Merge branch 'dev'
This commit is contained in:
Heng Li
commit
3dbe23b34e
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@ -0,0 +1,5 @@
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language: c
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compiler:
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- gcc
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- clang
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script: make
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65
format.c
65
format.c
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@ -1,7 +1,9 @@
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#include <stdarg.h>
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#include <stdarg.h>
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#include <stdlib.h>
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#include <stdlib.h>
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#include <string.h>
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#include <string.h>
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#include <assert.h>
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#include <stdio.h>
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#include <stdio.h>
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#include "kalloc.h"
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#include "mmpriv.h"
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#include "mmpriv.h"
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static inline void str_enlarge(kstring_t *s, int l)
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static inline void str_enlarge(kstring_t *s, int l)
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@ -54,6 +56,63 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
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s->s[s->l] = 0;
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s->s[s->l] = 0;
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}
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}
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static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
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{
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extern unsigned char seq_nt4_table[256];
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int i, q_off, t_off;
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uint8_t *qseq, *tseq;
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char *tmp;
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if (r->p == 0) return;
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mm_sprintf_lite(s, "\tcs:Z:");
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qseq = (uint8_t*)kmalloc(km, r->qe - r->qs);
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tseq = (uint8_t*)kmalloc(km, r->re - r->rs);
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tmp = (char*)kmalloc(km, r->re - r->rs > r->qe - r->qs? r->re - r->rs + 1 : r->qe - r->qs + 1);
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mm_idx_getseq(mi, r->rid, r->rs, r->re, tseq);
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if (!r->rev) {
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for (i = r->qs; i < r->qe; ++i)
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qseq[i - r->qs] = seq_nt4_table[(uint8_t)t->seq[i]];
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} else {
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for (i = r->qs; i < r->qe; ++i) {
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uint8_t c = seq_nt4_table[(uint8_t)t->seq[i]];
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qseq[r->qe - i - 1] = c >= 4? 4 : 3 - c;
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}
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}
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for (i = q_off = t_off = 0; i < r->p->n_cigar; ++i) {
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int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
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assert(op >= 0 && op <= 2);
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if (op == 0) {
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int l_tmp = 0;
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for (j = 0; j < len; ++j) {
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if (qseq[q_off + j] != tseq[t_off + j]) {
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if (l_tmp > 0) {
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tmp[l_tmp] = 0;
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mm_sprintf_lite(s, "=%s", tmp);
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l_tmp = 0;
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}
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mm_sprintf_lite(s, "*%c%c", "acgtn"[tseq[t_off + j]], "acgtn"[qseq[q_off + j]]);
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} else tmp[l_tmp++] = "ACGTN"[qseq[q_off + j]];
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}
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if (l_tmp > 0) {
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tmp[l_tmp] = 0;
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mm_sprintf_lite(s, "=%s", tmp);
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}
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q_off += len, t_off += len;
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} else if (op == 1) {
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for (j = 0, tmp[len] = 0; j < len; ++j)
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tmp[j] = "acgtn"[qseq[q_off + j]];
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mm_sprintf_lite(s, "+%s", tmp);
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q_off += len;
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} else if (op == 2) {
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for (j = 0, tmp[len] = 0; j < len; ++j)
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tmp[j] = "acgtn"[tseq[t_off + j]];
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mm_sprintf_lite(s, "-%s", tmp);
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t_off += len;
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}
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}
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assert(t_off == r->re - r->rs && q_off == r->qe - r->qs);
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kfree(km, qseq); kfree(km, tseq); kfree(km, tmp);
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}
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static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
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static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
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{
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{
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int type = r->inv? 'I' : r->id == r->parent? 'P' : 'S';
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int type = r->inv? 'I' : r->id == r->parent? 'P' : 'S';
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@ -63,7 +122,7 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
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if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
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if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
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}
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}
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void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
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void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag)
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{
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{
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s->l = 0;
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s->l = 0;
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mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
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mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
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@ -74,12 +133,14 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
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else mm_sprintf_lite(s, "\t%d\t%d", r->fuzzy_mlen, r->fuzzy_blen);
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else mm_sprintf_lite(s, "\t%d\t%d", r->fuzzy_mlen, r->fuzzy_blen);
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mm_sprintf_lite(s, "\t%d", r->mapq);
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mm_sprintf_lite(s, "\t%d", r->mapq);
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write_tags(s, r);
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write_tags(s, r);
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if (r->p) {
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if (r->p && (opt_flag & MM_F_OUT_CG)) {
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uint32_t k;
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uint32_t k;
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mm_sprintf_lite(s, "\tcg:Z:");
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mm_sprintf_lite(s, "\tcg:Z:");
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for (k = 0; k < r->p->n_cigar; ++k)
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for (k = 0; k < r->p->n_cigar; ++k)
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mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
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mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
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}
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}
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if (r->p && (opt_flag & MM_F_OUT_CS))
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write_cs(km, s, mi, t, r);
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}
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}
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static char comp_tab[] = {
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static char comp_tab[] = {
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@ -1,5 +1,6 @@
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#include <string.h>
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#include <string.h>
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#include <stdio.h>
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#include <stdio.h>
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#include <assert.h>
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#include "ksw2.h"
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#include "ksw2.h"
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#ifdef __SSE2__
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#ifdef __SSE2__
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@ -66,7 +67,8 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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if (w < 0) w = tlen > qlen? tlen : qlen;
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if (w < 0) w = tlen > qlen? tlen : qlen;
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wl = wr = w;
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wl = wr = w;
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tlen_ = (tlen + 15) / 16;
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tlen_ = (tlen + 15) / 16;
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n_col_ = ((w + 1 < tlen? (w + 1 < qlen? w + 1 : qlen): tlen) + 15) / 16 + 1;
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n_col_ = qlen < tlen? qlen : tlen;
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n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 15) / 16 + 1;
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qlen_ = (qlen + 15) / 16;
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qlen_ = (qlen + 15) / 16;
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for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
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for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
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max_sc = max_sc > mat[t]? max_sc : mat[t];
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max_sc = max_sc > mat[t]? max_sc : mat[t];
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@ -161,6 +163,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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x21_ = _mm_cvtsi32_si128((uint8_t)x21);
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x21_ = _mm_cvtsi32_si128((uint8_t)x21);
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v1_ = _mm_cvtsi32_si128((uint8_t)v1);
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v1_ = _mm_cvtsi32_si128((uint8_t)v1);
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st_ = st / 16, en_ = en / 16;
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st_ = st / 16, en_ = en / 16;
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assert(en_ - st_ + 1 <= n_col_);
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if (!with_cigar) { // score only
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if (!with_cigar) { // score only
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for (t = st_; t <= en_; ++t) {
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for (t = st_; t <= en_; ++t) {
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__m128i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
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__m128i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
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@ -1,4 +1,5 @@
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#include <string.h>
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#include <string.h>
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#include <assert.h>
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#include "ksw2.h"
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#include "ksw2.h"
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#ifdef __SSE2__
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#ifdef __SSE2__
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@ -58,7 +59,8 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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if (w < 0) w = tlen > qlen? tlen : qlen;
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if (w < 0) w = tlen > qlen? tlen : qlen;
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wl = wr = w;
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wl = wr = w;
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tlen_ = (tlen + 15) / 16;
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tlen_ = (tlen + 15) / 16;
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n_col_ = ((w + 1 < tlen? (w + 1 < qlen? w + 1 : qlen): tlen) + 15) / 16 + 1;
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n_col_ = qlen < tlen? qlen : tlen;
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n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 15) / 16 + 1;
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qlen_ = (qlen + 15) / 16;
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qlen_ = (qlen + 15) / 16;
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for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
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for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
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max_sc = max_sc > mat[t]? max_sc : mat[t];
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max_sc = max_sc > mat[t]? max_sc : mat[t];
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@ -130,6 +132,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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x1_ = _mm_cvtsi32_si128(x1);
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x1_ = _mm_cvtsi32_si128(x1);
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v1_ = _mm_cvtsi32_si128(v1);
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v1_ = _mm_cvtsi32_si128(v1);
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st_ = st / 16, en_ = en / 16;
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st_ = st / 16, en_ = en / 16;
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assert(en_ - st_ + 1 <= n_col_);
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if (!with_cigar) { // score only
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if (!with_cigar) { // score only
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for (t = st_; t <= en_; ++t) {
|
for (t = st_; t <= en_; ++t) {
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__m128i z, a, b, xt1, vt1, ut, tmp;
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__m128i z, a, b, xt1, vt1, ut, tmp;
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|
|
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8
main.c
8
main.c
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|
@ -8,7 +8,7 @@
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#include "minimap.h"
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#include "minimap.h"
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#include "mmpriv.h"
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#include "mmpriv.h"
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|
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#define MM_VERSION "2.0-r275"
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#define MM_VERSION "2.0-r276-dirty"
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void liftrlimit()
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void liftrlimit()
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{
|
{
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|
@ -54,7 +54,7 @@ int main(int argc, char *argv[])
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mm_realtime0 = realtime();
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mm_realtime0 = realtime();
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mm_mapopt_init(&opt);
|
mm_mapopt_init(&opt);
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||||||
|
|
||||||
while ((c = getopt_long(argc, argv, "aw:k:K:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Q", long_options, &long_idx)) >= 0) {
|
while ((c = getopt_long(argc, argv, "aSw:k:K:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Q", long_options, &long_idx)) >= 0) {
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||||||
if (c == 'w') w = atoi(optarg), idx_par_set = 1;
|
if (c == 'w') w = atoi(optarg), idx_par_set = 1;
|
||||||
else if (c == 'k') k = atoi(optarg), idx_par_set = 1;
|
else if (c == 'k') k = atoi(optarg), idx_par_set = 1;
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||||||
else if (c == 'H') is_hpc = 1, idx_par_set = 1;
|
else if (c == 'H') is_hpc = 1, idx_par_set = 1;
|
||||||
|
|
@ -67,7 +67,8 @@ int main(int argc, char *argv[])
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else if (c == 'N') opt.best_n = atoi(optarg);
|
else if (c == 'N') opt.best_n = atoi(optarg);
|
||||||
else if (c == 'p') opt.pri_ratio = atof(optarg);
|
else if (c == 'p') opt.pri_ratio = atof(optarg);
|
||||||
else if (c == 'M') opt.mask_level = atof(optarg);
|
else if (c == 'M') opt.mask_level = atof(optarg);
|
||||||
else if (c == 'c') opt.flag |= MM_F_CIGAR;
|
else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
|
||||||
|
else if (c == 'S') opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
|
||||||
else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
|
else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
|
||||||
else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
|
else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
|
||||||
else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
|
else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
|
||||||
|
|
@ -166,6 +167,7 @@ int main(int argc, char *argv[])
|
||||||
fprintf(stderr, " -Q ignore base quality in the input\n");
|
fprintf(stderr, " -Q ignore base quality in the input\n");
|
||||||
fprintf(stderr, " -a output in the SAM format (PAF by default)\n");
|
fprintf(stderr, " -a output in the SAM format (PAF by default)\n");
|
||||||
fprintf(stderr, " -c output CIGAR in PAF\n");
|
fprintf(stderr, " -c output CIGAR in PAF\n");
|
||||||
|
fprintf(stderr, " -S output the cs tag in PAF\n");
|
||||||
fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
|
fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
|
||||||
fprintf(stderr, " -K NUM minibatch size [200M]\n");
|
fprintf(stderr, " -K NUM minibatch size [200M]\n");
|
||||||
// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
|
// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
|
||||||
|
|
|
||||||
5
map.c
5
map.c
|
|
@ -338,16 +338,18 @@ static void *worker_pipeline(void *shared, int step, void *in)
|
||||||
kt_for(p->n_threads, worker_for, in, ((step_t*)in)->n_seq);
|
kt_for(p->n_threads, worker_for, in, ((step_t*)in)->n_seq);
|
||||||
return in;
|
return in;
|
||||||
} else if (step == 2) { // step 2: output
|
} else if (step == 2) { // step 2: output
|
||||||
|
void *km = 0;
|
||||||
step_t *s = (step_t*)in;
|
step_t *s = (step_t*)in;
|
||||||
const mm_idx_t *mi = p->mi;
|
const mm_idx_t *mi = p->mi;
|
||||||
for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
|
for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
|
||||||
free(s->buf);
|
free(s->buf);
|
||||||
|
if ((p->opt->flag & MM_F_OUT_CS) && !(mm_dbg_flag & MM_DBG_NO_KALLOC)) km = km_init();
|
||||||
for (i = 0; i < s->n_seq; ++i) {
|
for (i = 0; i < s->n_seq; ++i) {
|
||||||
mm_bseq1_t *t = &s->seq[i];
|
mm_bseq1_t *t = &s->seq[i];
|
||||||
for (j = 0; j < s->n_reg[i]; ++j) {
|
for (j = 0; j < s->n_reg[i]; ++j) {
|
||||||
mm_reg1_t *r = &s->reg[i][j];
|
mm_reg1_t *r = &s->reg[i][j];
|
||||||
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i]);
|
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i]);
|
||||||
else mm_write_paf(&p->str, mi, t, r);
|
else mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
|
||||||
puts(p->str.s);
|
puts(p->str.s);
|
||||||
}
|
}
|
||||||
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
|
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
|
||||||
|
|
@ -360,6 +362,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
|
||||||
if (s->seq[i].qual) free(s->seq[i].qual);
|
if (s->seq[i].qual) free(s->seq[i].qual);
|
||||||
}
|
}
|
||||||
free(s->reg); free(s->n_reg); free(s->seq);
|
free(s->reg); free(s->n_reg); free(s->seq);
|
||||||
|
km_destroy(km);
|
||||||
if (mm_verbose >= 3)
|
if (mm_verbose >= 3)
|
||||||
fprintf(stderr, "[M::%s::%.3f*%.2f] mapped %d sequences\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), s->n_seq);
|
fprintf(stderr, "[M::%s::%.3f*%.2f] mapped %d sequences\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), s->n_seq);
|
||||||
free(s);
|
free(s);
|
||||||
|
|
|
||||||
|
|
@ -12,6 +12,8 @@
|
||||||
#define MM_F_CIGAR 0x04
|
#define MM_F_CIGAR 0x04
|
||||||
#define MM_F_OUT_SAM 0x08
|
#define MM_F_OUT_SAM 0x08
|
||||||
#define MM_F_NO_QUAL 0x10
|
#define MM_F_NO_QUAL 0x10
|
||||||
|
#define MM_F_OUT_CG 0x20
|
||||||
|
#define MM_F_OUT_CS 0x40
|
||||||
|
|
||||||
#define MM_IDX_MAGIC "MMI\2"
|
#define MM_IDX_MAGIC "MMI\2"
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,28 @@
|
||||||
|
The [K8 Javascript shell][k8] is needed to run Javascripts in this directory.
|
||||||
|
Precompiled k8 binaries for Mac and Linux can be found at the [K8 release
|
||||||
|
page][k8bin].
|
||||||
|
|
||||||
|
* [paf2aln.js](paf2aln.js): convert PAF to [MAF][maf] or BLAST-like output for
|
||||||
|
eyeballing. PAF has to be generated with minimap2 option `-S`, which writes
|
||||||
|
the aligned sequences to the `cs` tag. An example:
|
||||||
|
```sh
|
||||||
|
../minimap2 -S ../test/MT-*.fa | k8 paf2aln.js /dev/stdin
|
||||||
|
```
|
||||||
|
|
||||||
|
* [mapstat.js](mapstat.js): output basic statistics such as the number of
|
||||||
|
non-redundant mapped bases, number of split and secondary alignments and
|
||||||
|
number of long gaps. This scripts seamlessly works with both SAM and PAF.
|
||||||
|
|
||||||
|
* [sim-pbsim.js](sim-pbsim.js): convert reads simulated with [PBSIM][pbsim] to
|
||||||
|
FASTA and encode the true mapping positions to read names in a format like
|
||||||
|
`S1_33!chr1!225258409!225267761!-`.
|
||||||
|
|
||||||
|
* [sim-eval.js](sim-eval.js): evaluate mapping accuracy for FASTA generated
|
||||||
|
with [sim-pbsim.js](sim-pbsim.js) or [sim-mason2.js](sim-mason2.js).
|
||||||
|
|
||||||
|
* [sam2paf.js](sam2paf.js): convert SAM to PAF.
|
||||||
|
|
||||||
|
[k8]: https://github.com/attractivechaos/k8
|
||||||
|
[k8bin]: https://github.com/attractivechaos/k8/releases
|
||||||
|
[maf]: https://genome.ucsc.edu/FAQ/FAQformat#format5
|
||||||
|
[pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator
|
||||||
|
|
@ -0,0 +1,171 @@
|
||||||
|
var getopt = function(args, ostr) {
|
||||||
|
var oli; // option letter list index
|
||||||
|
if (typeof(getopt.place) == 'undefined')
|
||||||
|
getopt.ind = 0, getopt.arg = null, getopt.place = -1;
|
||||||
|
if (getopt.place == -1) { // update scanning pointer
|
||||||
|
if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
|
||||||
|
getopt.place = -1;
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
|
||||||
|
++getopt.ind;
|
||||||
|
getopt.place = -1;
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
|
||||||
|
if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
|
||||||
|
if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
|
||||||
|
if (getopt.place < 0) ++getopt.ind;
|
||||||
|
return '?';
|
||||||
|
}
|
||||||
|
if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
|
||||||
|
getopt.arg = null;
|
||||||
|
if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
|
||||||
|
} else { // need an argument
|
||||||
|
if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
|
||||||
|
getopt.arg = args[getopt.ind].substr(getopt.place);
|
||||||
|
else if (args.length <= ++getopt.ind) { // no arg
|
||||||
|
getopt.place = -1;
|
||||||
|
if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
|
||||||
|
return '?';
|
||||||
|
} else getopt.arg = args[getopt.ind]; // white space
|
||||||
|
getopt.place = -1;
|
||||||
|
++getopt.ind;
|
||||||
|
}
|
||||||
|
return optopt;
|
||||||
|
}
|
||||||
|
|
||||||
|
var c, maf_out = false, line_len = 80;
|
||||||
|
while ((c = getopt(arguments, "ml:")) != null) {
|
||||||
|
if (c == 'm') maf_out = true;
|
||||||
|
else if (c == 'l') line_len = parseInt(getopt.arg); // TODO: not implemented yet
|
||||||
|
}
|
||||||
|
if (line_len == 0) line_len = 0x7fffffff;
|
||||||
|
|
||||||
|
if (getopt.ind == arguments.length) {
|
||||||
|
print("Usage: k8 paf2aln.js [options] <with-cs.paf>");
|
||||||
|
print("Options:");
|
||||||
|
print(" -m MAF output (BLAST-like output by default)");
|
||||||
|
print(" -l INT line length in BLAST-like output [80]");
|
||||||
|
print("");
|
||||||
|
print("Note: this script only works when minimap2 is run with option '-S'");
|
||||||
|
exit(1);
|
||||||
|
}
|
||||||
|
|
||||||
|
function padding_str(x, len, right)
|
||||||
|
{
|
||||||
|
var s = x.toString();
|
||||||
|
if (s.length < len) {
|
||||||
|
if (right) s += Array(len - s.length + 1).join(" ");
|
||||||
|
else s = Array(len - s.length + 1).join(" ") + s;
|
||||||
|
}
|
||||||
|
return s;
|
||||||
|
}
|
||||||
|
|
||||||
|
function update_aln(s_ref, s_qry, s_mid, type, seq, slen)
|
||||||
|
{
|
||||||
|
var l = type == '*'? 1 : seq.length;
|
||||||
|
if (type == '=') {
|
||||||
|
s_ref.set(seq);
|
||||||
|
s_qry.set(seq);
|
||||||
|
s_mid.set(Array(l+1).join("|"));
|
||||||
|
slen[0] += l, slen[1] += l;
|
||||||
|
} else if (type == '*') {
|
||||||
|
s_ref.set(seq.charAt(0));
|
||||||
|
s_qry.set(seq.charAt(1));
|
||||||
|
s_mid.set(' ');
|
||||||
|
slen[0] += 1, slen[1] += 1;
|
||||||
|
} else if (type == '+') {
|
||||||
|
s_ref.set(Array(l+1).join("-"));
|
||||||
|
s_qry.set(seq);
|
||||||
|
s_mid.set(Array(l+1).join(" "));
|
||||||
|
slen[1] += l;
|
||||||
|
} else if (type == '-') {
|
||||||
|
s_ref.set(seq);
|
||||||
|
s_qry.set(Array(l+1).join("-"));
|
||||||
|
s_mid.set(Array(l+1).join(" "));
|
||||||
|
slen[0] += l;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
function print_aln(rs, qs, strand, slen, elen, s_ref, s_qry, s_mid)
|
||||||
|
{
|
||||||
|
print(["Ref+:", padding_str(rs + slen[0] + 1, 10, false), s_ref.toString(), padding_str(rs + elen[0], 10, true)].join(" "));
|
||||||
|
print(" " + s_mid.toString());
|
||||||
|
var st, en;
|
||||||
|
if (strand == '+') st = qs + slen[1] + 1, en = qs + elen[1];
|
||||||
|
else st = qs - slen[1], en = qs - elen[1] + 1;
|
||||||
|
print(["Qry" + strand + ":", padding_str(st, 10, false), s_qry.toString(), padding_str(en , 10, true)].join(" "));
|
||||||
|
}
|
||||||
|
|
||||||
|
var s_ref = new Bytes(), s_qry = new Bytes(), s_mid = new Bytes();
|
||||||
|
var re = /([=\-\+\*])([A-Za-z]+)/g;
|
||||||
|
|
||||||
|
var buf = new Bytes();
|
||||||
|
var file = new File(arguments[getopt.ind]);
|
||||||
|
if (maf_out) print("##maf version=1\n");
|
||||||
|
while (file.readline(buf) >= 0) {
|
||||||
|
var m, line = buf.toString();
|
||||||
|
var t = line.split("\t", 12);
|
||||||
|
if ((m = /\tcs:Z:(\S+)/.exec(line)) == null) continue;
|
||||||
|
var cs = m[1];
|
||||||
|
s_ref.length = s_qry.length = s_mid.length = 0;
|
||||||
|
var slen = [0, 0], elen = [0, 0];
|
||||||
|
if (maf_out) {
|
||||||
|
while ((m = re.exec(cs)) != null)
|
||||||
|
update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
|
||||||
|
if (maf_out) {
|
||||||
|
var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
|
||||||
|
var len = t[0].length > t[5].length? t[0].length : t[5].length;
|
||||||
|
print("a " + score);
|
||||||
|
print(["s", padding_str(t[5], len, true), padding_str(t[7], 10, false), padding_str(parseInt(t[8]) - parseInt(t[7]), 10, false),
|
||||||
|
"+", padding_str(t[6], 10, false), s_ref.toString()].join(" "));
|
||||||
|
var qs, qe, ql = parseInt(t[1]);
|
||||||
|
if (t[4] == '+') {
|
||||||
|
qs = parseInt(t[2]);
|
||||||
|
qe = parseInt(t[3]);
|
||||||
|
} else {
|
||||||
|
qs = ql - parseInt(t[3]);
|
||||||
|
qe = ql - parseInt(t[2]);
|
||||||
|
}
|
||||||
|
print(["s", padding_str(t[0], len, true), padding_str(qs, 10, false), padding_str(qe - qs, 10, false),
|
||||||
|
t[4], padding_str(ql, 10, false), s_qry.toString()].join(" "));
|
||||||
|
print("");
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
line = line.replace(/\tc[sg]:Z:\S+/g, "");
|
||||||
|
print('>' + line);
|
||||||
|
var rs = parseInt(t[7]), qs = t[4] == '+'? parseInt(t[2]) : parseInt(t[3]);
|
||||||
|
var n_blocks = 0;
|
||||||
|
while ((m = re.exec(cs)) != null) {
|
||||||
|
var start = 0, rest = m[1] == '*'? 1 : m[2].length;
|
||||||
|
while (rest > 0) {
|
||||||
|
var l_proc;
|
||||||
|
if (s_ref.length + rest >= line_len) {
|
||||||
|
l_proc = line_len - s_ref.length;
|
||||||
|
update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
|
||||||
|
if (n_blocks > 0) print("");
|
||||||
|
print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
|
||||||
|
++n_blocks;
|
||||||
|
s_ref.length = s_qry.length = s_mid.length = 0;
|
||||||
|
slen[0] = elen[0], slen[1] = elen[1];
|
||||||
|
} else {
|
||||||
|
l_proc = rest;
|
||||||
|
update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
|
||||||
|
}
|
||||||
|
rest -= l_proc, start += l_proc;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (s_ref.length > 0) {
|
||||||
|
if (n_blocks > 0) print("");
|
||||||
|
print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
|
||||||
|
++n_blocks;
|
||||||
|
}
|
||||||
|
print("//");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
file.close();
|
||||||
|
buf.destroy();
|
||||||
|
|
||||||
|
s_ref.destroy(); s_qry.destroy(); s_mid.destroy();
|
||||||
|
|
@ -0,0 +1,111 @@
|
||||||
|
var getopt = function(args, ostr) {
|
||||||
|
var oli; // option letter list index
|
||||||
|
if (typeof(getopt.place) == 'undefined')
|
||||||
|
getopt.ind = 0, getopt.arg = null, getopt.place = -1;
|
||||||
|
if (getopt.place == -1) { // update scanning pointer
|
||||||
|
if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
|
||||||
|
getopt.place = -1;
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
|
||||||
|
++getopt.ind;
|
||||||
|
getopt.place = -1;
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
|
||||||
|
if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
|
||||||
|
if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
|
||||||
|
if (getopt.place < 0) ++getopt.ind;
|
||||||
|
return '?';
|
||||||
|
}
|
||||||
|
if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
|
||||||
|
getopt.arg = null;
|
||||||
|
if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
|
||||||
|
} else { // need an argument
|
||||||
|
if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
|
||||||
|
getopt.arg = args[getopt.ind].substr(getopt.place);
|
||||||
|
else if (args.length <= ++getopt.ind) { // no arg
|
||||||
|
getopt.place = -1;
|
||||||
|
if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
|
||||||
|
return '?';
|
||||||
|
} else getopt.arg = args[getopt.ind]; // white space
|
||||||
|
getopt.place = -1;
|
||||||
|
++getopt.ind;
|
||||||
|
}
|
||||||
|
return optopt;
|
||||||
|
}
|
||||||
|
|
||||||
|
var c, pri_only = false;
|
||||||
|
while ((c = getopt(arguments, "p")) != null)
|
||||||
|
if (c == 'p') pri_only = true;
|
||||||
|
|
||||||
|
var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
|
||||||
|
var buf = new Bytes();
|
||||||
|
var re = /(\d+)([MIDSHNX=])/g;
|
||||||
|
|
||||||
|
var len = {}, lineno = 0;
|
||||||
|
while (file.readline(buf) >= 0) {
|
||||||
|
var m, n_cigar = 0, line = buf.toString();
|
||||||
|
++lineno;
|
||||||
|
if (line.charAt(0) == '@') {
|
||||||
|
if (/^@SQ/.test(line)) {
|
||||||
|
var name = (m = /\tSN:(\S+)/.exec(line)) != null? m[1] : null;
|
||||||
|
var l = (m = /\tLN:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
|
||||||
|
if (name != null && l != null) len[name] = l;
|
||||||
|
}
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
var t = line.split("\t");
|
||||||
|
var flag = parseInt(t[1]);
|
||||||
|
if (t[9] != '*' && t[10] != '*' && t[9].length != t[10].length) throw Error("ERROR at line " + lineno + ": inconsistent SEQ and QUAL lengths - " + t[9].length + " != " + t[10].length);
|
||||||
|
if (t[2] == '*' || (flag&4)) continue;
|
||||||
|
if (pri_only && (flag&0x100)) continue;
|
||||||
|
var tlen = len[t[2]];
|
||||||
|
if (tlen == null) throw Error("ERROR at line " + lineno + ": can't find the length of contig " + t[2]);
|
||||||
|
var nn = (m = /\tnn:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
|
||||||
|
var NM = (m = /\tNM:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
|
||||||
|
var have_NM = NM == null? false : true;
|
||||||
|
NM += nn;
|
||||||
|
var clip = [0, 0], I = [0, 0], D = [0, 0], M = 0, N = 0, ql = 0, tl = 0, mm = 0, ext_cigar = false;
|
||||||
|
while ((m = re.exec(t[5])) != null) {
|
||||||
|
var l = parseInt(m[1]);
|
||||||
|
if (m[2] == 'M') M += l, ql += l, tl += l, ext_cigar = false;
|
||||||
|
else if (m[2] == 'I') ++I[0], I[1] += l, ql += l;
|
||||||
|
else if (m[2] == 'D') ++D[0], D[1] += l, tl += l;
|
||||||
|
else if (m[2] == 'N') N += l, tl += l;
|
||||||
|
else if (m[2] == 'S') clip[M == 0? 0 : 1] = l, ql += l;
|
||||||
|
else if (m[2] == 'H') clip[M == 0? 0 : 1] = l;
|
||||||
|
else if (m[2] == '=') M += l, ql += l, tl += l, ext_cigar = true;
|
||||||
|
else if (m[2] == 'X') M += l, ql += l, tl += l, mm += l, ext_cigar = true;
|
||||||
|
++n_cigar;
|
||||||
|
}
|
||||||
|
if (n_cigar > 65535)
|
||||||
|
warn("WARNING at line " + lineno + ": " + n_cigar + " CIGAR operations");
|
||||||
|
if (tl + parseInt(t[3]) - 1 > tlen) {
|
||||||
|
warn("WARNING at line " + lineno + ": alignment end position larger than ref length; skipped");
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
if (t[9] != '*' && t[9].length != ql) {
|
||||||
|
warn("WARNING at line " + lineno + ": SEQ length inconsistent with CIGAR (" + t[9].length + " != " + ql + "); skipped");
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
if (!have_NM || ext_cigar) NM = I[1] + D[1] + mm;
|
||||||
|
if (NM < I[1] + D[1] + mm) {
|
||||||
|
warn("WARNING at line " + lineno + ": NM is less than the total number of gaps (" + NM + " < " + (I[1]+D[1]+mm) + ")");
|
||||||
|
NM = I[1] + D[1] + mm;
|
||||||
|
}
|
||||||
|
var extra = ["mm:i:"+(NM-I[1]-D[1]), "io:i:"+I[0], "in:i:"+I[1], "do:i:"+D[0], "dn:i:"+D[1]];
|
||||||
|
var match = M - (NM - I[1] - D[1]);
|
||||||
|
var blen = M + I[1] + D[1];
|
||||||
|
var qlen = M + I[1] + clip[0] + clip[1];
|
||||||
|
var qs, qe;
|
||||||
|
if (flag&16) qs = clip[1], qe = qlen - clip[0];
|
||||||
|
else qs = clip[0], qe = qlen - clip[1];
|
||||||
|
var ts = parseInt(t[3]) - 1, te = ts + M + D[1] + N;
|
||||||
|
var a = [t[0], qlen, qs, qe, flag&16? '-' : '+', t[2], tlen, ts, te, match, blen, t[4]];
|
||||||
|
print(a.join("\t"), extra.join("\t"));
|
||||||
|
}
|
||||||
|
|
||||||
|
buf.destroy();
|
||||||
|
file.close();
|
||||||
|
|
@ -36,11 +36,12 @@ var getopt = function(args, ostr) {
|
||||||
return optopt;
|
return optopt;
|
||||||
}
|
}
|
||||||
|
|
||||||
var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.333;
|
var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.1, cap_short_mapq = false;
|
||||||
while ((c = getopt(arguments, "Q:r:m:")) != null) {
|
while ((c = getopt(arguments, "Q:r:m:c")) != null) {
|
||||||
if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true;
|
if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true;
|
||||||
else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg);
|
else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg);
|
||||||
else if (c == 'm') mode = parseInt(getopt.arg);
|
else if (c == 'm') mode = parseInt(getopt.arg);
|
||||||
|
else if (c == 'c') cap_short_mapq = true;
|
||||||
}
|
}
|
||||||
|
|
||||||
var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
|
var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
|
||||||
|
|
@ -68,20 +69,27 @@ function is_correct(s, b)
|
||||||
|
|
||||||
function count_err(qname, a, tot, err, mode)
|
function count_err(qname, a, tot, err, mode)
|
||||||
{
|
{
|
||||||
var s = qname.split("!");
|
|
||||||
if (a.length == 0) return;
|
if (a.length == 0) return;
|
||||||
if (s.length < 5 || (s[4] != '+' && s[4] != '-'))
|
|
||||||
throw Error("Failed to parse pbsim2fa read names '" + qname + "'");
|
var m, s;
|
||||||
s[2] = parseInt(s[2]);
|
if ((m = /^(\S+)!(\S+)!(\d+)!(\d+)!([\+\-])$/.exec(qname)) != null) { // pbsim single-end reads
|
||||||
s[3] = parseInt(s[3]);
|
s = [m[1], m[2], parseInt(m[3]), parseInt(m[4]), m[5]];
|
||||||
s.shift(); // skip pbsim orginal read name
|
} else if ((m = /^(\S+)!(\S+)!(\d+)_(\d+)!(\d+)_(\d+)!([\+\-])([\+\-])\/([12])$/.exec(qname)) != null) { // mason2 paired-end reads
|
||||||
|
if (m[9] == '1') {
|
||||||
|
s = [m[1], m[2], parseInt(m[3]), parseInt(m[5]), m[7]];
|
||||||
|
} else {
|
||||||
|
s = [m[1], m[2], parseInt(m[4]), parseInt(m[6]), m[8]];
|
||||||
|
}
|
||||||
|
} else throw Error("Failed to parse simulated read names '" + qname + "'");
|
||||||
|
s.shift(); // skip the orginal read name
|
||||||
|
|
||||||
if (mode == 0 || mode == 1) { // longest only or first only
|
if (mode == 0 || mode == 1) { // longest only or first only
|
||||||
var max_i = 0;
|
var max_i = 0;
|
||||||
if (mode == 0) {
|
if (mode == 0) { // longest only
|
||||||
var max = 0;
|
var max = 0;
|
||||||
for (var i = 0; i < a.length; ++i)
|
for (var i = 0; i < a.length; ++i)
|
||||||
if (a[i][2] - a[i][1] > max)
|
if (a[i][5] > max)
|
||||||
max = a[i][2] - a[i][1], max_i = i;
|
max = a[i][5], max_i = i;
|
||||||
}
|
}
|
||||||
var mapq = a[max_i][4];
|
var mapq = a[max_i][4];
|
||||||
++tot[mapq];
|
++tot[mapq];
|
||||||
|
|
@ -92,6 +100,14 @@ function count_err(qname, a, tot, err, mode)
|
||||||
}
|
}
|
||||||
} else if (mode == 2) { // all primary mode
|
} else if (mode == 2) { // all primary mode
|
||||||
var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
|
var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
|
||||||
|
if (cap_short_mapq) {
|
||||||
|
var max = 0, max_q = 0;
|
||||||
|
for (var i = 0; i < a.length; ++i)
|
||||||
|
if (a[i][5] > max)
|
||||||
|
max = a[i][5], max_q = a[i][4];
|
||||||
|
for (var i = 0; i < a.length; ++i)
|
||||||
|
a[i][4] = max_q < a[i][4]? max_q : a[i][4];
|
||||||
|
}
|
||||||
for (var i = 0; i < a.length; ++i) {
|
for (var i = 0; i < a.length; ++i) {
|
||||||
max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
|
max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
|
||||||
if (!is_correct(s, a[i]))
|
if (!is_correct(s, a[i]))
|
||||||
|
|
@ -106,22 +122,53 @@ function count_err(qname, a, tot, err, mode)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
var lineno = 0, last = null, a = [];
|
var lineno = 0, last = null, a = [], n_unmapped = null;
|
||||||
|
var re_cigar = /(\d+)([MIDSHN])/g;
|
||||||
while (file.readline(buf) >= 0) {
|
while (file.readline(buf) >= 0) {
|
||||||
var line = buf.toString();
|
var m, line = buf.toString();
|
||||||
++lineno;
|
++lineno;
|
||||||
if (line[0] != '@') {
|
if (line[0] != '@') {
|
||||||
var t = line.split("\t");
|
var t = line.split("\t");
|
||||||
if (last != t[0]) {
|
|
||||||
if (last != null) count_err(last, a, tot, err, mode);
|
|
||||||
a = [], last = t[0];
|
|
||||||
}
|
|
||||||
if (t[4] == '+' || t[4] == '-') { // PAF
|
if (t[4] == '+' || t[4] == '-') { // PAF
|
||||||
|
if (last != t[0]) {
|
||||||
|
if (last != null) count_err(last, a, tot, err, mode);
|
||||||
|
a = [], last = t[0];
|
||||||
|
}
|
||||||
if (/\ts1:i:\d+/.test(line) && !/\ts2:i:\d+/.test(line)) // secondary alignment in minimap2 PAF
|
if (/\ts1:i:\d+/.test(line) && !/\ts2:i:\d+/.test(line)) // secondary alignment in minimap2 PAF
|
||||||
continue;
|
continue;
|
||||||
var mapq = parseInt(t[11]);
|
var mapq = parseInt(t[11]);
|
||||||
if (mapq > max_mapq) mapq = max_mapq;
|
if (mapq > max_mapq) mapq = max_mapq;
|
||||||
a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq]);
|
a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq, parseInt(t[9])]);
|
||||||
|
} else { // SAM
|
||||||
|
var flag = parseInt(t[1]);
|
||||||
|
var read_no = flag>>6&0x3;
|
||||||
|
var qname = read_no == 1 || read_no == 2? t[0] + '/' + read_no : t[0];
|
||||||
|
if (last != qname) {
|
||||||
|
if (last != null) count_err(last, a, tot, err, mode);
|
||||||
|
a = [], last = qname;
|
||||||
|
}
|
||||||
|
if (flag&0x100) continue; // secondary alignment
|
||||||
|
if ((flag&0x4) || t[2] == '*') { // unmapped
|
||||||
|
if (n_unmapped == null) n_unmapped = 0;
|
||||||
|
++n_unmapped;
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
var mapq = parseInt(t[4]);
|
||||||
|
if (mapq > max_mapq) mapq = max_mapq;
|
||||||
|
var pos = parseInt(t[3]) - 1, pos_end = pos;
|
||||||
|
var n_gap = 0, mlen = 0;
|
||||||
|
while ((m = re_cigar.exec(t[5])) != null) {
|
||||||
|
var len = parseInt(m[1]);
|
||||||
|
if (m[2] == 'M') pos_end += len, mlen += len;
|
||||||
|
else if (m[2] == 'I') n_gap += len;
|
||||||
|
else if (m[2] == 'D') n_gap += len, pos_end += len;
|
||||||
|
}
|
||||||
|
var score = pos_end - pos;
|
||||||
|
if ((m = /\tNM:i:(\d+)/.exec(line)) != null) {
|
||||||
|
var NM = parseInt(m[1]);
|
||||||
|
if (NM >= n_gap) score = mlen - (NM - n_gap);
|
||||||
|
}
|
||||||
|
a.push([t[2], pos, pos_end, (flag&16)? '-' : '+', mapq, score]);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -141,3 +188,4 @@ for (var q = max_mapq; q >= 0; --q) {
|
||||||
sum_tot2 += tot[q], sum_err2 += err[q];
|
sum_tot2 += tot[q], sum_err2 += err[q];
|
||||||
}
|
}
|
||||||
print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9));
|
print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9));
|
||||||
|
if (n_unmapped != null) print('U', n_unmapped);
|
||||||
|
|
@ -0,0 +1,105 @@
|
||||||
|
Bytes.prototype.reverse = function()
|
||||||
|
{
|
||||||
|
for (var i = 0; i < this.length>>1; ++i) {
|
||||||
|
var tmp = this[i];
|
||||||
|
this[i] = this[this.length - i - 1];
|
||||||
|
this[this.length - i - 1] = tmp;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// reverse complement a DNA string
|
||||||
|
Bytes.prototype.revcomp = function()
|
||||||
|
{
|
||||||
|
if (Bytes.rctab == null) {
|
||||||
|
var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
|
||||||
|
var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
|
||||||
|
Bytes.rctab = [];
|
||||||
|
for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
|
||||||
|
for (var i = 0; i < s1.length; ++i)
|
||||||
|
Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
|
||||||
|
}
|
||||||
|
for (var i = 0; i < this.length>>1; ++i) {
|
||||||
|
var tmp = this[this.length - i - 1];
|
||||||
|
this[this.length - i - 1] = Bytes.rctab[this[i]];
|
||||||
|
this[i] = Bytes.rctab[tmp];
|
||||||
|
}
|
||||||
|
if (this.length&1)
|
||||||
|
this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
|
||||||
|
}
|
||||||
|
|
||||||
|
if (arguments.length == 0) {
|
||||||
|
print("Usage: k8 sim-mason2.js <mason.sam>");
|
||||||
|
exit(1);
|
||||||
|
}
|
||||||
|
|
||||||
|
function print_se(a)
|
||||||
|
{
|
||||||
|
print('@' + a.slice(0, 5).join("!") + " " + a[8]);
|
||||||
|
print(a[5]);
|
||||||
|
print("+");
|
||||||
|
print(a[6]);
|
||||||
|
}
|
||||||
|
|
||||||
|
var buf = new Bytes(), buf2 = new Bytes();
|
||||||
|
var file = new File(arguments[0]);
|
||||||
|
var re = /(\d+)([MIDSHN])/g;
|
||||||
|
var last = null;
|
||||||
|
while (file.readline(buf) >= 0) {
|
||||||
|
var t = buf.toString().split("\t");
|
||||||
|
if (t[0].charAt(0) == '@') continue;
|
||||||
|
var m, l_ref = 0;
|
||||||
|
while ((m = re.exec(t[5])) != null)
|
||||||
|
if (m[2] == 'D' || m[2] == 'M' || m[2] == 'N')
|
||||||
|
l_ref += parseInt(m[1]);
|
||||||
|
var flag = parseInt(t[1]);
|
||||||
|
var rev = !!(flag&16);
|
||||||
|
var seq, qual;
|
||||||
|
if (rev) {
|
||||||
|
buf2.length = 0;
|
||||||
|
buf2.set(t[9], 0);
|
||||||
|
buf2.revcomp();
|
||||||
|
seq = buf2.toString();
|
||||||
|
buf2.set(t[10], 0);
|
||||||
|
buf2.reverse();
|
||||||
|
qual = buf2.toString();
|
||||||
|
} else seq = t[9], qual = t[10];
|
||||||
|
var qname = t[0];
|
||||||
|
qname = qname.replace(/^simulated./, "");
|
||||||
|
var chr = t[2];
|
||||||
|
var pos = parseInt(t[3]) - 1;
|
||||||
|
var strand = (flag&16)? '-' : '+';
|
||||||
|
var read_no = flag&0xc0;
|
||||||
|
if (read_no == 0x40) read_no = 1;
|
||||||
|
else if (read_no == 0x80) read_no = 2;
|
||||||
|
else read_no = 0;
|
||||||
|
var err = 0, snp = 0, indel = 0;
|
||||||
|
for (var i = 11; i < t.length; ++i) {
|
||||||
|
if ((m = /^XE:i:(\d+)/.exec(t[i])) != null) err = m[1];
|
||||||
|
else if ((m = /^XS:i:(\d+)/.exec(t[i])) != null) snp = m[1];
|
||||||
|
else if ((m = /^XI:i:(\d+)/.exec(t[i])) != null) indel = m[1];
|
||||||
|
}
|
||||||
|
var comment = [err, snp, indel].join(":");
|
||||||
|
if (last == null) {
|
||||||
|
last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
|
||||||
|
} else if (last[0] != qname) {
|
||||||
|
print_se(last);
|
||||||
|
last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
|
||||||
|
} else {
|
||||||
|
if (read_no == 2) { // last[] is the first read
|
||||||
|
if (last[7] != 1) throw Error("ERROR: can't find read1");
|
||||||
|
var name = [qname, chr, last[2] + "_" + pos, last[3] + "_" + (pos + l_ref), last[4] + strand].join("!");
|
||||||
|
print('@' + name + '/1' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
|
||||||
|
print('@' + name + '/2' + ' ' + comment); print(seq); print("+"); print(qual);
|
||||||
|
} else {
|
||||||
|
if (last[7] != 2) throw Error("ERROR: can't find read2");
|
||||||
|
var name = [qname, chr, pos + "_" + last[2], (pos + l_ref) + "_" + last[3], strand + last[4]].join("!");
|
||||||
|
print('@' + name + '/1' + ' ' + comment); print(seq); print("+"); print(qual);
|
||||||
|
print('@' + name + '/2' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
|
||||||
|
}
|
||||||
|
last = null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (last != null) print_se(last);
|
||||||
|
file.close();
|
||||||
|
buf.destroy();
|
||||||
|
buf2.destroy();
|
||||||
|
|
@ -28,7 +28,7 @@ Bytes.prototype.revcomp = function()
|
||||||
}
|
}
|
||||||
|
|
||||||
if (arguments.length < 2) {
|
if (arguments.length < 2) {
|
||||||
print("Usage: k8 pbsim2paf.js <chr.list> <pbsim1.maf> [[pbsim2.maf] ...]");
|
print("Usage: k8 sim-pbsim.js <ref.fa.fai> <pbsim1.maf> [[pbsim2.maf] ...]");
|
||||||
exit(1);
|
exit(1);
|
||||||
}
|
}
|
||||||
|
|
||||||
2
mmpriv.h
2
mmpriv.h
|
|
@ -40,7 +40,7 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end);
|
||||||
void radix_sort_64(uint64_t *beg, uint64_t *end);
|
void radix_sort_64(uint64_t *beg, uint64_t *end);
|
||||||
uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
|
uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
|
||||||
|
|
||||||
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r);
|
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag);
|
||||||
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
|
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
|
||||||
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km);
|
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km);
|
||||||
mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
|
mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,21 @@
|
||||||
|
.SUFFIXES: .gp .tex .eps .pdf .eps.gz
|
||||||
|
|
||||||
|
.eps.pdf:
|
||||||
|
epstopdf --outfile $@ $<
|
||||||
|
|
||||||
|
.eps.gz.pdf:
|
||||||
|
gzip -dc $< | epstopdf --filter > $@
|
||||||
|
|
||||||
|
.pdf.eps:
|
||||||
|
pdftops -eps $< $@
|
||||||
|
|
||||||
|
all:minimap2.pdf
|
||||||
|
|
||||||
|
roc-color.eps:roc.gp
|
||||||
|
gnuplot roc.gp
|
||||||
|
|
||||||
|
minimap2.pdf:minimap2.tex minimap2.bib roc-color.pdf
|
||||||
|
pdflatex minimap2; bibtex minimap2; pdflatex minimap2; pdflatex minimap2;
|
||||||
|
|
||||||
|
clean:
|
||||||
|
rm -fr *.toc *.aux *.bbl *.blg *.idx *.log *.out *~ minimap2.pdf
|
||||||
|
|
@ -0,0 +1,930 @@
|
||||||
|
\newcommand\classname{bioinfo}
|
||||||
|
\newcommand\lastmodifieddate{2003/02/08}
|
||||||
|
\newcommand\versionnumber{0.1}
|
||||||
|
|
||||||
|
% Are we printing crop marks?
|
||||||
|
\newif\if@cropmarkson \@cropmarksontrue
|
||||||
|
|
||||||
|
\NeedsTeXFormat{LaTeX2e}[2001/06/01]
|
||||||
|
\ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber]
|
||||||
|
|
||||||
|
\setlength{\paperheight}{11truein}
|
||||||
|
\setlength{\paperwidth}{8.5truein}
|
||||||
|
|
||||||
|
\newif\if@final
|
||||||
|
|
||||||
|
\DeclareOption{draft}{\PassOptionsToPackage{draft}{graphicx}}
|
||||||
|
\DeclareOption{a4paper}{\PassOptionsToPackage{a4}{crop}}
|
||||||
|
\DeclareOption{centre}{\PassOptionsToPackage{center}{crop}}
|
||||||
|
\DeclareOption{crop}{\PassOptionsToPackage{cam}{crop}\global\@cropmarksontrue}
|
||||||
|
\DeclareOption{nocrop}{\PassOptionsToPackage{off}{crop}\global\@cropmarksonfalse}
|
||||||
|
\DeclareOption{info}{\PassOptionsToPackage{info}{crop}}
|
||||||
|
\DeclareOption{noinfo}{\PassOptionsToPackage{noinfo}{crop}}
|
||||||
|
\DeclareOption{final}{\global\@finaltrue}
|
||||||
|
|
||||||
|
\ExecuteOptions{a4paper,nocrop,centre,info}
|
||||||
|
|
||||||
|
\ProcessOptions
|
||||||
|
|
||||||
|
% Load all necessary packages
|
||||||
|
\RequirePackage{inputenc,crop,graphicx,amsmath,array,color,amssymb,flushend,stfloats,amsthm,chngpage,times}
|
||||||
|
%\RequirePackage[LY1]{fontenc}
|
||||||
|
%\RequirePackage[LY1,mtbold]{mathtime}
|
||||||
|
\def\authoraffliate{\fontfamily{phv}\selectfont}
|
||||||
|
\def\helvetica{\fontfamily{phv}\selectfont}
|
||||||
|
\def\helveticaitalic{\fontfamily{phv}\itshape\selectfont}
|
||||||
|
\def\helveticabold{\fontfamily{phv}\bfseries\selectfont}
|
||||||
|
\def\helveticabolditalic{\fontfamily{phv}\bfseries\itshape\selectfont}
|
||||||
|
|
||||||
|
% Not sure if needed.
|
||||||
|
\newcommand\@ptsize{0}
|
||||||
|
|
||||||
|
% Set twoside printing
|
||||||
|
\@twosidetrue
|
||||||
|
|
||||||
|
% Marginal notes are on the outside edge
|
||||||
|
\@mparswitchfalse
|
||||||
|
|
||||||
|
\reversemarginpar
|
||||||
|
|
||||||
|
\renewcommand\normalsize{%
|
||||||
|
\@setfontsize\normalsize{9}{11}%
|
||||||
|
\abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@
|
||||||
|
\abovedisplayshortskip \z@ \@plus3\p@
|
||||||
|
\belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@
|
||||||
|
\belowdisplayskip \abovedisplayskip
|
||||||
|
\let\@listi\@listI}
|
||||||
|
\normalsize
|
||||||
|
\let\@bls\baselineskip
|
||||||
|
|
||||||
|
\newcommand\small{%
|
||||||
|
\@setfontsize\small{9}{11}%
|
||||||
|
\abovedisplayskip 11\p@ minus 3\p@
|
||||||
|
\belowdisplayskip \abovedisplayskip
|
||||||
|
\abovedisplayshortskip \z@ plus 2\p@
|
||||||
|
\belowdisplayshortskip 4\p@ plus 2\p@ minus2\p@
|
||||||
|
\def\@listi{\topsep 4.5\p@ plus 2\p@ minus 1\p@
|
||||||
|
\itemsep \parsep
|
||||||
|
\topsep 4\p@ plus 2\p@ minus 2\p@}}
|
||||||
|
|
||||||
|
\newcommand\footnotesize{%
|
||||||
|
\@setfontsize\footnotesize{8}{10}%
|
||||||
|
\abovedisplayskip 6\p@ minus 3\p@
|
||||||
|
\belowdisplayskip\abovedisplayskip
|
||||||
|
\abovedisplayshortskip \z@ plus 3\p@
|
||||||
|
\belowdisplayshortskip 6\p@ plus 3\p@ minus 3\p@
|
||||||
|
\def\@listi{\topsep 3\p@ plus 1\p@ minus 1\p@
|
||||||
|
\parsep 2\p@ plus 1\p@ minus 1\p@\itemsep \parsep}}
|
||||||
|
|
||||||
|
\def\scriptsize{\@setfontsize\scriptsize{7pt}{9pt}}
|
||||||
|
\def\tiny{\@setfontsize\tiny{5pt}{7pt}}
|
||||||
|
\def\large{\@setfontsize\large{11.5pt}{12pt}}
|
||||||
|
\def\Large{\@setfontsize\Large{14pt}{16}}
|
||||||
|
\def\LARGE{\@setfontsize\LARGE{15pt}{17pt}}
|
||||||
|
\def\huge{\@setfontsize\huge{22pt}{22pt}}
|
||||||
|
\def\Huge{\@setfontsize\Huge{30pt}{30pt}}
|
||||||
|
|
||||||
|
\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
|
||||||
|
\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
|
||||||
|
\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
|
||||||
|
\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
|
||||||
|
\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
|
||||||
|
\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
|
||||||
|
\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
|
||||||
|
|
||||||
|
% Line spacing
|
||||||
|
\setlength\lineskip{1\p@}
|
||||||
|
\setlength\normallineskip{1\p@}
|
||||||
|
\renewcommand\baselinestretch{}
|
||||||
|
|
||||||
|
% Paragraph dimensions and inter-para spacing
|
||||||
|
\setlength\parskip{0\p@}
|
||||||
|
\setlength\parindent{3mm}
|
||||||
|
|
||||||
|
% Set inter-para skips
|
||||||
|
\setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@}
|
||||||
|
\setlength\medskipamount{6\p@ \@plus 2\p@}
|
||||||
|
\setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@}
|
||||||
|
|
||||||
|
% Page break penalties
|
||||||
|
\@lowpenalty 51
|
||||||
|
\@medpenalty 151
|
||||||
|
\@highpenalty 301
|
||||||
|
|
||||||
|
% Disallow widows and orphans
|
||||||
|
\clubpenalty 10000
|
||||||
|
\widowpenalty 10000
|
||||||
|
|
||||||
|
% Disable page breaks before equations, allow pagebreaks after
|
||||||
|
% equations and discourage widow lines before equations.
|
||||||
|
\displaywidowpenalty 100
|
||||||
|
\predisplaypenalty 10000
|
||||||
|
\postdisplaypenalty 2500
|
||||||
|
|
||||||
|
% Allow breaking the page in the middle of a paragraph
|
||||||
|
\interlinepenalty 0
|
||||||
|
|
||||||
|
% Disallow breaking the page after a hyphenated line
|
||||||
|
\brokenpenalty 10000
|
||||||
|
|
||||||
|
% Hyphenation; don't split words into less than three characters
|
||||||
|
\lefthyphenmin=3
|
||||||
|
\righthyphenmin=3
|
||||||
|
|
||||||
|
%
|
||||||
|
% Set page layout dimensions
|
||||||
|
%
|
||||||
|
\setlength\headheight{16\p@} % height of running head
|
||||||
|
\setlength\topmargin{2.9pc} % head margin
|
||||||
|
\addtolength\topmargin{-1in} % subtract out the 1 inch driver margin
|
||||||
|
|
||||||
|
\setlength\topskip{10\p@} % height of first line of text
|
||||||
|
\setlength\headsep{19\p@} % space below running head --
|
||||||
|
|
||||||
|
\setlength\footskip{34\p@} % space above footer line
|
||||||
|
\setlength\maxdepth{.5\topskip} % pages can be short or deep by half a line?
|
||||||
|
|
||||||
|
\setlength\textwidth{42pc} % text measure excluding margins
|
||||||
|
|
||||||
|
\setlength\textheight{58\baselineskip} % 54 lines on a full page,
|
||||||
|
\addtolength\textheight{\topskip} % including the first
|
||||||
|
% line on the page
|
||||||
|
|
||||||
|
% Set the margins
|
||||||
|
\setlength\marginparsep{3\p@}
|
||||||
|
\setlength\marginparpush{3\p@}
|
||||||
|
\setlength\marginparwidth{35\p@}
|
||||||
|
|
||||||
|
\setlength\oddsidemargin{4.5pc}
|
||||||
|
\addtolength\oddsidemargin{-1in} % subtract out the 1 inch driver margin
|
||||||
|
\setlength\@tempdima{\paperwidth}
|
||||||
|
\addtolength\@tempdima{-\textwidth}
|
||||||
|
\addtolength\@tempdima{-4.5pc}
|
||||||
|
\setlength\evensidemargin{\@tempdima}
|
||||||
|
\addtolength\evensidemargin{-1in}
|
||||||
|
|
||||||
|
\setlength\columnsep{1.5pc} % space between columns for double-column text
|
||||||
|
\setlength\columnseprule{0\p@} % width of rule between two columns
|
||||||
|
|
||||||
|
% Footnotes
|
||||||
|
\setlength\footnotesep{9\p@} % space between footnotes
|
||||||
|
% space between text and footnote
|
||||||
|
\setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
|
||||||
|
|
||||||
|
% Float placement parameters
|
||||||
|
|
||||||
|
% The total number of floats that can be allowed on a page.
|
||||||
|
\setcounter{totalnumber}{10}
|
||||||
|
% The maximum number of floats at the top and bottom of a page.
|
||||||
|
\setcounter{topnumber}{5}
|
||||||
|
\setcounter{bottomnumber}{5}
|
||||||
|
% The maximum part of the top or bottom of a text page that can be
|
||||||
|
% occupied by floats. This is set so that at least four lines of text
|
||||||
|
% fit on the page.
|
||||||
|
\renewcommand\topfraction{.9}
|
||||||
|
\renewcommand\bottomfraction{.9}
|
||||||
|
% The minimum amount of a text page that must be occupied by text.
|
||||||
|
% This should accomodate four lines of text.
|
||||||
|
\renewcommand\textfraction{.06}
|
||||||
|
% The minimum amount of a float page that must be occupied by floats.
|
||||||
|
\renewcommand\floatpagefraction{.94}
|
||||||
|
|
||||||
|
% The same parameters repeated for double column output
|
||||||
|
\renewcommand\dbltopfraction{.9}
|
||||||
|
\renewcommand\dblfloatpagefraction{.9}
|
||||||
|
|
||||||
|
% Space between floats
|
||||||
|
\setlength\floatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
|
||||||
|
% Space between floats and text
|
||||||
|
\setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
|
||||||
|
% Space above and below an inline figure
|
||||||
|
\setlength\intextsep {18\p@ \@plus 2\p@ \@minus 2\p@}
|
||||||
|
|
||||||
|
% For double column floats
|
||||||
|
\setlength\dblfloatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
|
||||||
|
\setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
|
||||||
|
|
||||||
|
% Space left at top, bottom and inbetween floats on a float page.
|
||||||
|
\setlength\@fptop{0\p@} % no space above float page figures
|
||||||
|
\setlength\@fpsep{12\p@ \@plus 1fil}
|
||||||
|
\setlength\@fpbot{0\p@}
|
||||||
|
|
||||||
|
% The same for double column
|
||||||
|
\setlength\@dblfptop{0\p@}
|
||||||
|
\setlength\@dblfpsep{12\p@ \@plus 1fil}
|
||||||
|
\setlength\@dblfpbot{0\p@}
|
||||||
|
|
||||||
|
% Override settings in mathtime back to TeX defaults
|
||||||
|
\DeclareMathSizes{5} {5} {5} {5}
|
||||||
|
\DeclareMathSizes{6} {6} {5} {5}
|
||||||
|
\DeclareMathSizes{7} {7} {5} {5}
|
||||||
|
\DeclareMathSizes{8} {8} {6} {5}
|
||||||
|
\DeclareMathSizes{9} {9} {6.5} {5}
|
||||||
|
\DeclareMathSizes{10} {10} {7.5} {5}
|
||||||
|
\DeclareMathSizes{12} {12} {9} {7}
|
||||||
|
|
||||||
|
% Page styles
|
||||||
|
\def\ps@headings
|
||||||
|
{%
|
||||||
|
\def\@oddfoot{\vbox to 12.5\p@{\hbox{\rule{\textwidth}{0.5\p@}}\vss
|
||||||
|
\hbox to \textwidth{\hfill\helveticabold\small\thepage}%
|
||||||
|
}}%
|
||||||
|
\def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
|
||||||
|
\hbox to \textwidth{\helveticabold\small\thepage\hfill}%
|
||||||
|
}}%
|
||||||
|
\def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{8}{10}\selectfont
|
||||||
|
\helveticabold{\fontshape{it}\selectfont
|
||||||
|
\strut\leftmark}\hfill}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
|
||||||
|
\def\@oddhead{\vbox{\hbox to \textwidth{\hfill\fontsize{8}{10}\selectfont
|
||||||
|
\helveticabold{\fontshape{it}\selectfont\strut\rightmark}}%
|
||||||
|
\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
|
||||||
|
\def\titlemark##1{\markboth{##1}{##1}}%
|
||||||
|
\def\authormark##1{\gdef\leftmark{##1}}%
|
||||||
|
}
|
||||||
|
|
||||||
|
\def\ps@opening
|
||||||
|
{%
|
||||||
|
\def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
|
||||||
|
\hbox to \textwidth{\helvetica
|
||||||
|
\fontsize{7}{9}\fontshape{n}\selectfont%
|
||||||
|
\hfill\small\helveticabold\thepage}%
|
||||||
|
}}%
|
||||||
|
\def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}\vss
|
||||||
|
\hbox to \textwidth{\helvetica\thepage\hfill
|
||||||
|
\fontsize{7}{9}\fontshape{n}\selectfont}%
|
||||||
|
}}%
|
||||||
|
\let\@evenhead\relax
|
||||||
|
\let\@oddhead\relax}
|
||||||
|
|
||||||
|
% Page range
|
||||||
|
\newif\iflastpagegiven \lastpagegivenfalse
|
||||||
|
\newcommand\firstpage[1]{%
|
||||||
|
\gdef\@firstpage{#1}%
|
||||||
|
\ifnum\@firstpage>\c@page
|
||||||
|
\setcounter{page}{#1}%
|
||||||
|
\ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
|
||||||
|
\else \ifnum\@firstpage<\c@page
|
||||||
|
\ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
|
||||||
|
\xdef\@firstpage{\the\c@page}%
|
||||||
|
}
|
||||||
|
\def\@firstpage{1}
|
||||||
|
\def\pagenumbering#1{%
|
||||||
|
\global\c@page \@ne
|
||||||
|
\gdef\thepage{\csname @#1\endcsname \c@page}%
|
||||||
|
\gdef\thefirstpage{%
|
||||||
|
\csname @#1\endcsname \@firstpage}%
|
||||||
|
\gdef\thelastpage{%
|
||||||
|
\csname @#1\endcsname \@lastpage}%
|
||||||
|
}
|
||||||
|
|
||||||
|
\newcommand\lastpage[1]{\xdef\@lastpage{#1}%
|
||||||
|
\global\lastpagegiventrue}
|
||||||
|
\def\@lastpage{0}
|
||||||
|
\def\setlastpage{\iflastpagegiven\else
|
||||||
|
\edef\@tempa{@lastpage@}%
|
||||||
|
\expandafter
|
||||||
|
\ifx \csname \@tempa \endcsname \relax
|
||||||
|
\gdef\@lastpage{0}%
|
||||||
|
\else
|
||||||
|
\xdef\@lastpage{\@nameuse{@lastpage@}}%
|
||||||
|
\fi
|
||||||
|
\fi }
|
||||||
|
\def\writelastpage{%
|
||||||
|
\iflastpagegiven \else
|
||||||
|
\immediate\write\@auxout%
|
||||||
|
{\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
|
||||||
|
\fi
|
||||||
|
}
|
||||||
|
\def\thepagerange{%
|
||||||
|
\ifnum\@lastpage =0 {\ \bf ???} \else
|
||||||
|
\ifnum\@lastpage = \@firstpage \ \thefirstpage\else
|
||||||
|
\thefirstpage--\thelastpage \fi\fi}
|
||||||
|
|
||||||
|
\AtBeginDocument{\setlastpage
|
||||||
|
\pagenumbering{arabic}%
|
||||||
|
}
|
||||||
|
\AtEndDocument{%
|
||||||
|
\writelastpage
|
||||||
|
\if@final
|
||||||
|
\clearemptydoublepage
|
||||||
|
\else
|
||||||
|
\clearpage
|
||||||
|
\fi}
|
||||||
|
|
||||||
|
%
|
||||||
|
% Sectional units
|
||||||
|
%
|
||||||
|
|
||||||
|
% Counters
|
||||||
|
\newcounter{section}
|
||||||
|
\newcounter{subsection}[section]
|
||||||
|
\newcounter{subsubsection}[subsection]
|
||||||
|
\newcounter{paragraph}[subsubsection]
|
||||||
|
\newcounter{subparagraph}[paragraph]
|
||||||
|
\newcounter{figure}
|
||||||
|
\newcounter{table}
|
||||||
|
|
||||||
|
% Form of the numbers
|
||||||
|
\newcommand\thepage{\arabic{page}}
|
||||||
|
\renewcommand\thesection{\arabic{section}}
|
||||||
|
\renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
|
||||||
|
\renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
|
||||||
|
\renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
|
||||||
|
\renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
|
||||||
|
\renewcommand\theequation{\arabic{equation}}
|
||||||
|
|
||||||
|
% Form of the words
|
||||||
|
\newcommand\contentsname{Contents}
|
||||||
|
\newcommand\listfigurename{List of Figures}
|
||||||
|
\newcommand\listtablename{List of Tables}
|
||||||
|
\newcommand\partname{Part}
|
||||||
|
\newcommand\appendixname{Appendix}
|
||||||
|
\newcommand\abstractname{Abstract}
|
||||||
|
\newcommand\refname{References}
|
||||||
|
\newcommand\bibname{References}
|
||||||
|
\newcommand\indexname{Index}
|
||||||
|
\newcommand\figurename{Fig.}
|
||||||
|
\newcommand\tablename{Table}
|
||||||
|
|
||||||
|
% Clearemptydoublepage should really clear the running heads too
|
||||||
|
\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
|
||||||
|
|
||||||
|
% Frontmatter, mainmatter and backmatter
|
||||||
|
|
||||||
|
\newif\if@mainmatter \@mainmattertrue
|
||||||
|
|
||||||
|
\newcommand\frontmatter{%
|
||||||
|
\clearpage
|
||||||
|
\@mainmatterfalse
|
||||||
|
\pagenumbering{roman}}
|
||||||
|
|
||||||
|
\newcommand\mainmatter{%
|
||||||
|
\clearpage
|
||||||
|
\@mainmattertrue
|
||||||
|
\pagenumbering{arabic}}
|
||||||
|
|
||||||
|
\newcommand\backmatter{%
|
||||||
|
\clearpage
|
||||||
|
\@mainmatterfalse}
|
||||||
|
|
||||||
|
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% TITLE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||||
|
\newlength{\dropfromtop}
|
||||||
|
\setlength{\dropfromtop}{\z@}
|
||||||
|
|
||||||
|
% Application Notes
|
||||||
|
\newif\if@appnotes
|
||||||
|
\newcommand{\application}{%
|
||||||
|
% \setlength{\dropfromtop}{-2.25pc}%
|
||||||
|
\global\@appnotestrue}
|
||||||
|
|
||||||
|
\long\def\title{\@ifnextchar[{\short@title}{\@@title}}
|
||||||
|
\def\short@title[#1]{\titlemark{#1}\@@@title}
|
||||||
|
\def\@@title#1{\authormark{#1}\@@@title{#1}}
|
||||||
|
\long\def\@@@title#1{\gdef\@title{#1}}
|
||||||
|
|
||||||
|
\long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
|
||||||
|
\def\short@uthor[#1]{\authormark{#1}\@@author}
|
||||||
|
\def\@uthor#1{\authormark{#1}\@@author{#1}}
|
||||||
|
\long\def\@@author#1{\gdef\@author{#1}}
|
||||||
|
|
||||||
|
\def\vol#1{\global\def\@vol{#1}}
|
||||||
|
\def\issue#1{\global\def\@issue{#1}}
|
||||||
|
\def\address#1{\global\def\@issue{#1}}
|
||||||
|
\def\history#1{\global\def\@history{#1}}
|
||||||
|
\def\editor#1{\global\def\@editor{#1}}
|
||||||
|
\def\pubyear#1{\global\def\@pubyear{#1}}
|
||||||
|
\def\copyrightyear#1{\global\def\@copyrightyear{#1}}
|
||||||
|
\def\address#1{\global\def\@address{#1}}
|
||||||
|
\def\DOI#1{\global\def\@DOI{#1}}
|
||||||
|
|
||||||
|
\definecolor{gray}{cmyk}{0, 0, 0, 0.15}
|
||||||
|
\newlength{\extraspace}
|
||||||
|
\setlength{\extraspace}{\z@}
|
||||||
|
|
||||||
|
\newcommand\maketitle{\par
|
||||||
|
\begingroup
|
||||||
|
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
|
||||||
|
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
|
||||||
|
\long\def\@makefntext##1{\parindent 3mm\noindent
|
||||||
|
% \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
|
||||||
|
\@textsuperscript{\normalfont\@thefnmark}##1}%
|
||||||
|
\if@twocolumn
|
||||||
|
\ifnum \col@number=\@ne
|
||||||
|
\@maketitle
|
||||||
|
\else
|
||||||
|
\twocolumn[\@maketitle]%
|
||||||
|
\fi
|
||||||
|
\else
|
||||||
|
\newpage
|
||||||
|
\global\@topnum\z@ % Prevents figures from going at top of page.
|
||||||
|
\@maketitle
|
||||||
|
\fi
|
||||||
|
\thispagestyle{opening}\@thanks
|
||||||
|
\endgroup
|
||||||
|
\setcounter{footnote}{0}%
|
||||||
|
\global\let\thanks\relax
|
||||||
|
\global\let\maketitle\relax
|
||||||
|
\global\let\@maketitle\relax
|
||||||
|
\global\let\@address\@empty
|
||||||
|
\global\let\@history\@empty
|
||||||
|
\global\let\@editor\@empty
|
||||||
|
\global\let\@thanks\@empty
|
||||||
|
\global\let\@author\@empty
|
||||||
|
\global\let\@date\@empty
|
||||||
|
\global\let\@title\@empty
|
||||||
|
\global\let\@pubyear\@empty
|
||||||
|
\global\let\address\relax
|
||||||
|
\global\let\history\relax
|
||||||
|
\global\let\editor\relax
|
||||||
|
\global\let\title\relax
|
||||||
|
\global\let\author\relax
|
||||||
|
\global\let\date\relax
|
||||||
|
\global\let\pubyear\relax
|
||||||
|
\global\let\@copyrightline\@empty
|
||||||
|
\global\let\and\relax
|
||||||
|
\@afterindentfalse\@afterheading
|
||||||
|
}
|
||||||
|
|
||||||
|
\newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
|
||||||
|
\setlength{\aboveskipchk}{\z@}%
|
||||||
|
|
||||||
|
\def\@maketitle{%
|
||||||
|
\let\footnote\thanks
|
||||||
|
\clearemptydoublepage
|
||||||
|
\checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-3pc}\else\setlength{\aboveskipchk}{-5pc}\fi%for checking oddpage or evenpage top skip%%
|
||||||
|
\vspace*{\aboveskipchk}%
|
||||||
|
\vspace{\dropfromtop}%
|
||||||
|
\hbox to \textwidth{%
|
||||||
|
{\helvetica\itshape\bfseries\fontsize{19}{12}\selectfont {\color{gray}TECHNICAL REPORT}
|
||||||
|
\hfil
|
||||||
|
\if@appnotes APPLICATIONS NOTE\hfil\fi
|
||||||
|
}%
|
||||||
|
\enskip \parbox[b]{11.3pc}{%
|
||||||
|
\helvetica
|
||||||
|
\flushright\fontsize{8}{10}\fontshape{it}\selectfont
|
||||||
|
\hfill
|
||||||
|
}}
|
||||||
|
\rule{\textwidth}{1\p@}\par%
|
||||||
|
\helvetica
|
||||||
|
\hbox to \textwidth{%
|
||||||
|
\parbox[t]{41pc}{%
|
||||||
|
\vspace*{1sp}
|
||||||
|
{\helveticabold\fontsize{16}{21}\selectfont\raggedright \@title \par}%
|
||||||
|
\vspace{4.5\p@}
|
||||||
|
{\authoraffliate\fontsize{11}{13}\selectfont\raggedright \@author \par}%
|
||||||
|
\vspace{4\p@}
|
||||||
|
{\authoraffliate\fontsize{9}{11}\selectfont\raggedright \@address \par}%
|
||||||
|
\vspace{4\p@}
|
||||||
|
%{\helvetica\fontsize{8}{10}\selectfont\raggedright \@history \par}
|
||||||
|
%\vspace{24\p@}
|
||||||
|
%{\helvetica\fontsize{10}{12}\selectfont\raggedright \@editor \par}
|
||||||
|
%\vspace{20\p@}
|
||||||
|
}%
|
||||||
|
}
|
||||||
|
\vspace{4.5\p@}%
|
||||||
|
\rule{\textwidth}{1\p@}%
|
||||||
|
\vspace{12\p@ plus 6\p@ minus 6\p@}%
|
||||||
|
\vspace{\extraspace}
|
||||||
|
}
|
||||||
|
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||||
|
|
||||||
|
%%%%%%%%%%%%%%%%%%%%%%%%%%%% Abstract %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||||
|
\newcommand{\absection}[1]{%
|
||||||
|
\par\noindent{\bfseries #1}\space\ignorespaces}
|
||||||
|
|
||||||
|
\newenvironment{abstract}{%
|
||||||
|
\begingroup
|
||||||
|
\let\section\absection
|
||||||
|
\fontfamily{\sfdefault}\fontsize{8}{11}\sffamily\selectfont
|
||||||
|
{\fontseries{b}\selectfont ABSTRACT}\par}
|
||||||
|
{\endgroup\bigskip\@afterheading\@afterindentfalse\vskip 12pt plus 3pt minus 1pt}
|
||||||
|
|
||||||
|
% Section macros
|
||||||
|
|
||||||
|
% Lowest level heading that takes a number by default
|
||||||
|
\setcounter{secnumdepth}{3}
|
||||||
|
|
||||||
|
\renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad}
|
||||||
|
|
||||||
|
\def\section{%
|
||||||
|
\@startsection{section}{1}{\z@}
|
||||||
|
{-22\p@ plus -3\p@}{3\p@}
|
||||||
|
{\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
|
||||||
|
|
||||||
|
\def\subsection{%
|
||||||
|
\@startsection{subsection}{2}{\z@}
|
||||||
|
{-11\p@ plus -2\p@}{3\p@}
|
||||||
|
{\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
|
||||||
|
|
||||||
|
\def\subsubsection{%
|
||||||
|
\@startsection{subsubsection}{3}{\z@}
|
||||||
|
%{-11\p@ plus -1\p@}{-1em}
|
||||||
|
{-11\p@ plus -1\p@}{0.001em}
|
||||||
|
{\reset@font\normalfont\normalsize\itshape}}
|
||||||
|
|
||||||
|
\def\textcolon{\text{\rm :}}
|
||||||
|
|
||||||
|
\def\paragraph{%
|
||||||
|
\@startsection{paragraph}{4}{\z@}
|
||||||
|
{-6\p@}
|
||||||
|
{-.4em}
|
||||||
|
{\reset@font\itshape}}
|
||||||
|
|
||||||
|
% ********************
|
||||||
|
% Figures and tables *
|
||||||
|
% ********************
|
||||||
|
|
||||||
|
% Table and array parameters
|
||||||
|
\setlength\arraycolsep{.5em}
|
||||||
|
\setlength\tabcolsep{.5em}
|
||||||
|
\setlength\arrayrulewidth{.5pt}
|
||||||
|
\setlength\doublerulesep{2.5pt}
|
||||||
|
\setlength\extrarowheight{\z@}
|
||||||
|
\renewcommand\arraystretch{1}
|
||||||
|
|
||||||
|
\newlength{\abovecaptionskip}
|
||||||
|
\newlength{\belowcaptionskip}
|
||||||
|
\setlength{\abovecaptionskip}{13pt}
|
||||||
|
\setlength{\belowcaptionskip}{10.5pt}
|
||||||
|
|
||||||
|
\long\def\@makecaption#1#2{\vspace{\abovecaptionskip}%
|
||||||
|
\begingroup
|
||||||
|
\footnotesize
|
||||||
|
\textbf{#1.}\enskip{#2}\par
|
||||||
|
\endgroup}
|
||||||
|
|
||||||
|
\long\def\@tablecaption#1#2{%
|
||||||
|
\begingroup
|
||||||
|
\footnotesize
|
||||||
|
\textbf{#1.}\enskip{#2\strut\par}
|
||||||
|
\endgroup\vspace{\belowcaptionskip}}
|
||||||
|
|
||||||
|
% Table rules
|
||||||
|
\def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet
|
||||||
|
\@tempa\@xhline}
|
||||||
|
\def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt
|
||||||
|
\hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline}
|
||||||
|
\def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet
|
||||||
|
\@tempa\@xhline}
|
||||||
|
\def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@}
|
||||||
|
|
||||||
|
\def\thefigure{\@arabic\c@figure}
|
||||||
|
\def\fps@figure{tbp}
|
||||||
|
\def\ftype@figure{1}
|
||||||
|
\def\ext@figure{lof}
|
||||||
|
\def\fnum@figure{\figurename~\thefigure}
|
||||||
|
\def\figure{\@float{figure}}
|
||||||
|
\let\endfigure\end@float
|
||||||
|
\@namedef{figure*}{\@dblfloat{figure}}
|
||||||
|
\@namedef{endfigure*}{\end@dblfloat}
|
||||||
|
\def\thetable{\@arabic\c@table}
|
||||||
|
\def\fps@table{tbp}
|
||||||
|
\def\ftype@table{2}
|
||||||
|
\def\ext@table{lot}
|
||||||
|
\def\fnum@table{Table~\thetable}
|
||||||
|
\def\table{\let\@makecaption\@tablecaption\let\source\tablesource\@float{table}}
|
||||||
|
\def\endtable{\end@float}
|
||||||
|
\@namedef{table*}{\let\@makecaption\@tablecaption\@dblfloat{table}}
|
||||||
|
\@namedef{endtable*}{\end@dblfloat}
|
||||||
|
|
||||||
|
\newif\if@rotate \@rotatefalse
|
||||||
|
\newif\if@rotatecenter \@rotatecenterfalse
|
||||||
|
\def\rotatecenter{\global\@rotatecentertrue}
|
||||||
|
\def\rotateendcenter{\global\@rotatecenterfalse}
|
||||||
|
\def\rotate{\global\@rotatetrue}
|
||||||
|
\def\endrotate{\global\@rotatefalse}
|
||||||
|
\newdimen\rotdimen
|
||||||
|
\def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate
|
||||||
|
#1 neg exch neg exch translate}}
|
||||||
|
\def\rotfinish{\special{ps: currentpoint grestore moveto}}
|
||||||
|
\def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1
|
||||||
|
\hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1
|
||||||
|
\rotstart{270 rotate}\box #1\vss}\hss}\rotfinish}
|
||||||
|
\def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1
|
||||||
|
\hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1
|
||||||
|
\rotstart{90 rotate}\box #1\vss}\hss}\rotfinish}
|
||||||
|
|
||||||
|
\newdimen\tempdime
|
||||||
|
\newbox\temptbox
|
||||||
|
|
||||||
|
% From ifmtarg.sty
|
||||||
|
% Copyright Peter Wilson and Donald Arseneau, 2000
|
||||||
|
\begingroup
|
||||||
|
\catcode`\Q=3
|
||||||
|
\long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil}
|
||||||
|
\long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4}
|
||||||
|
\long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil}
|
||||||
|
\endgroup
|
||||||
|
|
||||||
|
\def\tablesize{\@setfontsize\tablesize{8\p@}{10\p@}}
|
||||||
|
|
||||||
|
\newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}%
|
||||||
|
\tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}}
|
||||||
|
{\relax}
|
||||||
|
|
||||||
|
\newcommand{\@processtable}[4]{%
|
||||||
|
\if@rotate
|
||||||
|
\setbox4=\vbox to \hsize{\vss\hbox to \textheight{%
|
||||||
|
\begin{minipage}{#4}%
|
||||||
|
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
|
||||||
|
\vskip7\p@\noindent
|
||||||
|
\parbox{#4}{\fontsize{7}{9}\selectfont #3\par}%
|
||||||
|
\end{minipage}}\vss}%
|
||||||
|
\rotr{4}
|
||||||
|
\else
|
||||||
|
\hbox to \hsize{\hss\begin{minipage}[t]{#4}%
|
||||||
|
\vskip2.9pt
|
||||||
|
\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
|
||||||
|
\vskip6\p@\noindent
|
||||||
|
\parbox{#4}{\fontsize{7}{9}\selectfont #3\par}%
|
||||||
|
\end{minipage}\hss}\fi}%
|
||||||
|
|
||||||
|
\newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}}
|
||||||
|
|
||||||
|
% ******************************
|
||||||
|
% List numbering and lettering *
|
||||||
|
% ******************************
|
||||||
|
\def\labelenumi{{\rm\arabic{enumi}.}}
|
||||||
|
\def\theenumi{\arabic{enumi}}
|
||||||
|
\def\labelenumii{{\rm\alph{enumii}.}}
|
||||||
|
\def\theenumii{\alph{enumii}}
|
||||||
|
\def\p@enumii{\theenumi}
|
||||||
|
\def\labelenumiii{{\rm(\arabic{enumiii})}}
|
||||||
|
\def\theenumiii{\roman{enumiii}}
|
||||||
|
\def\p@enumiii{\theenumi(\theenumii)}
|
||||||
|
\def\labelenumiv{{\rm(\arabic{enumiv})}}
|
||||||
|
\def\theenumiv{\Alph{enumiv}}
|
||||||
|
\def\p@enumiv{\p@enumiii\theenumiii}
|
||||||
|
\def\labelitemi{{\small$\bullet$}}
|
||||||
|
\def\labelitemii{{\small$\bullet$}}
|
||||||
|
\def\labelitemiii{{\small$\bullet$}}
|
||||||
|
\def\labelitemiv{{\small$\bullet$}}
|
||||||
|
|
||||||
|
\def\@listI{\leftmargin\leftmargini \topsep\medskipamount}
|
||||||
|
\let\@listi\@listI
|
||||||
|
\@listi
|
||||||
|
\def\@listii{\topsep\z@\leftmargin\leftmarginii}
|
||||||
|
\def\@listiii{\leftmargin\leftmarginiii \topsep\z@}
|
||||||
|
\def\@listiv{\leftmargin\leftmarginiv \topsep\z@}
|
||||||
|
\def\@listv{\leftmargin\leftmarginv \topsep\z@}
|
||||||
|
\def\@listvi{\leftmargin\leftmarginvi \topsep\z@}
|
||||||
|
|
||||||
|
\setlength{\leftmargini}{3mm}
|
||||||
|
\setlength{\leftmarginii}{\z@}
|
||||||
|
\setlength{\leftmarginiii}{\z@}
|
||||||
|
\setlength{\leftmarginiv}{\z@}
|
||||||
|
|
||||||
|
% Changes to the list parameters for enumerate
|
||||||
|
\def\enumargs{%
|
||||||
|
\partopsep \z@
|
||||||
|
\itemsep 3\p@
|
||||||
|
\parsep \z@
|
||||||
|
\labelsep 0.5em
|
||||||
|
\listparindent \parindent
|
||||||
|
\itemindent \z@
|
||||||
|
\topsep 11\p@
|
||||||
|
}
|
||||||
|
|
||||||
|
\def\enumerate{%
|
||||||
|
\@ifnextchar[{\@numerate}{\@numerate[0]}}
|
||||||
|
|
||||||
|
\def\@numerate[#1]{%
|
||||||
|
\ifnum \@enumdepth >3 \@toodeep\else
|
||||||
|
\advance\@enumdepth \@ne
|
||||||
|
\edef\@enumctr{enum\romannumeral\the\@enumdepth}
|
||||||
|
\list{\csname label\@enumctr\endcsname}{%
|
||||||
|
\enumargs
|
||||||
|
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname}
|
||||||
|
\usecounter{\@enumctr}
|
||||||
|
\settowidth\labelwidth{#1}
|
||||||
|
\addtolength{\leftmargin}{\labelwidth}
|
||||||
|
\addtolength{\leftmargin}{\labelsep}
|
||||||
|
\def\makelabel##1{\hss \llap{##1}}}%
|
||||||
|
\fi
|
||||||
|
}
|
||||||
|
\let\endenumerate\endlist
|
||||||
|
|
||||||
|
% Changes to the list parameters for itemize
|
||||||
|
\def\itemargs{%
|
||||||
|
\partopsep \z@
|
||||||
|
\itemsep 3\p@
|
||||||
|
\parsep \z@
|
||||||
|
\labelsep 0.5em
|
||||||
|
\rightmargin \z@
|
||||||
|
\listparindent \parindent
|
||||||
|
\itemindent \z@
|
||||||
|
\topsep11\p@
|
||||||
|
}
|
||||||
|
|
||||||
|
\def\itemize{%
|
||||||
|
\@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
|
||||||
|
|
||||||
|
\def\@itemize[#1]{%
|
||||||
|
\ifnum \@itemdepth >3 \@toodeep\else
|
||||||
|
\advance\@itemdepth \@ne
|
||||||
|
\edef\@itemctr{item\romannumeral\the\@itemdepth}
|
||||||
|
\list{\csname label\@itemctr\endcsname}{%
|
||||||
|
\itemargs
|
||||||
|
\setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname}
|
||||||
|
\settowidth\labelwidth{#1}
|
||||||
|
\addtolength{\leftmargin}{\labelwidth}
|
||||||
|
\addtolength{\leftmargin}{\labelsep}
|
||||||
|
\def\makelabel##1{\hss \llap{##1}}}%
|
||||||
|
\fi
|
||||||
|
}
|
||||||
|
\let\enditemize\endlist
|
||||||
|
|
||||||
|
\newenvironment{unlist}{%
|
||||||
|
\begin{list}{}%
|
||||||
|
{\setlength{\labelwidth}{\z@}%
|
||||||
|
\setlength{\labelsep}{\z@}%
|
||||||
|
\setlength{\topsep}{\medskipamount}%
|
||||||
|
\setlength{\itemsep}{3\p@}%
|
||||||
|
\setlength{\leftmargin}{2em}%
|
||||||
|
\setlength{\itemindent}{-2em}}}
|
||||||
|
{\end{list}}
|
||||||
|
|
||||||
|
|
||||||
|
% ***********************
|
||||||
|
% Quotes and Quotations *
|
||||||
|
% ***********************
|
||||||
|
\def\quotation{\par\begin{list}{}{
|
||||||
|
\setlength{\topsep}{\medskipamount}
|
||||||
|
\setlength{\leftmargin}{2em}%
|
||||||
|
\setlength{\rightmargin}{\z@}%
|
||||||
|
\setlength\labelwidth{0pt}%
|
||||||
|
\setlength\labelsep{0pt}%
|
||||||
|
\listparindent\parindent}%
|
||||||
|
\item[]}
|
||||||
|
\def\endquotation{\end{list}}
|
||||||
|
\let\quote\quotation
|
||||||
|
\let\endquote\endquotation
|
||||||
|
|
||||||
|
\skip\@mpfootins = \skip\footins
|
||||||
|
\fboxsep=6\p@
|
||||||
|
\fboxrule=1\p@
|
||||||
|
|
||||||
|
% *******************
|
||||||
|
% Table of contents *
|
||||||
|
% *******************
|
||||||
|
\newcommand\@pnumwidth{4em}
|
||||||
|
\newcommand\@tocrmarg{2.55em plus 1fil}
|
||||||
|
\newcommand\@dotsep{1000}
|
||||||
|
\setcounter{tocdepth}{4}
|
||||||
|
|
||||||
|
\def\numberline#1{\hbox to \@tempdima{{#1}}}
|
||||||
|
|
||||||
|
\def\@authortocline#1#2#3#4#5{%
|
||||||
|
\vskip 1.5\p@
|
||||||
|
\ifnum #1>\c@tocdepth \else
|
||||||
|
{\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
|
||||||
|
\parindent #2\relax\@afterindenttrue
|
||||||
|
\interlinepenalty\@M
|
||||||
|
\leavevmode
|
||||||
|
\@tempdima #3\relax
|
||||||
|
\advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
|
||||||
|
{\itshape #4}\nobreak
|
||||||
|
\leaders\hbox{$\m@th
|
||||||
|
\mkern \@dotsep mu\hbox{.}\mkern \@dotsep
|
||||||
|
mu$}\hfill
|
||||||
|
\nobreak
|
||||||
|
\hb@xt@\@pnumwidth{\hfil}%
|
||||||
|
\par}%
|
||||||
|
\fi}
|
||||||
|
|
||||||
|
\newcommand*\l@author{\@authortocline{2}{0pt}{30pt}}
|
||||||
|
\newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}}
|
||||||
|
\newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}}
|
||||||
|
\newcommand*\l@subsubsection[2]{}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
% ***********
|
||||||
|
% Footnotes *
|
||||||
|
% ***********
|
||||||
|
|
||||||
|
\def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}}
|
||||||
|
\def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}%
|
||||||
|
\newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1}
|
||||||
|
|
||||||
|
% ***********
|
||||||
|
% References *
|
||||||
|
% ***********
|
||||||
|
|
||||||
|
\providecommand{\newblock}{}
|
||||||
|
\newenvironment{thebibliography}{%
|
||||||
|
\section{\bibname}%
|
||||||
|
\begingroup
|
||||||
|
\small
|
||||||
|
\begin{list}{}{%
|
||||||
|
\setlength{\topsep}{\z@}%
|
||||||
|
\setlength{\labelsep}{\z@}%
|
||||||
|
\settowidth{\labelwidth}{\z@}%
|
||||||
|
\setlength{\leftmargin}{4mm}%
|
||||||
|
\setlength{\itemindent}{-4mm}}\small}
|
||||||
|
{\end{list}\endgroup}
|
||||||
|
|
||||||
|
\RequirePackage{natbib}
|
||||||
|
|
||||||
|
% **********
|
||||||
|
% Appendix *
|
||||||
|
% **********
|
||||||
|
\newif\ifappend % Are we in the Appendix?
|
||||||
|
\def\appendix{\par
|
||||||
|
\setcounter{section}{0}
|
||||||
|
\setcounter{subsection}{0}
|
||||||
|
\appendtrue
|
||||||
|
}
|
||||||
|
|
||||||
|
%Math parameters
|
||||||
|
|
||||||
|
\setlength{\jot}{5\p@}
|
||||||
|
\mathchardef\@m=1500 % adapted value
|
||||||
|
|
||||||
|
\def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m
|
||||||
|
\sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m}
|
||||||
|
|
||||||
|
% Theorems
|
||||||
|
\def\th@plain{%
|
||||||
|
%% \let\thm@indent\noindent % no indent
|
||||||
|
\thm@headfont{\quad\scshape}% heading font is bold
|
||||||
|
\thm@notefont{\upshape\mdseries}% same as heading font
|
||||||
|
\thm@headpunct{.}% no period after heading
|
||||||
|
\thm@headsep 5\p@ plus\p@ minus\p@\relax
|
||||||
|
%% \let\thm@swap\@gobble
|
||||||
|
%% \thm@preskip\topsep
|
||||||
|
%% \thm@postskip\theorempreskipamount
|
||||||
|
\itshape % body font
|
||||||
|
}
|
||||||
|
|
||||||
|
\vbadness=9999
|
||||||
|
\tolerance=9999
|
||||||
|
\doublehyphendemerits=10000
|
||||||
|
\doublehyphendemerits 640000 % corresponds to badness 800
|
||||||
|
\finalhyphendemerits 1000000 % corresponds to badness 1000
|
||||||
|
|
||||||
|
\flushbottom
|
||||||
|
\frenchspacing
|
||||||
|
\ps@headings
|
||||||
|
\twocolumn
|
||||||
|
|
||||||
|
% Screen PDF compatability
|
||||||
|
\newcommand{\medline}[1]{%
|
||||||
|
\unskip\unskip\ignorespaces}
|
||||||
|
|
||||||
|
|
||||||
|
%%%%for smaller size text
|
||||||
|
\newenvironment{methods}{%
|
||||||
|
\begingroup
|
||||||
|
\def\section{%
|
||||||
|
\@startsection{section}{1}{\z@}
|
||||||
|
{-24\p@ plus -3\p@}{4\p@}
|
||||||
|
{\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
|
||||||
|
\def\subsection{%
|
||||||
|
\@startsection{subsection}{2}{\z@}
|
||||||
|
{-5\p@ plus -2\p@}{4\p@}
|
||||||
|
{\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
|
||||||
|
\def\subsubsection{%
|
||||||
|
\@startsection{subsubsection}{3}{\z@}
|
||||||
|
% {-6\p@ plus -1\p@}{-1em}
|
||||||
|
{-6\p@ plus -1\p@}{0.001em}
|
||||||
|
{\reset@font\normalfont\normalsize\itshape}}
|
||||||
|
\footnotesize
|
||||||
|
\par}
|
||||||
|
{\par\endgroup\bigskip\@afterheading\@afterindentfalse}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
\graphicspath{{g:/artwork/oup/bioinfo/}}
|
||||||
|
|
||||||
|
\language=2
|
||||||
|
|
||||||
|
\hyphenation{Figure Table Figures Tables}
|
||||||
|
|
||||||
|
\newcommand{\href}[2]{#2}
|
||||||
|
|
||||||
|
\renewenvironment{proof}[1][\proofname]{\par
|
||||||
|
\normalfont \topsep6\p@\@plus6\p@\relax
|
||||||
|
\labelsep 0.5em
|
||||||
|
\trivlist
|
||||||
|
\item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces
|
||||||
|
}{\endtrivlist\@endpefalse}
|
||||||
|
|
||||||
|
%%Different Bonds
|
||||||
|
|
||||||
|
\def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt}
|
||||||
|
\def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}}
|
||||||
|
\def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}}
|
||||||
|
|
||||||
|
% Author queries
|
||||||
|
%\fboxsep=4\p@
|
||||||
|
%\fboxrule=0.5\p@
|
||||||
|
\newcommand{\query}[2][0pt]{}%
|
||||||
|
% \marginpar{\vspace*{#1}%
|
||||||
|
% {\parbox{\marginparwidth}{%
|
||||||
|
% \raggedright\fontsize{6}{8}\selectfont
|
||||||
|
% #2}}}}
|
||||||
|
|
||||||
|
\renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}}
|
||||||
|
|
||||||
|
\endinput
|
||||||
|
|
@ -0,0 +1,17 @@
|
||||||
|
Q 60 32681 57 0.001744133
|
||||||
|
Q 39 3 1 0.001774569
|
||||||
|
Q 38 3 1 0.001804999
|
||||||
|
Q 35 5 1 0.001835311
|
||||||
|
Q 34 31 2 0.001894692
|
||||||
|
Q 20 11 2 0.001955154
|
||||||
|
Q 19 4 1 0.001985460
|
||||||
|
Q 15 29 5 0.002136296
|
||||||
|
Q 14 6 1 0.002166417
|
||||||
|
Q 10 11 1 0.002196193
|
||||||
|
Q 6 11 2 0.002256442
|
||||||
|
Q 5 1 1 0.002286864
|
||||||
|
Q 4 1 1 0.002317285
|
||||||
|
Q 3 36 15 0.002771602
|
||||||
|
Q 2 5 2 0.002832085
|
||||||
|
Q 1 12 9 0.003105023
|
||||||
|
Q 0 220 83 0.005594194
|
||||||
|
|
@ -0,0 +1,55 @@
|
||||||
|
Q 60 31721 27 0.000851171
|
||||||
|
Q 59 54 4 0.000975610
|
||||||
|
Q 58 29 5 0.001131933
|
||||||
|
Q 57 21 2 0.001194030
|
||||||
|
Q 56 14 4 0.001319137
|
||||||
|
Q 55 22 6 0.001506544
|
||||||
|
Q 54 12 4 0.001631475
|
||||||
|
Q 53 16 3 0.001724733
|
||||||
|
Q 51 10 1 0.001755541
|
||||||
|
Q 50 10 1 0.001786330
|
||||||
|
Q 49 11 3 0.001879699
|
||||||
|
Q 47 8 2 0.001941869
|
||||||
|
Q 46 17 1 0.001972140
|
||||||
|
Q 44 8 3 0.002065534
|
||||||
|
Q 43 10 1 0.002096174
|
||||||
|
Q 42 13 1 0.002126595
|
||||||
|
Q 41 14 3 0.002219444
|
||||||
|
Q 40 13 2 0.002281036
|
||||||
|
Q 38 17 4 0.002404747
|
||||||
|
Q 37 15 4 0.002528484
|
||||||
|
Q 36 12 1 0.002558742
|
||||||
|
Q 35 19 3 0.002650783
|
||||||
|
Q 34 12 3 0.002743313
|
||||||
|
Q 33 7 1 0.002773882
|
||||||
|
Q 32 21 3 0.002865508
|
||||||
|
Q 31 11 2 0.002926799
|
||||||
|
Q 30 14 3 0.003018891
|
||||||
|
Q 29 17 1 0.003048401
|
||||||
|
Q 28 11 2 0.003109549
|
||||||
|
Q 27 20 5 0.003262998
|
||||||
|
Q 26 11 1 0.003292948
|
||||||
|
Q 25 14 4 0.003415725
|
||||||
|
Q 24 16 5 0.003569212
|
||||||
|
Q 23 43 6 0.003750426
|
||||||
|
Q 21 15 1 0.003779664
|
||||||
|
Q 20 29 7 0.003992943
|
||||||
|
Q 19 22 2 0.004052089
|
||||||
|
Q 18 28 4 0.004172204
|
||||||
|
Q 16 25 5 0.004323390
|
||||||
|
Q 15 24 5 0.004474480
|
||||||
|
Q 14 25 5 0.004625204
|
||||||
|
Q 13 23 3 0.004714365
|
||||||
|
Q 12 22 1 0.004741963
|
||||||
|
Q 11 32 11 0.005075674
|
||||||
|
Q 10 35 7 0.005285315
|
||||||
|
Q 9 32 12 0.005648503
|
||||||
|
Q 8 33 8 0.005888126
|
||||||
|
Q 7 39 7 0.006095506
|
||||||
|
Q 6 42 14 0.006515953
|
||||||
|
Q 5 38 15 0.006966725
|
||||||
|
Q 4 37 12 0.007325113
|
||||||
|
Q 3 49 18 0.007862737
|
||||||
|
Q 2 63 21 0.008486434
|
||||||
|
Q 1 55 27 0.009292156
|
||||||
|
Q 0 153 77 0.011576593
|
||||||
|
|
@ -0,0 +1,33 @@
|
||||||
|
#!/usr/bin/perl
|
||||||
|
|
||||||
|
use strict;
|
||||||
|
use warnings;
|
||||||
|
use Getopt::Std;
|
||||||
|
|
||||||
|
my %opts = (n=>33088, s=>100);
|
||||||
|
getopts('n:', \%opts);
|
||||||
|
|
||||||
|
my $pseudo = .5;
|
||||||
|
my $tot = $pseudo;
|
||||||
|
my $err = $pseudo;
|
||||||
|
my $tot_last_out = -$opts{s};
|
||||||
|
my $state = 0;
|
||||||
|
my $mapq = 0;
|
||||||
|
while (<>) {
|
||||||
|
chomp;
|
||||||
|
if (/^Q\t(\d+)\t(\d+)\t(\d+)/) {
|
||||||
|
$tot += $2;
|
||||||
|
$err += $3;
|
||||||
|
if ($tot - $tot_last_out >= $opts{s}) {
|
||||||
|
print join("\t", $1, $err/$tot, $tot / $opts{n}), "\n";
|
||||||
|
$tot_last_out = $tot;
|
||||||
|
$state = 0;
|
||||||
|
} else {
|
||||||
|
$state = 1;
|
||||||
|
$mapq = $1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if ($state) {
|
||||||
|
print join("\t", $mapq, $err/$tot, $tot / $opts{n}), "\n";
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,4 @@
|
||||||
|
Q 40 31897 63 0.001975107
|
||||||
|
Q 3 423 267 0.010210396
|
||||||
|
Q 2 162 120 0.013853827
|
||||||
|
Q 1 188 172 0.019038874
|
||||||
|
|
@ -0,0 +1,4 @@
|
||||||
|
./pbsim --prefix pb-1 --depth 0.1 --sample-fastq m131017_060208_42213_c100579642550000001823095604021496_s1_p0.1.subreads.fastq --length-min 1000 --length-max 30000 --seed 11 hs38.fa
|
||||||
|
|
||||||
|
bin/mason_variator -ir hs38.fa -s 1 -ov hs38-s1.vcf --snp-rate 1e-3 --small-indel-rate 2e-4 --sv-indel-rate 0 --sv-inversion-rate 0 --sv-translocation-rate 0 --sv-duplication-rate 0 --max-small-indel-size 10
|
||||||
|
bin/mason_simulator -ir hs38.fa -iv hs38-s1.vcf -n 1000000 --seed 1 -o s1_1.fq -or s1_2.fq -oa s1.sam --illumina-prob-mismatch-scale 2.5
|
||||||
|
|
@ -0,0 +1,49 @@
|
||||||
|
Q 60 32070 190 0.005924540
|
||||||
|
Q 59 62 2 0.005975352
|
||||||
|
Q 58 37 5 0.006123908
|
||||||
|
Q 57 40 7 0.006333633
|
||||||
|
Q 56 39 6 0.006512032
|
||||||
|
Q 55 32 2 0.006567534
|
||||||
|
Q 54 54 2 0.006618420
|
||||||
|
Q 53 33 4 0.006735255
|
||||||
|
Q 52 39 2 0.006788866
|
||||||
|
Q 51 48 3 0.006871264
|
||||||
|
Q 50 34 2 0.006925634
|
||||||
|
Q 49 32 3 0.007011070
|
||||||
|
Q 48 35 2 0.007064967
|
||||||
|
Q 47 36 4 0.007179896
|
||||||
|
Q 46 23 1 0.007205495
|
||||||
|
Q 45 25 1 0.007230614
|
||||||
|
Q 44 17 3 0.007318716
|
||||||
|
Q 43 17 2 0.007376121
|
||||||
|
Q 42 31 5 0.007522016
|
||||||
|
Q 41 25 4 0.007638486
|
||||||
|
Q 40 26 4 0.007754541
|
||||||
|
Q 39 35 2 0.007807258
|
||||||
|
Q 37 18 4 0.007924896
|
||||||
|
Q 36 13 3 0.008013162
|
||||||
|
Q 35 15 2 0.008070411
|
||||||
|
Q 34 20 3 0.008156805
|
||||||
|
Q 33 11 1 0.008184501
|
||||||
|
Q 32 15 3 0.008272003
|
||||||
|
Q 31 25 1 0.008296107
|
||||||
|
Q 29 8 1 0.008324472
|
||||||
|
Q 28 7 2 0.008383452
|
||||||
|
Q 27 9 2 0.008441894
|
||||||
|
Q 26 30 2 0.008494888
|
||||||
|
Q 23 2 1 0.008524710
|
||||||
|
Q 22 11 3 0.008612846
|
||||||
|
Q 20 23 3 0.008697760
|
||||||
|
Q 19 6 1 0.008726479
|
||||||
|
Q 18 8 1 0.008754658
|
||||||
|
Q 16 6 1 0.008783354
|
||||||
|
Q 13 2 1 0.008813108
|
||||||
|
Q 12 4 2 0.008872604
|
||||||
|
Q 11 7 2 0.008931275
|
||||||
|
Q 10 4 3 0.009021009
|
||||||
|
Q 9 6 4 0.009140436
|
||||||
|
Q 8 6 3 0.009229559
|
||||||
|
Q 7 5 1 0.009258419
|
||||||
|
Q 6 8 3 0.009346925
|
||||||
|
Q 4 8 5 0.009495872
|
||||||
|
Q 3 17 8 0.009732801
|
||||||
|
|
@ -0,0 +1,181 @@
|
||||||
|
@article{Chaisson:2012aa,
|
||||||
|
Author = {Chaisson, Mark J and Tesler, Glenn},
|
||||||
|
Journal = {BMC Bioinformatics},
|
||||||
|
Pages = {238},
|
||||||
|
Title = {{Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory}},
|
||||||
|
Volume = {13},
|
||||||
|
Year = {2012}}
|
||||||
|
|
||||||
|
@article{Liu:2016ab,
|
||||||
|
Author = {Liu, Bo and others},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {1625-31},
|
||||||
|
Title = {{rHAT}: fast alignment of noisy long reads with regional hashing},
|
||||||
|
Volume = {32},
|
||||||
|
Year = {2016}}
|
||||||
|
|
||||||
|
@article{Liu:2017aa,
|
||||||
|
Author = {Liu, Bo and others},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {192-201},
|
||||||
|
Title = {{LAMSA}: fast split read alignment with long approximate matches},
|
||||||
|
Volume = {33},
|
||||||
|
Year = {2017}}
|
||||||
|
|
||||||
|
@article{Lin:2017aa,
|
||||||
|
Author = {Lin, Hsin-Nan and Hsu, Wen-Lian},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Title = {Kart: a divide-and-conquer algorithm for {NGS} read alignment},
|
||||||
|
Year = {2017}}
|
||||||
|
|
||||||
|
@article{Li:2013aa,
|
||||||
|
Author = {Li, Heng},
|
||||||
|
Journal = {arXiv:1303.3997},
|
||||||
|
Title = {Aligning sequence reads, clone sequences and assembly contigs with {BWA-MEM}},
|
||||||
|
archivePrefix = "arXiv",
|
||||||
|
eprint = {1303.3997},
|
||||||
|
primaryClass = "q-bio",
|
||||||
|
Year = {2013}}
|
||||||
|
|
||||||
|
@article{Sovic:2016aa,
|
||||||
|
Author = {Sovi{\'c}, Ivan and others},
|
||||||
|
Journal = {Nat Commun},
|
||||||
|
Pages = {11307},
|
||||||
|
Title = {Fast and sensitive mapping of nanopore sequencing reads with {GraphMap}},
|
||||||
|
Volume = {7},
|
||||||
|
Year = {2016}}
|
||||||
|
|
||||||
|
@article{Langmead:2012fk,
|
||||||
|
Author = {Langmead, Ben and Salzberg, Steven L},
|
||||||
|
Journal = {Nat Methods},
|
||||||
|
Pages = {357-9},
|
||||||
|
Title = {Fast gapped-read alignment with {Bowtie} 2},
|
||||||
|
Volume = {9},
|
||||||
|
Year = {2012}}
|
||||||
|
|
||||||
|
@article{Li:2016aa,
|
||||||
|
Author = {Li, Heng},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {2103-10},
|
||||||
|
Title = {Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences},
|
||||||
|
Volume = {32},
|
||||||
|
Year = {2016}}
|
||||||
|
|
||||||
|
@misc{Suzuki:2016,
|
||||||
|
title = {Fast and accurate alignment tool for PacBio and Nanopore long reads},
|
||||||
|
author = {Hajime Suzuki},
|
||||||
|
journal = {Unpublished},
|
||||||
|
howpublished = {\href{https://github.com/ocxtal/minialign}{https://github.com/ocxtal/minialign}},
|
||||||
|
year = {2016}}
|
||||||
|
|
||||||
|
@misc{Ruan:2016,
|
||||||
|
title = {Ultra-fast de novo assembler using long noisy reads},
|
||||||
|
author = {Jue Ruan},
|
||||||
|
journal = {Unpulished},
|
||||||
|
howpublished = {\href{https://github.com/ruanjue/smartdenovo}{https://github.com/ruanjue/smartdenovo}},
|
||||||
|
year = {2016}}
|
||||||
|
|
||||||
|
@article{Miller:1988aa,
|
||||||
|
Author = {Miller, W and Myers, E W},
|
||||||
|
Journal = {Bull Math Biol},
|
||||||
|
Number = {2},
|
||||||
|
Pages = {97-120},
|
||||||
|
Title = {Sequence comparison with concave weighting functions},
|
||||||
|
Volume = {50},
|
||||||
|
Year = {1988}}
|
||||||
|
|
||||||
|
@article{Gotoh:1990aa,
|
||||||
|
Author = {Gotoh, O},
|
||||||
|
Journal = {Bull Math Biol},
|
||||||
|
Pages = {359-73},
|
||||||
|
Title = {Optimal sequence alignment allowing for long gaps},
|
||||||
|
Volume = {52},
|
||||||
|
Year = {1990}}
|
||||||
|
|
||||||
|
@article{Wu:1996aa,
|
||||||
|
Author = {Wu, Sun and others},
|
||||||
|
Journal = {Algorithmica},
|
||||||
|
Pages = {50-67},
|
||||||
|
Title = {A subquadratic algorithm for approximate limited expression matching},
|
||||||
|
Volume = {15},
|
||||||
|
Year = {1996}}
|
||||||
|
|
||||||
|
@article{Daily:2016aa,
|
||||||
|
Author = {Daily, Jeff},
|
||||||
|
Journal = {BMC Bioinformatics},
|
||||||
|
Month = {Feb},
|
||||||
|
Pages = {81},
|
||||||
|
Title = {Parasail: {SIMD C} library for global, semi-global, and local pairwise sequence alignments},
|
||||||
|
Volume = {17},
|
||||||
|
Year = {2016}}
|
||||||
|
|
||||||
|
@article{Sedlazeck169557,
|
||||||
|
author = {Sedlazeck, Fritz J and others},
|
||||||
|
title = {Accurate detection of complex structural variations using single molecule sequencing},
|
||||||
|
note = {doi:10.1101/169557},
|
||||||
|
journal = {bioRxiv},
|
||||||
|
year = {2017}}
|
||||||
|
|
||||||
|
@article{Altschul:1997vn,
|
||||||
|
Author = {Altschul, S F and others},
|
||||||
|
Journal = {Nucleic Acids Res},
|
||||||
|
Pages = {3389-402},
|
||||||
|
Title = {Gapped {BLAST} and {PSI-BLAST}: a new generation of protein database search programs},
|
||||||
|
Volume = {25},
|
||||||
|
Year = {1997}}
|
||||||
|
|
||||||
|
@article{Sosic:2017aa,
|
||||||
|
Author = {{\v S}o{\v s}i\'{c}, Martin and {\v S}ikic, Mile},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {1394-1395},
|
||||||
|
Title = {Edlib: a {C/C++} library for fast, exact sequence alignment using edit distance},
|
||||||
|
Volume = {33},
|
||||||
|
Year = {2017}}
|
||||||
|
|
||||||
|
@article{Abouelhoda:2005aa,
|
||||||
|
Author = {Mohamed Ibrahim Abouelhoda and Enno Ohlebusch},
|
||||||
|
Journal = {J. Discrete Algorithms},
|
||||||
|
Pages = {321-41},
|
||||||
|
Title = {Chaining algorithms for multiple genome comparison},
|
||||||
|
Volume = {3},
|
||||||
|
Year = {2005}}
|
||||||
|
|
||||||
|
@article{Ono:2013aa,
|
||||||
|
Author = {Ono, Yukiteru and others},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {119-21},
|
||||||
|
Title = {{PBSIM}: {PacBio} reads simulator--toward accurate genome assembly},
|
||||||
|
Volume = {29},
|
||||||
|
Year = {2013}}
|
||||||
|
|
||||||
|
@article {Jain128835,
|
||||||
|
author = {Jain, Miten and others},
|
||||||
|
title = {Nanopore sequencing and assembly of a human genome with ultra-long reads},
|
||||||
|
year = {2017},
|
||||||
|
note = {doi:10.1101/128835},
|
||||||
|
publisher = {Cold Spring Harbor Labs Journals},
|
||||||
|
journal = {bioRxiv}}
|
||||||
|
|
||||||
|
@article{Lau:2016aa,
|
||||||
|
Author = {Lau, Bayo and others},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {3829-3832},
|
||||||
|
Title = {{LongISLND}: in silico sequencing of lengthy and noisy datatypes},
|
||||||
|
Volume = {32},
|
||||||
|
Year = {2016}}
|
||||||
|
|
||||||
|
@article{Robinson:2011aa,
|
||||||
|
Author = {Robinson, James T and others},
|
||||||
|
Journal = {Nat Biotechnol},
|
||||||
|
Pages = {24-6},
|
||||||
|
Title = {Integrative genomics viewer},
|
||||||
|
Volume = {29},
|
||||||
|
Year = {2011}}
|
||||||
|
|
||||||
|
@article {Suzuki130633,
|
||||||
|
author = {Suzuki, Hajime and Kasahara, Masahiro},
|
||||||
|
title = {Acceleration Of Nucleotide Semi-Global Alignment With Adaptive Banded Dynamic Programming},
|
||||||
|
year = {2017},
|
||||||
|
note = {doi:10.1101/130633},
|
||||||
|
publisher = {Cold Spring Harbor Labs Journals},
|
||||||
|
journal = {bioRxiv}}
|
||||||
|
|
@ -0,0 +1,344 @@
|
||||||
|
\documentclass{bioinfo}
|
||||||
|
\copyrightyear{2017}
|
||||||
|
\pubyear{2017}
|
||||||
|
|
||||||
|
\usepackage{graphicx}
|
||||||
|
\usepackage{hyperref}
|
||||||
|
\usepackage{url}
|
||||||
|
\usepackage{amsmath}
|
||||||
|
\usepackage[ruled,vlined]{algorithm2e}
|
||||||
|
\newcommand\mycommfont[1]{\footnotesize\rmfamily{\it #1}}
|
||||||
|
\SetCommentSty{mycommfont}
|
||||||
|
\SetKwComment{Comment}{$\triangleright$\ }{}
|
||||||
|
|
||||||
|
\usepackage{natbib}
|
||||||
|
\bibliographystyle{apalike}
|
||||||
|
\usepackage{hyperref}
|
||||||
|
|
||||||
|
\DeclareMathOperator*{\argmax}{argmax}
|
||||||
|
|
||||||
|
\begin{document}
|
||||||
|
\firstpage{1}
|
||||||
|
|
||||||
|
\title[Long DNA sequence alignment with minimap2]{Minimap2: fast pairwise alignment for long DNA sequences}
|
||||||
|
\author[Li]{Heng Li}
|
||||||
|
\address{Broad Institute, 415 Main Street, Cambridge, MA 02142, USA}
|
||||||
|
|
||||||
|
\maketitle
|
||||||
|
|
||||||
|
\begin{abstract}
|
||||||
|
\section{Summary:} Minimap2 is a general-purpose mapper to align long noisy DNA
|
||||||
|
sequences against a large reference database. It targets query sequences of
|
||||||
|
1kb--100Mb in length with per-base divergence typically below 25\%. Minimap2 is
|
||||||
|
$\sim$30 times faster than many mainstream long-read aligners and achieves
|
||||||
|
higher accuracy on simulated data. It also employs concave gap cost and rescues
|
||||||
|
inversions for improved alignment around potential structural variations.
|
||||||
|
|
||||||
|
\section{Availability and implementation:}
|
||||||
|
\href{https://github.com/lh3/minimap2}{https://github.com/lh3/minimap2}
|
||||||
|
|
||||||
|
\section{Contact:} hengli@broadinstitute.org
|
||||||
|
\end{abstract}
|
||||||
|
|
||||||
|
\section{Introduction}
|
||||||
|
|
||||||
|
Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore
|
||||||
|
technologies (ONT) produce reads over 10kbp in length at an error rate
|
||||||
|
$\sim$15\%. Several aligners have been developed for such
|
||||||
|
data~\citep{Chaisson:2012aa,Li:2013aa,Liu:2016ab,Sovic:2016aa,Liu:2017aa,Lin:2017aa,Sedlazeck169557}.
|
||||||
|
They are usually five times as slow as mainstream short-read
|
||||||
|
aligners~\citep{Langmead:2012fk,Li:2013aa}. We speculated there could be
|
||||||
|
substantial room for speedup on the thought that 10kb long sequences should be
|
||||||
|
easier to map than 100bp reads because we can more effectively skip repetitive
|
||||||
|
regions, which are often the bottleneck of short-read alignment. We confirmed
|
||||||
|
our speculation by achieving approximate mapping 50 times faster than
|
||||||
|
BWA-MEM~\citep{Li:2016aa}. \citet{Suzuki:2016} extended our work with a fast
|
||||||
|
and novel algorithm on generating detailed alignment, which in turn inspired us
|
||||||
|
to develop minimap2 towards higher accuracy and more practical functionality.
|
||||||
|
|
||||||
|
\begin{methods}
|
||||||
|
\section{Methods}
|
||||||
|
|
||||||
|
Minimap2 is the successor of minimap~\citep{Li:2016aa}. It uses similar
|
||||||
|
indexing and seeding algorithms, and furthers it with more accurate chaining
|
||||||
|
and the ability to produce detailed alignment.
|
||||||
|
|
||||||
|
\subsection{Chaining}
|
||||||
|
|
||||||
|
%\subsubsection{Chaining}
|
||||||
|
An \emph{anchor} is a 3-tuple $(x,y,w)$, indicating interval $[x-w+1,x]$ on the
|
||||||
|
reference matching interval $[y-w+1,y]$ on the query. Given a list of anchors
|
||||||
|
sorted by ending reference position $x$, let $f(i)$ be the maximal chaining
|
||||||
|
score up to the $i$-th anchor in the list. $f(i)$ can be calculated with
|
||||||
|
dynamic programming (DP):
|
||||||
|
\begin{equation}\label{eq:chain}
|
||||||
|
f(i)=\max\big\{\max_{i>j\ge 1} \{ f(j)+d(j,i)-\gamma(j,i) \},w_i\big\}
|
||||||
|
\end{equation}
|
||||||
|
where $d(j,i)=\min\big\{\min\{y_i-y_j,x_i-x_j\},w_i\big\}$ is the number of
|
||||||
|
matching bases between the two anchors. $\gamma(j,i)>0$ is the gap cost. It
|
||||||
|
equals $\infty$ if $y_j\ge y_i$ or $\max\{y_i-y_j,x_i-x_j\}>G$ (i.e. the
|
||||||
|
distance between two anchors is too large); otherwise
|
||||||
|
\[
|
||||||
|
\gamma(j,i)=\gamma'(\max\{y_i-y_j,x_i-x_j\}-\min\{y_i-y_j,x_i-x_j\})
|
||||||
|
\]
|
||||||
|
In implementation, a gap of length $l$ costs $\gamma'(l)=\alpha\cdot
|
||||||
|
l+\beta\log_2(l)$. For $m$ anchors, directly computing all $f(\cdot)$ with
|
||||||
|
Eq.~(\ref{eq:chain}) takes $O(m^2)$ time. Although theoretically faster
|
||||||
|
chaining algorithms exist~\citep{Abouelhoda:2005aa}, they
|
||||||
|
are inapplicable to generic gap cost, complex to implement and usually
|
||||||
|
associated with a large constant. We introduced a simple heuristic to
|
||||||
|
accelerate chaining.
|
||||||
|
|
||||||
|
We note that if anchor $i$ is chained to $j$, chaining $i$ to a predecessor
|
||||||
|
of $j$ is likely to yield a lower score. When evaluating Eq.~(\ref{eq:chain}),
|
||||||
|
we start from anchor $i-1$ and stop the evaluation if we cannot find a better
|
||||||
|
score after up to $h$ iterations. This approach reduces the average time to
|
||||||
|
$O(h\cdot m)$. In practice, we can almost always find the optimal chain with
|
||||||
|
$h=50$; even if the heuristic fails, the optimal chain is often close.
|
||||||
|
|
||||||
|
%\subsubsection{Backtracking}
|
||||||
|
For backtracking, let $P(i)$ be the index of the best predecessor of anchor
|
||||||
|
$i$. It equals 0 if $f(i)=w_i$ or $\argmax_j\{f(j)+\eta(j,i)-\gamma(j,i)\}$
|
||||||
|
otherwise. For each anchor $i$ in the descending order of $f(i)$, we apply
|
||||||
|
$P(\cdot)$ repeatedly to find its predecessor and mark each visited $i$ as
|
||||||
|
`used', until $P(i)=0$ or we reach an already `used' $i$. This way we find all
|
||||||
|
chains with no anchors used in more than one chains.
|
||||||
|
|
||||||
|
%\subsubsection{Identifying primary chains}
|
||||||
|
In the absence of copy number changes, each query segment should not be mapped
|
||||||
|
to two places in the reference. However, chains found at the previous step may
|
||||||
|
have significant or complete overlaps due to repeats in the reference.
|
||||||
|
Minimap2 used the following procedure to identify \emph{primary chains} that do
|
||||||
|
not greatly overlap on the query. Let $Q$ be an empty set initially. For each
|
||||||
|
chain from the best to the worst according to their chaining scores: if on the
|
||||||
|
query, the chain overlaps with a chain in $Q$ by 50\% or higher percentage of
|
||||||
|
the shorter chain, mark the chain as secondary to the chain in $Q$; otherwise,
|
||||||
|
add the chain to $Q$. In the end, $Q$ contains all the primary chains. We did
|
||||||
|
not choose a more sophisticated data structure (e.g. range tree or k-d tree)
|
||||||
|
because this step is not the performance bottleneck.
|
||||||
|
|
||||||
|
\subsection{Alignment}
|
||||||
|
|
||||||
|
Minimap2 performs global alignment between adjacent anchors in a chain. It
|
||||||
|
adopted difference-based formulation to derive
|
||||||
|
alignment~\citep{Wu:1996aa,Suzuki:2016}. When combined with SSE vectorization,
|
||||||
|
this formulation has two advantages. First, because each score in the DP matrix
|
||||||
|
is bounded by the gap cost and the maximum matching score, we can usually
|
||||||
|
achieve 16-way SSE vectorization regardless of the peak score of the
|
||||||
|
alignment. Second, filling the DP matrix along the diagonal, we can simplify
|
||||||
|
banded alignment, which is critical to performance. In practice, our
|
||||||
|
implementation is three times as fast as Parasail's 4-way
|
||||||
|
vectorization~\citep{Daily:2016aa} for global alignment.
|
||||||
|
Without banding, our implementation is slower than Edlib~\citep{Sosic:2017aa},
|
||||||
|
but with a 1000bp band, it is considerably faster. When performing global
|
||||||
|
alignment between anchors, we expect the alignment to stay close to the
|
||||||
|
diagonal of the DP matrix. Banding is often applicable.
|
||||||
|
|
||||||
|
Minimap2 uses a 2-piece affine gap cost
|
||||||
|
$\gamma(l)=\min\{q+l\cdot e,\tilde{q}+l\cdot\tilde{e}\}$.
|
||||||
|
On the condition that $q+e<\tilde{q}+\tilde{e}$ and $e>\tilde{e}$, this
|
||||||
|
cost function is concave. It applies cost $q+l\cdot e$ to gaps shorter than
|
||||||
|
$\lceil(\tilde{q}-q)/(e-\tilde{e})\rceil$ and applies
|
||||||
|
$\tilde{q}+l\cdot\tilde{e}$ to longer gaps. This scheme helps to recover
|
||||||
|
longer insertions and deletions~(INDEL; \citealp{Gotoh:1990aa}).
|
||||||
|
|
||||||
|
With global alignment, minimap2 may force to align unrelated sequences between
|
||||||
|
two adjacent anchors. To avoid such an artifact, we compute accumulative
|
||||||
|
alignment score along the alignment path and break the alignment where the
|
||||||
|
score drops too fast in the diagonal direction. More precisely, let $S(i,j)$ be
|
||||||
|
the alignment score along the alignment path ending at cell $(i,j)$ in the DP
|
||||||
|
matrix. We break the alignment if there exist $(i',j')$ and $(i,j)$, $i'<i$ and
|
||||||
|
$j'<j$, such that
|
||||||
|
\[
|
||||||
|
S(i',j')-S(i,j)>Z+e\cdot(\max\{i-i',j-j'\}-\min\{i-i',j-j'\})
|
||||||
|
\]
|
||||||
|
where $e$ is the gap extension cost and $Z$ is an arbitrary threshold.
|
||||||
|
This strategy is similar to X-drop employed in BLAST~\citep{Altschul:1997vn}.
|
||||||
|
However, unlike X-drop, it would not break the alignment in the presence of a
|
||||||
|
single long gap.
|
||||||
|
|
||||||
|
When minimap2 breaks a global alignment between two anchors, it performs local
|
||||||
|
alignment between the two subsequences involved in the global alignment, but
|
||||||
|
this time with the one subsequence reverse complemented. This additional
|
||||||
|
alignment step may identify short inversions that are missed during chaining.
|
||||||
|
|
||||||
|
\end{methods}
|
||||||
|
|
||||||
|
\section{Results}
|
||||||
|
\begin{figure}[!tb]
|
||||||
|
\centering
|
||||||
|
\includegraphics[width=.5\textwidth]{roc-color.pdf}
|
||||||
|
\caption{Evaluation on simulated SMRT reads aligned against human genome
|
||||||
|
GRCh38. (a) ROC-like curve. (b) Accumulative mapping error rate as a function
|
||||||
|
of mapping quality. 33,088 $\ge$1000bp reads were simulated using
|
||||||
|
pbsim~\citep{Ono:2013aa} with error profile sampled from file
|
||||||
|
`m131017\_060208\_42213\_*.1.*' downloaded at
|
||||||
|
\href{http://bit.ly/chm1p5c3}{http://bit.ly/chm1p5c3}. The N50 read length is
|
||||||
|
11,628. A read is considered correctly mapped if the true position overlaps
|
||||||
|
with the best mapping position by 10\% of the read length. All aligners were
|
||||||
|
run under the default setting for SMRT reads.}\label{fig:eval}
|
||||||
|
\end{figure}
|
||||||
|
|
||||||
|
As a sanity check, we evaluated minimap2 on simulated human reads along with
|
||||||
|
BLASR~\citep{Chaisson:2012aa},
|
||||||
|
BWA-MEM~\citep{Li:2013aa},
|
||||||
|
GraphMap~\citep{Sovic:2016aa},
|
||||||
|
minialign~\citep{Suzuki:2016} and
|
||||||
|
NGMLR~\citep{Sedlazeck169557}. We excluded rHAT~\citep{Liu:2016ab},
|
||||||
|
LAMSA~\citep{Liu:2017aa} and Kart~\citep{Lin:2017aa} because they either
|
||||||
|
crashed or produced malformatted output. In this evaluation, Minimap2 has
|
||||||
|
higher power to distinguish unique and repetitive hits, and achieves overall
|
||||||
|
higher mapping accuracy (Fig.~\ref{fig:eval}a). It is still the most accurate
|
||||||
|
even if we skip DP-based alignment (data not shown), suggesting chaining alone
|
||||||
|
is sufficient to achieve high accuracy for approximate mapping. Minimap2 and
|
||||||
|
NGMLR provide better mapping quality estimate: they rarely give repetitive hits
|
||||||
|
high mapping quality (Fig.~\ref{fig:eval}b). Apparently, other aligners may
|
||||||
|
occasionally miss close suboptimal hits and be overconfident in wrong mappings.
|
||||||
|
On run time, minialign is slightly faster than minimap2. They are over 30 times
|
||||||
|
faster than the rest. Minimap2 consumed 6.1GB memory at the peak, more than
|
||||||
|
BWA-MEM but less than others.
|
||||||
|
|
||||||
|
On real human SMRT reads, the relative performance and sensitivity of
|
||||||
|
these aligners are broadly similar to those on simulated data. We are unable to
|
||||||
|
provide a good estimate of mapping error rate due to the lack of the truth. On
|
||||||
|
ONT ultra-long human reads~\citep{Jain128835}, BWA-MEM failed. Minialign and
|
||||||
|
minimap2 are over 70 times faster than others. We have also examined tens of
|
||||||
|
$\ge$100bp INDELs in IGV~\citep{Robinson:2011aa} and can confirm the
|
||||||
|
observation by~\citet{Sedlazeck169557} that BWA-MEM often breaks them into
|
||||||
|
shorter gaps. Minimap2 does not have this issue.
|
||||||
|
|
||||||
|
\section{Discussions}
|
||||||
|
|
||||||
|
Minialign and minimap2 are fast because a) with chaining, they can quickly
|
||||||
|
filter out most false seed hits~\citep{Li:2016aa} and reduce unsuccessful but
|
||||||
|
costly DP-based alignments; b) they implemented so far the fastest DP-based
|
||||||
|
alignment algorithm for long sequences~\citep{Suzuki:2016}. It is possible to
|
||||||
|
further accelerate minimap2 with a few other tweaks such as adaptive
|
||||||
|
banding~\citep{Suzuki130633} or incremental banding.
|
||||||
|
|
||||||
|
In addition to reference-based read mapping, minimap2 inherits minimap's
|
||||||
|
ability to search against huge multi-species databases and to find read
|
||||||
|
overlaps. On a few test data sets, minimap2 appears to yield slightly better
|
||||||
|
miniasm assembly. Minimap2 can also align closely related genomes, though it
|
||||||
|
would benefit from more thorough evaluations. Genome alignment is an intricate
|
||||||
|
topic.
|
||||||
|
|
||||||
|
\section*{Acknowledgements}
|
||||||
|
We owe a debt of gratitude to Hajime Suzuki for releasing his masterpiece and
|
||||||
|
insightful notes before formal publication. We thank M. Schatz, P. Rescheneder
|
||||||
|
and F. Sedlazeck for pointing out the limitation of BWA-MEM. We are also
|
||||||
|
grateful to early minimap2 testers who have greatly helped to fix various
|
||||||
|
issues.
|
||||||
|
|
||||||
|
\bibliography{minimap2}
|
||||||
|
|
||||||
|
\pagebreak
|
||||||
|
\appendix
|
||||||
|
|
||||||
|
\begin{methods}
|
||||||
|
\section*{Appendix}
|
||||||
|
A 2-piece gap cost function is
|
||||||
|
\[
|
||||||
|
\gamma(l)=\min\{q+l\cdot e,\tilde{q}+l\cdot\tilde{e}\}
|
||||||
|
\]
|
||||||
|
Without losing generality, we assume $q+e\le\tilde{q}+\tilde{e}$. The equation
|
||||||
|
to compute the optimal alignment under such a gap cost is~\citep{Gotoh:1990aa}
|
||||||
|
\begin{equation}\label{eq:ae86}
|
||||||
|
\left\{\begin{array}{l}
|
||||||
|
H_{ij} = \max\{H_{i-1,j-1}+s(i,j),E_{ij},F_{ij},\tilde{E}_{ij},\tilde{F}_{ij}\}\\
|
||||||
|
E_{i+1,j}= \max\{H_{ij}-q,E_{ij}\}-e\\
|
||||||
|
F_{i,j+1}= \max\{H_{ij}-q,F_{ij}\}-e\\
|
||||||
|
\tilde{E}_{i+1,j}= \max\{H_{ij}-\tilde{q},\tilde{E}_{ij}\}-\tilde{e}\\
|
||||||
|
\tilde{F}_{i,j+1}= \max\{H_{ij}-\tilde{q},\tilde{F}_{ij}\}-\tilde{e}
|
||||||
|
\end{array}\right.
|
||||||
|
\end{equation}
|
||||||
|
where $s(i,j)$ is the score between the $i$-th reference base and $j$-th query
|
||||||
|
base. If we define
|
||||||
|
\[
|
||||||
|
\left\{\begin{array}{ll}
|
||||||
|
u_{ij}\triangleq H_{ij}-H_{i-1,j} & v_{ij}\triangleq H_{ij}-H_{i,j-1} \\
|
||||||
|
x_{ij}\triangleq E_{i+1,j}-H_{ij} & \tilde{x}_{ij}\triangleq \tilde{E}_{i+1,j}-\tilde{H}_{ij} \\
|
||||||
|
y_{ij}\triangleq F_{i,j+1}-H_{ij} & \tilde{y}_{ij}\triangleq \tilde{F}_{i,j+1}-\tilde{H}_{ij}
|
||||||
|
\end{array}\right.
|
||||||
|
\]
|
||||||
|
we can transform Eq.~(\ref{eq:ae86}) to
|
||||||
|
\begin{equation}\label{eq:suzuki}
|
||||||
|
\left\{\begin{array}{lll}
|
||||||
|
z_{ij}&=&\max\{s(i,j),x_{i-1,j}+v_{i-1,j},y_{i,j-1}+u_{i,j-1},\\
|
||||||
|
&&\tilde{x}_{i-1,j}+v_{i-1,j},\tilde{y}_{i,j-1}+u_{i,j-1}\}\\
|
||||||
|
u_{ij}&=&z_{ij}-v_{i-1,j}\\
|
||||||
|
v_{ij}&=&z_{ij}-u_{i,j-1}\\
|
||||||
|
x_{ij}&=&\max\{0,x_{i-1,j}+v_{i-1,j}-z_{ij}+q\}-q-e\\
|
||||||
|
y_{ij}&=&\max\{0,y_{i,j-1}+u_{i,j-1}-z_{ij}+q\}-q-e\\
|
||||||
|
\tilde{x}_{ij}&=&\max\{0,\tilde{x}_{i-1,j}+v_{i-1,j}-z_{ij}+\tilde{q}\}-\tilde{q}-\tilde{e}\\
|
||||||
|
\tilde{y}_{ij}&=&\max\{0,\tilde{y}_{i,j-1}+u_{i,j-1}-z_{ij}+\tilde{q}\}-\tilde{q}-\tilde{e}
|
||||||
|
\end{array}\right.
|
||||||
|
\end{equation}
|
||||||
|
where $z_{ij}$ is a temporary variable that does not need to be stored.
|
||||||
|
|
||||||
|
All values in Eq.~(\ref{eq:suzuki}) are bounded. To see that,
|
||||||
|
\[
|
||||||
|
x_{ij}=E_{i+1,j}-H_{ij}=\max\{-q,E_{ij}-H_{ij}\}-e
|
||||||
|
\]
|
||||||
|
With $E_{ij}\le H_{ij}$, we have
|
||||||
|
\[
|
||||||
|
-q-e\le x_{ij}\le\max\{-q,0\}-e=-e
|
||||||
|
\]
|
||||||
|
and similar inequations for $y_{ij}$, $\tilde{x}_{ij}$ and $\tilde{y}_{ij}$.
|
||||||
|
In addition,
|
||||||
|
\[
|
||||||
|
u_{ij}=z_{ij}-v_{i-1,j}\ge\max\{x_{i-1,j},\tilde{x}_{i-1,j}\}\ge-q-e
|
||||||
|
\]
|
||||||
|
As the maximum value of $z_{ij}=H_{ij}-H_{i-1,j-1}$ is $M$, the maximal
|
||||||
|
matching score, we can derive
|
||||||
|
\[
|
||||||
|
u_{ij}\le M-v_{i-1,j}\le M+q+e
|
||||||
|
\]
|
||||||
|
In conclusion, $x$ and $y$ are bounded by $[-q-e,-e]$, $\tilde{x}$ and $\tilde{y}$ by
|
||||||
|
$[-\tilde{q}-\tilde{e},-\tilde{e}]$, and $u$ and $v$ by $[-q-e,M+q+e]$. When
|
||||||
|
matching score and gap cost are small, each of them can be stored as a 8-bit
|
||||||
|
integer. This enables 16-way SSE vectorization regardless of the peak score of
|
||||||
|
the alignment.
|
||||||
|
|
||||||
|
For a more efficient SSE implementation, we transform the row-column coordinate
|
||||||
|
to diagonal-anti-diagonal coordinate by letting $r\gets i+j$ and $t\gets i$.
|
||||||
|
Eq.~(\ref{eq:suzuki}) becomes:
|
||||||
|
\begin{equation*}
|
||||||
|
\left\{\begin{array}{lll}
|
||||||
|
z_{rt}&=&\max\{s(t,r-t),x_{r-1,t-1}+v_{r-1,t-1},y_{r-1,t}+u_{r-1,t},\\
|
||||||
|
&&\tilde{x}_{r-1,t-1}+v_{r-1,t-1},\tilde{y}_{r-1,t}+u_{r-1,t}\}\\
|
||||||
|
u_{rt}&=&z_{rt}-v_{r-1,t-1}\\
|
||||||
|
v_{rt}&=&z_{rt}-u_{r-1,t}\\
|
||||||
|
x_{rt}&=&\max\{0,x_{r-1,t-1}+v_{r-1,t-1}-z_{rt}+q\}-q-e\\
|
||||||
|
y_{rt}&=&\max\{0,y_{r-1,t}+u_{r-1,t}-z_{rt}+q\}-q-e\\
|
||||||
|
\tilde{x}_{rt}&=&\max\{0,\tilde{x}_{r-1,t-1}+v_{r-1,t-1}-z_{rt}+\tilde{q}\}-\tilde{q}-\tilde{e}\\
|
||||||
|
\tilde{y}_{rt}&=&\max\{0,\tilde{y}_{r-1,t}+u_{r-1,t}-z_{rt}+\tilde{q}\}-\tilde{q}-\tilde{e}
|
||||||
|
\end{array}\right.
|
||||||
|
\end{equation*}
|
||||||
|
In this formulation, cells with the same diagonal index $r$ are independent of
|
||||||
|
each other. This allows us to fully vectorize the computation of all cells on
|
||||||
|
the same anti-diagonal in one inner loop.
|
||||||
|
|
||||||
|
On the condition that $q+e<\tilde{q}+\tilde{e}$ and $e>\tilde{e}$, the boundary
|
||||||
|
condition of this equation in the diagonal-anti-diagonal coordinate is
|
||||||
|
\[
|
||||||
|
\left\{\begin{array}{l}
|
||||||
|
x_{r-1,-1}=y_{r-1,r}=-q-e\\
|
||||||
|
\tilde{x}_{r-1,-1}=\tilde{y}_{r-1,r}=-\tilde{q}-\tilde{e}\\
|
||||||
|
u_{r-1,r}=v_{r-1,-1}=\eta(r)\\
|
||||||
|
\end{array}\right.
|
||||||
|
\]
|
||||||
|
where
|
||||||
|
\[
|
||||||
|
\eta(r)=\left\{\begin{array}{ll}
|
||||||
|
-q-e & (r=0) \\
|
||||||
|
-e & (r<\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil) \\
|
||||||
|
r\cdot(e-\tilde{e})-(\tilde{q}-q)-\tilde{e} & (r=\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil) \\
|
||||||
|
-\tilde{e} & (r>\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil)
|
||||||
|
\end{array}\right.
|
||||||
|
\]
|
||||||
|
|
||||||
|
\citet{Suzuki:2016} first derived a similar set of equations under affine gap
|
||||||
|
cost but with different notations.
|
||||||
|
\end{methods}
|
||||||
|
\end{document}
|
||||||
|
|
@ -0,0 +1,30 @@
|
||||||
|
Q 60 32066 0 0.000000000
|
||||||
|
Q 40 32 1 0.000031155
|
||||||
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Q 38 19 1 0.000062272
|
||||||
|
Q 36 11 1 0.000093376
|
||||||
|
Q 35 32 1 0.000124378
|
||||||
|
Q 33 15 1 0.000155400
|
||||||
|
Q 32 58 1 0.000186145
|
||||||
|
Q 27 11 1 0.000217095
|
||||||
|
Q 26 80 1 0.000247494
|
||||||
|
Q 21 19 2 0.000309186
|
||||||
|
Q 20 16 1 0.000339936
|
||||||
|
Q 19 19 1 0.000370622
|
||||||
|
Q 18 22 2 0.000432099
|
||||||
|
Q 17 37 5 0.000585751
|
||||||
|
Q 15 24 2 0.000646930
|
||||||
|
Q 14 18 3 0.000738939
|
||||||
|
Q 13 30 6 0.000922821
|
||||||
|
Q 12 18 1 0.000953054
|
||||||
|
Q 11 29 2 0.001013638
|
||||||
|
Q 10 30 1 0.001043393
|
||||||
|
Q 9 20 5 0.001196099
|
||||||
|
Q 8 25 8 0.001440348
|
||||||
|
Q 7 28 6 0.001622830
|
||||||
|
Q 6 35 12 0.001988132
|
||||||
|
Q 5 34 12 0.002352725
|
||||||
|
Q 4 29 8 0.002594865
|
||||||
|
Q 3 36 14 0.003018937
|
||||||
|
Q 2 46 15 0.003471482
|
||||||
|
Q 1 69 36 0.004558162
|
||||||
|
Q 0 167 94 0.007377173
|
||||||
|
|
@ -0,0 +1,17 @@
|
||||||
|
Q 60 32072 0 0.000000000
|
||||||
|
Q 43 206 1 0.000030981
|
||||||
|
Q 27 201 1 0.000061578
|
||||||
|
Q 15 59 1 0.000092200
|
||||||
|
Q 12 25 1 0.000122839
|
||||||
|
Q 11 16 1 0.000153473
|
||||||
|
Q 10 24 1 0.000184032
|
||||||
|
Q 9 17 2 0.000245248
|
||||||
|
Q 8 27 3 0.000336938
|
||||||
|
Q 7 23 1 0.000367309
|
||||||
|
Q 6 20 1 0.000397675
|
||||||
|
Q 5 18 4 0.000519751
|
||||||
|
Q 4 17 1 0.000550038
|
||||||
|
Q 3 29 5 0.000702204
|
||||||
|
Q 2 32 4 0.000823522
|
||||||
|
Q 1 54 6 0.001004872
|
||||||
|
Q 0 234 106 0.004202697
|
||||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,803 @@
|
||||||
|
%%
|
||||||
|
%% This is file `natbib.sty',
|
||||||
|
%% generated with the docstrip utility.
|
||||||
|
%%
|
||||||
|
%% The original source files were:
|
||||||
|
%%
|
||||||
|
%% natbib.dtx (with options: `package,all')
|
||||||
|
%% =============================================
|
||||||
|
%% IMPORTANT NOTICE:
|
||||||
|
%%
|
||||||
|
%% This program can be redistributed and/or modified under the terms
|
||||||
|
%% of the LaTeX Project Public License Distributed from CTAN
|
||||||
|
%% archives in directory macros/latex/base/lppl.txt; either
|
||||||
|
%% version 1 of the License, or any later version.
|
||||||
|
%%
|
||||||
|
%% This is a generated file.
|
||||||
|
%% It may not be distributed without the original source file natbib.dtx.
|
||||||
|
%%
|
||||||
|
%% Full documentation can be obtained by LaTeXing that original file.
|
||||||
|
%% Only a few abbreviated comments remain here to describe the usage.
|
||||||
|
%% =============================================
|
||||||
|
%% Copyright 1993-2000 Patrick W Daly
|
||||||
|
%% Max-Planck-Institut f\"ur Aeronomie
|
||||||
|
%% Max-Planck-Str. 2
|
||||||
|
%% D-37191 Katlenburg-Lindau
|
||||||
|
%% Germany
|
||||||
|
%% E-mail: daly@linmpi.mpg.de
|
||||||
|
\NeedsTeXFormat{LaTeX2e}[1995/06/01]
|
||||||
|
\ProvidesPackage{natbib}
|
||||||
|
[2000/07/24 7.0a (PWD)]
|
||||||
|
% This package reimplements the LaTeX \cite command to be used for various
|
||||||
|
% citation styles, both author-year and numerical. It accepts BibTeX
|
||||||
|
% output intended for many other packages, and therefore acts as a
|
||||||
|
% general, all-purpose citation-style interface.
|
||||||
|
%
|
||||||
|
% With standard numerical .bst files, only numerical citations are
|
||||||
|
% possible. With an author-year .bst file, both numerical and
|
||||||
|
% author-year citations are possible.
|
||||||
|
%
|
||||||
|
% If author-year citations are selected, \bibitem must have one of the
|
||||||
|
% following forms:
|
||||||
|
% \bibitem[Jones et al.(1990)]{key}...
|
||||||
|
% \bibitem[Jones et al.(1990)Jones, Baker, and Williams]{key}...
|
||||||
|
% \bibitem[Jones et al., 1990]{key}...
|
||||||
|
% \bibitem[\protect\citeauthoryear{Jones, Baker, and Williams}{Jones
|
||||||
|
% et al.}{1990}]{key}...
|
||||||
|
% \bibitem[\protect\citeauthoryear{Jones et al.}{1990}]{key}...
|
||||||
|
% \bibitem[\protect\astroncite{Jones et al.}{1990}]{key}...
|
||||||
|
% \bibitem[\protect\citename{Jones et al., }1990]{key}...
|
||||||
|
% \harvarditem[Jones et al.]{Jones, Baker, and Williams}{1990}{key}...
|
||||||
|
%
|
||||||
|
% This is either to be made up manually, or to be generated by an
|
||||||
|
% appropriate .bst file with BibTeX.
|
||||||
|
% Author-year mode || Numerical mode
|
||||||
|
% Then, \citet{key} ==>> Jones et al. (1990) || Jones et al. [21]
|
||||||
|
% \citep{key} ==>> (Jones et al., 1990) || [21]
|
||||||
|
% Multiple citations as normal:
|
||||||
|
% \citep{key1,key2} ==>> (Jones et al., 1990; Smith, 1989) || [21,24]
|
||||||
|
% or (Jones et al., 1990, 1991) || [21,24]
|
||||||
|
% or (Jones et al., 1990a,b) || [21,24]
|
||||||
|
% \cite{key} is the equivalent of \citet{key} in author-year mode
|
||||||
|
% and of \citep{key} in numerical mode
|
||||||
|
% Full author lists may be forced with \citet* or \citep*, e.g.
|
||||||
|
% \citep*{key} ==>> (Jones, Baker, and Williams, 1990)
|
||||||
|
% Optional notes as:
|
||||||
|
% \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2)
|
||||||
|
% \citep[e.g.,][]{key} ==>> (e.g., Jones et al., 1990)
|
||||||
|
% \citep[see][pg. 34]{key}==>> (see Jones et al., 1990, pg. 34)
|
||||||
|
% (Note: in standard LaTeX, only one note is allowed, after the ref.
|
||||||
|
% Here, one note is like the standard, two make pre- and post-notes.)
|
||||||
|
% \citealt{key} ==>> Jones et al. 1990
|
||||||
|
% \citealt*{key} ==>> Jones, Baker, and Williams 1990
|
||||||
|
% \citealp{key} ==>> Jones et al., 1990
|
||||||
|
% \citealp*{key} ==>> Jones, Baker, and Williams, 1990
|
||||||
|
% Additional citation possibilities (both author-year and numerical modes)
|
||||||
|
% \citeauthor{key} ==>> Jones et al.
|
||||||
|
% \citeauthor*{key} ==>> Jones, Baker, and Williams
|
||||||
|
% \citeyear{key} ==>> 1990
|
||||||
|
% \citeyearpar{key} ==>> (1990)
|
||||||
|
% \citetext{priv. comm.} ==>> (priv. comm.)
|
||||||
|
% Note: full author lists depends on whether the bib style supports them;
|
||||||
|
% if not, the abbreviated list is printed even when full requested.
|
||||||
|
%
|
||||||
|
% For names like della Robbia at the start of a sentence, use
|
||||||
|
% \Citet{dRob98} ==>> Della Robbia (1998)
|
||||||
|
% \Citep{dRob98} ==>> (Della Robbia, 1998)
|
||||||
|
% \Citeauthor{dRob98} ==>> Della Robbia
|
||||||
|
%
|
||||||
|
%
|
||||||
|
% Citation aliasing is achieved with
|
||||||
|
% \defcitealias{key}{text}
|
||||||
|
% \citetalias{key} ==>> text
|
||||||
|
% \citepalias{key} ==>> (text)
|
||||||
|
%
|
||||||
|
% Defining the citation style of a given bib style:
|
||||||
|
% Use \bibpunct (in the preamble only) with 6 mandatory arguments:
|
||||||
|
% 1. opening bracket for citation
|
||||||
|
% 2. closing bracket
|
||||||
|
% 3. citation separator (for multiple citations in one \cite)
|
||||||
|
% 4. the letter n for numerical styles, s for superscripts
|
||||||
|
% else anything for author-year
|
||||||
|
% 5. punctuation between authors and date
|
||||||
|
% 6. punctuation between years (or numbers) when common authors missing
|
||||||
|
% One optional argument is the character coming before post-notes. It
|
||||||
|
% appears in square braces before all other arguments. May be left off.
|
||||||
|
% Example (and default) \bibpunct[, ]{(}{)}{;}{a}{,}{,}
|
||||||
|
%
|
||||||
|
% To make this automatic for a given bib style, named newbib, say, make
|
||||||
|
% a local configuration file, natbib.cfg, with the definition
|
||||||
|
% \newcommand{\bibstyle@newbib}{\bibpunct...}
|
||||||
|
% Then the \bibliographystyle{newbib} will cause \bibstyle@newbib to
|
||||||
|
% be called on THE NEXT LATEX RUN (via the aux file).
|
||||||
|
%
|
||||||
|
% Such preprogrammed definitions may be invoked in the text (preamble only)
|
||||||
|
% by calling \citestyle{newbib}. This is only useful if the style specified
|
||||||
|
% differs from that in \bibliographystyle.
|
||||||
|
%
|
||||||
|
% With \citeindextrue and \citeindexfalse, one can control whether the
|
||||||
|
% \cite commands make an automatic entry of the citation in the .idx
|
||||||
|
% indexing file. For this, \makeindex must also be given in the preamble.
|
||||||
|
%
|
||||||
|
% LaTeX2e Options: (for selecting punctuation)
|
||||||
|
% round - round parentheses are used (default)
|
||||||
|
% square - square brackets are used [option]
|
||||||
|
% curly - curly braces are used {option}
|
||||||
|
% angle - angle brackets are used <option>
|
||||||
|
% colon - multiple citations separated by colon (default)
|
||||||
|
% comma - separated by comma
|
||||||
|
% authoryear - selects author-year citations (default)
|
||||||
|
% numbers- selects numerical citations
|
||||||
|
% super - numerical citations as superscripts
|
||||||
|
% sort - sorts multiple citations according to order in ref. list
|
||||||
|
% sort&compress - like sort, but also compresses numerical citations
|
||||||
|
% longnamesfirst - makes first citation full author list
|
||||||
|
% sectionbib - puts bibliography in a \section* instead of \chapter*
|
||||||
|
% Punctuation so selected dominates over any predefined ones.
|
||||||
|
% LaTeX2e options are called as, e.g.
|
||||||
|
% \usepackage[square,comma]{natbib}
|
||||||
|
% LaTeX the source file natbib.dtx to obtain more details
|
||||||
|
% or the file natnotes.tex for a brief reference sheet.
|
||||||
|
%-----------------------------------------------------------
|
||||||
|
\@ifclassloaded{aguplus}{\PackageError{natbib}
|
||||||
|
{The aguplus class already includes natbib coding,\MessageBreak
|
||||||
|
so you should not add it explicitly}
|
||||||
|
{Type <Return> for now, but then later remove\MessageBreak
|
||||||
|
the command \protect\usepackage{natbib} from the document}
|
||||||
|
\endinput}{}
|
||||||
|
\@ifclassloaded{nlinproc}{\PackageError{natbib}
|
||||||
|
{The nlinproc class already includes natbib coding,\MessageBreak
|
||||||
|
so you should not add it explicitly}
|
||||||
|
{Type <Return> for now, but then later remove\MessageBreak
|
||||||
|
the command \protect\usepackage{natbib} from the document}
|
||||||
|
\endinput}{}
|
||||||
|
\@ifclassloaded{egs}{\PackageError{natbib}
|
||||||
|
{The egs class already includes natbib coding,\MessageBreak
|
||||||
|
so you should not add it explicitly}
|
||||||
|
{Type <Return> for now, but then later remove\MessageBreak
|
||||||
|
the command \protect\usepackage{natbib} from the document}
|
||||||
|
\endinput}{}
|
||||||
|
% Define citation punctuation for some author-year styles
|
||||||
|
% One may add and delete at this point
|
||||||
|
% Or put additions into local configuration file natbib.cfg
|
||||||
|
\newcommand\bibstyle@chicago{\bibpunct{(}{)}{;}{a}{,}{,}}
|
||||||
|
\newcommand\bibstyle@named{\bibpunct{[}{]}{;}{a}{,}{,}}
|
||||||
|
\newcommand\bibstyle@agu{\bibpunct{[}{]}{;}{a}{,}{,~}}%Amer. Geophys. Union
|
||||||
|
\newcommand\bibstyle@egs{\bibpunct{(}{)}{;}{a}{,}{,}}%Eur. Geophys. Soc.
|
||||||
|
\newcommand\bibstyle@agsm{\bibpunct{(}{)}{,}{a}{}{,}\gdef\harvardand{\&}}
|
||||||
|
\newcommand\bibstyle@kluwer{\bibpunct{(}{)}{,}{a}{}{,}\gdef\harvardand{\&}}
|
||||||
|
\newcommand\bibstyle@dcu{\bibpunct{(}{)}{;}{a}{;}{,}\gdef\harvardand{and}}
|
||||||
|
\newcommand\bibstyle@aa{\bibpunct{(}{)}{;}{a}{}{,}} %Astronomy & Astrophysics
|
||||||
|
\newcommand\bibstyle@pass{\bibpunct{(}{)}{;}{a}{,}{,}}%Planet. & Space Sci
|
||||||
|
\newcommand\bibstyle@anngeo{\bibpunct{(}{)}{;}{a}{,}{,}}%Annales Geophysicae
|
||||||
|
\newcommand\bibstyle@nlinproc{\bibpunct{(}{)}{;}{a}{,}{,}}%Nonlin.Proc.Geophys.
|
||||||
|
% Define citation punctuation for some numerical styles
|
||||||
|
\newcommand\bibstyle@cospar{\bibpunct{/}{/}{,}{n}{}{}%
|
||||||
|
\gdef\NAT@biblabelnum##1{##1.}}
|
||||||
|
\newcommand\bibstyle@esa{\bibpunct{(Ref.~}{)}{,}{n}{}{}%
|
||||||
|
\gdef\NAT@biblabelnum##1{##1.\hspace{1em}}}
|
||||||
|
\newcommand\bibstyle@nature{\bibpunct{}{}{,}{s}{}{\textsuperscript{,}}%
|
||||||
|
\gdef\NAT@biblabelnum##1{##1.}}
|
||||||
|
% The standard LaTeX styles
|
||||||
|
\newcommand\bibstyle@plain{\bibpunct{[}{]}{,}{n}{}{,}}
|
||||||
|
\let\bibstyle@alpha=\bibstyle@plain
|
||||||
|
\let\bibstyle@abbrv=\bibstyle@plain
|
||||||
|
\let\bibstyle@unsrt=\bibstyle@plain
|
||||||
|
% The author-year modifications of the standard styles
|
||||||
|
\newcommand\bibstyle@plainnat{\bibpunct{[}{]}{,}{a}{,}{,}}
|
||||||
|
\let\bibstyle@abbrvnat=\bibstyle@plainnat
|
||||||
|
\let\bibstyle@unsrtnat=\bibstyle@plainnat
|
||||||
|
\newif\ifNAT@numbers \NAT@numbersfalse
|
||||||
|
\newif\ifNAT@super \NAT@superfalse
|
||||||
|
\DeclareOption{numbers}{\NAT@numberstrue
|
||||||
|
\ExecuteOptions{square,comma,nobibstyle}}
|
||||||
|
\DeclareOption{super}{\NAT@supertrue\NAT@numberstrue
|
||||||
|
\renewcommand\NAT@open{}\renewcommand\NAT@close{}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{authoryear}{\NAT@numbersfalse
|
||||||
|
\ExecuteOptions{round,colon,bibstyle}}
|
||||||
|
\DeclareOption{round}{%
|
||||||
|
\renewcommand\NAT@open{(} \renewcommand\NAT@close{)}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{square}{%
|
||||||
|
\renewcommand\NAT@open{[} \renewcommand\NAT@close{]}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{angle}{%
|
||||||
|
\renewcommand\NAT@open{$<$} \renewcommand\NAT@close{$>$}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{curly}{%
|
||||||
|
\renewcommand\NAT@open{\{} \renewcommand\NAT@close{\}}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{comma}{\renewcommand\NAT@sep{,}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{colon}{\renewcommand\NAT@sep{;}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{nobibstyle}{\let\bibstyle=\@gobble}
|
||||||
|
\DeclareOption{bibstyle}{\let\bibstyle=\@citestyle}
|
||||||
|
\newif\ifNAT@openbib \NAT@openbibfalse
|
||||||
|
\DeclareOption{openbib}{\NAT@openbibtrue}
|
||||||
|
\DeclareOption{sectionbib}{\def\NAT@sectionbib{on}}
|
||||||
|
\def\NAT@sort{0}
|
||||||
|
\DeclareOption{sort}{\def\NAT@sort{1}}
|
||||||
|
\DeclareOption{sort&compress}{\def\NAT@sort{2}}
|
||||||
|
\@ifpackageloaded{cite}{\PackageWarningNoLine{natbib}
|
||||||
|
{The `cite' package should not be used\MessageBreak
|
||||||
|
with natbib. Use option `sort' instead}\ExecuteOptions{sort}}{}
|
||||||
|
\newif\ifNAT@longnames\NAT@longnamesfalse
|
||||||
|
\DeclareOption{longnamesfirst}{\NAT@longnamestrue}
|
||||||
|
\DeclareOption{nonamebreak}{\def\NAT@nmfmt#1{\mbox{\NAT@up#1}}}
|
||||||
|
\def\NAT@nmfmt#1{{\NAT@up#1}}
|
||||||
|
\renewcommand\bibstyle[1]{\@ifundefined{bibstyle@#1}{\relax}
|
||||||
|
{\csname bibstyle@#1\endcsname}}
|
||||||
|
\AtBeginDocument{\global\let\bibstyle=\@gobble}
|
||||||
|
\let\@citestyle\bibstyle
|
||||||
|
\newcommand\citestyle[1]{\@citestyle{#1}\let\bibstyle\@gobble}
|
||||||
|
\@onlypreamble{\citestyle}\@onlypreamble{\@citestyle}
|
||||||
|
\newcommand\bibpunct[7][, ]%
|
||||||
|
{\gdef\NAT@open{#2}\gdef\NAT@close{#3}\gdef
|
||||||
|
\NAT@sep{#4}\global\NAT@numbersfalse\ifx #5n\global\NAT@numberstrue
|
||||||
|
\else
|
||||||
|
\ifx #5s\global\NAT@numberstrue\global\NAT@supertrue
|
||||||
|
\fi\fi
|
||||||
|
\gdef\NAT@aysep{#6}\gdef\NAT@yrsep{#7}%
|
||||||
|
\gdef\NAT@cmt{#1}%
|
||||||
|
\global\let\bibstyle\@gobble
|
||||||
|
}
|
||||||
|
\@onlypreamble{\bibpunct}
|
||||||
|
\newcommand\NAT@open{(} \newcommand\NAT@close{)}
|
||||||
|
\newcommand\NAT@sep{;}
|
||||||
|
\ProcessOptions
|
||||||
|
\newcommand\NAT@aysep{,} \newcommand\NAT@yrsep{,}
|
||||||
|
\newcommand\NAT@cmt{, }
|
||||||
|
\newcommand\NAT@cite%
|
||||||
|
[3]{\ifNAT@swa\NAT@@open\if*#2*\else#2\ \fi
|
||||||
|
#1\if*#3*\else\NAT@cmt#3\fi\NAT@@close\else#1\fi\endgroup}
|
||||||
|
\newcommand\NAT@citenum%
|
||||||
|
[3]{\ifNAT@swa\NAT@@open\if*#2*\else#2\ \fi
|
||||||
|
#1\if*#3*\else\NAT@cmt#3\fi\NAT@@close\else#1\fi\endgroup}
|
||||||
|
\newcommand\NAT@citesuper[3]{\ifNAT@swa
|
||||||
|
\unskip\hspace{1\p@}\textsuperscript{#1}%
|
||||||
|
\if*#3*\else\ (#3)\fi\else #1\fi\endgroup}
|
||||||
|
\providecommand
|
||||||
|
\textsuperscript[1]{\mbox{$^{\mbox{\scriptsize#1}}$}}
|
||||||
|
\providecommand\@firstofone[1]{#1}
|
||||||
|
\newcommand\NAT@citexnum{}
|
||||||
|
\def\NAT@citexnum[#1][#2]#3{%
|
||||||
|
\NAT@sort@cites{#3}%
|
||||||
|
\let\@citea\@empty
|
||||||
|
\@cite{\def\NAT@num{-1}\let\NAT@last@yr\relax\let\NAT@nm\@empty
|
||||||
|
\@for\@citeb:=\NAT@cite@list\do
|
||||||
|
{\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi
|
||||||
|
\@ifundefined{b@\@citeb\@extra@b@citeb}{%
|
||||||
|
{\reset@font\bfseries?}
|
||||||
|
\NAT@citeundefined\PackageWarning{natbib}%
|
||||||
|
{Citation `\@citeb' on page \thepage \space undefined}}%
|
||||||
|
{\let\NAT@last@num\NAT@num\let\NAT@last@nm\NAT@nm
|
||||||
|
\NAT@parse{\@citeb}%
|
||||||
|
\ifNAT@longnames\@ifundefined{bv@\@citeb\@extra@b@citeb}{%
|
||||||
|
\let\NAT@name=\NAT@all@names
|
||||||
|
\global\@namedef{bv@\@citeb\@extra@b@citeb}{}}{}%
|
||||||
|
\fi
|
||||||
|
\ifNAT@full\let\NAT@nm\NAT@all@names\else
|
||||||
|
\let\NAT@nm\NAT@name\fi
|
||||||
|
\ifNAT@swa
|
||||||
|
\ifnum\NAT@ctype>1\relax\@citea
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\ifnum\NAT@ctype=2\relax\NAT@test{\NAT@ctype}%
|
||||||
|
\else\NAT@alias
|
||||||
|
\fi\hyper@natlinkend\else
|
||||||
|
\ifnum\NAT@sort>1
|
||||||
|
\begingroup\catcode`\_=8
|
||||||
|
\ifcat _\ifnum\z@<0\NAT@num _\else A\fi
|
||||||
|
\global\let\NAT@nm=\NAT@num \else \gdef\NAT@nm{-2}\fi
|
||||||
|
\ifcat _\ifnum\z@<0\NAT@last@num _\else A\fi
|
||||||
|
\global\@tempcnta=\NAT@last@num \global\advance\@tempcnta by\@ne
|
||||||
|
\else \global\@tempcnta\m@ne\fi
|
||||||
|
\endgroup
|
||||||
|
\ifnum\NAT@nm=\@tempcnta
|
||||||
|
\ifx\NAT@last@yr\relax
|
||||||
|
\edef\NAT@last@yr{\@citea \mbox{\noexpand\citenumfont{\NAT@num}}}%
|
||||||
|
\else
|
||||||
|
\edef\NAT@last@yr{--\penalty\@m\mbox{\noexpand\citenumfont{\NAT@num}}}%
|
||||||
|
\fi
|
||||||
|
\else
|
||||||
|
\NAT@last@yr \@citea \mbox{\citenumfont{\NAT@num}}%
|
||||||
|
\let\NAT@last@yr\relax
|
||||||
|
\fi
|
||||||
|
\else
|
||||||
|
\@citea \mbox{\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
{\citenumfont{\NAT@num}}\hyper@natlinkend}%
|
||||||
|
\fi
|
||||||
|
\fi
|
||||||
|
\def\@citea{\NAT@sep\penalty\@m\NAT@space}%
|
||||||
|
\else
|
||||||
|
\ifcase\NAT@ctype\relax
|
||||||
|
\ifx\NAT@last@nm\NAT@nm \NAT@yrsep\penalty\@m\NAT@space\else
|
||||||
|
\@citea \NAT@test{1}\ \NAT@@open
|
||||||
|
\if*#1*\else#1\ \fi\fi \NAT@mbox{%
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
{\citenumfont{\NAT@num}}\hyper@natlinkend}%
|
||||||
|
\def\@citea{\NAT@@close\NAT@sep\penalty\@m\ }%
|
||||||
|
\or\@citea
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@test{\NAT@ctype}\hyper@natlinkend
|
||||||
|
\def\@citea{\NAT@sep\penalty\@m\ }%
|
||||||
|
\or\@citea
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@test{\NAT@ctype}\hyper@natlinkend
|
||||||
|
\def\@citea{\NAT@sep\penalty\@m\ }%
|
||||||
|
\or\@citea
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@alias\hyper@natlinkend
|
||||||
|
\def\@citea{\NAT@sep\penalty\@m\ }%
|
||||||
|
\fi
|
||||||
|
\fi
|
||||||
|
}}%
|
||||||
|
\ifnum\NAT@sort>1\relax\NAT@last@yr\fi
|
||||||
|
\ifNAT@swa\else\ifnum\NAT@ctype=0\if*#2*\else
|
||||||
|
\NAT@cmt#2\fi \NAT@@close\fi\fi}{#1}{#2}}
|
||||||
|
\newcommand\NAT@test[1]{\ifnum#1=1 \ifx\NAT@nm\NAT@noname
|
||||||
|
{\reset@font\bfseries(author?)}\PackageWarning{natbib}
|
||||||
|
{Author undefined for citation`\@citeb'
|
||||||
|
\MessageBreak
|
||||||
|
on page \thepage}\else \NAT@nm \fi
|
||||||
|
\else \if\relax\NAT@date\relax
|
||||||
|
{\reset@font\bfseries(year?)}\PackageWarning{natbib}
|
||||||
|
{Year undefined for citation`\@citeb'
|
||||||
|
\MessageBreak
|
||||||
|
on page \thepage}\else \NAT@date \fi \fi}
|
||||||
|
\let\citenumfont=\relax
|
||||||
|
\newcommand\NAT@citex{}
|
||||||
|
\def\NAT@citex%
|
||||||
|
[#1][#2]#3{%
|
||||||
|
\NAT@sort@cites{#3}%
|
||||||
|
\let\@citea\@empty
|
||||||
|
\@cite{\let\NAT@nm\@empty\let\NAT@year\@empty
|
||||||
|
\@for\@citeb:=\NAT@cite@list\do
|
||||||
|
{\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi
|
||||||
|
\@ifundefined{b@\@citeb\@extra@b@citeb}{\@citea%
|
||||||
|
{\reset@font\bfseries ?}\NAT@citeundefined
|
||||||
|
\PackageWarning{natbib}%
|
||||||
|
{Citation `\@citeb' on page \thepage \space undefined}\def\NAT@date{}}%
|
||||||
|
{\let\NAT@last@nm=\NAT@nm\let\NAT@last@yr=\NAT@year
|
||||||
|
\NAT@parse{\@citeb}%
|
||||||
|
\ifNAT@longnames\@ifundefined{bv@\@citeb\@extra@b@citeb}{%
|
||||||
|
\let\NAT@name=\NAT@all@names
|
||||||
|
\global\@namedef{bv@\@citeb\@extra@b@citeb}{}}{}%
|
||||||
|
\fi
|
||||||
|
\ifNAT@full\let\NAT@nm\NAT@all@names\else
|
||||||
|
\let\NAT@nm\NAT@name\fi
|
||||||
|
\ifNAT@swa\ifcase\NAT@ctype
|
||||||
|
\if\relax\NAT@date\relax
|
||||||
|
\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}\NAT@date\hyper@natlinkend
|
||||||
|
\else
|
||||||
|
\ifx\NAT@last@nm\NAT@nm\NAT@yrsep
|
||||||
|
\ifx\NAT@last@yr\NAT@year
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@exlab
|
||||||
|
\hyper@natlinkend
|
||||||
|
\else\unskip\
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@date
|
||||||
|
\hyper@natlinkend
|
||||||
|
\fi
|
||||||
|
\else\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}%
|
||||||
|
\hyper@natlinkbreak{\NAT@aysep\ }{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@date\hyper@natlinkend
|
||||||
|
\fi
|
||||||
|
\fi
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}\hyper@natlinkend
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@date\hyper@natlinkend
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@alias\hyper@natlinkend
|
||||||
|
\fi \def\@citea{\NAT@sep\ }%
|
||||||
|
\else\ifcase\NAT@ctype
|
||||||
|
\if\relax\NAT@date\relax
|
||||||
|
\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}\hyper@natlinkend
|
||||||
|
\else
|
||||||
|
\ifx\NAT@last@nm\NAT@nm\NAT@yrsep
|
||||||
|
\ifx\NAT@last@yr\NAT@year
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@exlab
|
||||||
|
\hyper@natlinkend
|
||||||
|
\else\unskip\
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@date
|
||||||
|
\hyper@natlinkend
|
||||||
|
\fi
|
||||||
|
\else\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}%
|
||||||
|
\hyper@natlinkbreak{\ \NAT@@open\if*#1*\else#1\ \fi}%
|
||||||
|
{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@date\hyper@natlinkend\fi
|
||||||
|
\fi
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}\hyper@natlinkend
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@date\hyper@natlinkend
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@alias\hyper@natlinkend
|
||||||
|
\fi \if\relax\NAT@date\relax\def\@citea{\NAT@sep\ }%
|
||||||
|
\else\def\@citea{\NAT@@close\NAT@sep\ }\fi
|
||||||
|
\fi
|
||||||
|
}}\ifNAT@swa\else\if*#2*\else\NAT@cmt#2\fi
|
||||||
|
\if\relax\NAT@date\relax\else\NAT@@close\fi\fi}{#1}{#2}}
|
||||||
|
\newif\ifNAT@par \NAT@partrue
|
||||||
|
\newcommand\NAT@@open{\ifNAT@par\NAT@open\fi}
|
||||||
|
\newcommand\NAT@@close{\ifNAT@par\NAT@close\fi}
|
||||||
|
\newcommand\NAT@alias{\@ifundefined{al@\@citeb\@extra@b@citeb}{%
|
||||||
|
{\reset@font\bfseries(alias?)}\PackageWarning{natbib}
|
||||||
|
{Alias undefined for citation `\@citeb'
|
||||||
|
\MessageBreak on page \thepage}}{\@nameuse{al@\@citeb\@extra@b@citeb}}}
|
||||||
|
\let\NAT@up\relax
|
||||||
|
\newcommand\NAT@Up[1]{{\let\protect\@unexpandable@protect\let~\relax
|
||||||
|
\expandafter\NAT@deftemp#1}\expandafter\NAT@UP\NAT@temp}
|
||||||
|
\newcommand\NAT@deftemp[1]{\xdef\NAT@temp{#1}}
|
||||||
|
\newcommand\NAT@UP[1]{\let\@tempa\NAT@UP\ifcat a#1\MakeUppercase{#1}%
|
||||||
|
\let\@tempa\relax\else#1\fi\@tempa}
|
||||||
|
\newcommand\shortcites[1]{%
|
||||||
|
\@bsphack\@for\@citeb:=#1\do
|
||||||
|
{\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\global\@namedef{bv@\@citeb\@extra@b@citeb}{}}\@esphack}
|
||||||
|
\newcommand\NAT@biblabel[1]{\hfill}
|
||||||
|
\newcommand\NAT@biblabelnum[1]{\bibnumfmt{#1}}
|
||||||
|
\newcommand\bibnumfmt[1]{[#1]}
|
||||||
|
\def\@tempa#1{[#1]}
|
||||||
|
\ifx\@tempa\@biblabel\let\@biblabel\@empty\fi
|
||||||
|
\newcommand\NAT@bibsetnum[1]{\settowidth\labelwidth{\@biblabel{#1}}%
|
||||||
|
\setlength{\leftmargin}{\labelwidth}\addtolength{\leftmargin}{\labelsep}%
|
||||||
|
\setlength{\itemsep}{\bibsep}\setlength{\parsep}{\z@}%
|
||||||
|
\ifNAT@openbib
|
||||||
|
\addtolength{\leftmargin}{4mm}%
|
||||||
|
\setlength{\itemindent}{-4mm}%
|
||||||
|
\setlength{\listparindent}{\itemindent}%
|
||||||
|
\setlength{\parsep}{0pt}%
|
||||||
|
\fi
|
||||||
|
}
|
||||||
|
\newlength{\bibhang}
|
||||||
|
\setlength{\bibhang}{1em}
|
||||||
|
\newlength{\bibsep}
|
||||||
|
{\@listi \global\bibsep\itemsep \global\advance\bibsep by\parsep}
|
||||||
|
|
||||||
|
\newcommand\NAT@bibsetup%
|
||||||
|
[1]{\setlength{\leftmargin}{\bibhang}\setlength{\itemindent}{-\leftmargin}%
|
||||||
|
\setlength{\itemsep}{\bibsep}\setlength{\parsep}{\z@}}
|
||||||
|
\newcommand\NAT@set@cites{\ifNAT@numbers
|
||||||
|
\ifNAT@super \let\@cite\NAT@citesuper
|
||||||
|
\def\NAT@mbox##1{\unskip\nobreak\hspace{1\p@}\textsuperscript{##1}}%
|
||||||
|
\let\citeyearpar=\citeyear
|
||||||
|
\let\NAT@space\relax\else
|
||||||
|
\let\NAT@mbox=\mbox
|
||||||
|
\let\@cite\NAT@citenum \def\NAT@space{ }\fi
|
||||||
|
\let\@citex\NAT@citexnum
|
||||||
|
\ifx\@biblabel\@empty\let\@biblabel\NAT@biblabelnum\fi
|
||||||
|
\let\@bibsetup\NAT@bibsetnum
|
||||||
|
\def\natexlab##1{}%
|
||||||
|
\else
|
||||||
|
\let\@cite\NAT@cite
|
||||||
|
\let\@citex\NAT@citex
|
||||||
|
\let\@biblabel\NAT@biblabel
|
||||||
|
\let\@bibsetup\NAT@bibsetup
|
||||||
|
\def\natexlab##1{##1}%
|
||||||
|
\fi}
|
||||||
|
\AtBeginDocument{\NAT@set@cites}
|
||||||
|
\AtBeginDocument{\ifx\SK@def\@undefined\else
|
||||||
|
\ifx\SK@cite\@empty\else
|
||||||
|
\SK@def\@citex[#1][#2]#3{\SK@\SK@@ref{#3}\SK@@citex[#1][#2]{#3}}\fi
|
||||||
|
\ifx\SK@citeauthor\@undefined\def\HAR@checkdef{}\else
|
||||||
|
\let\citeauthor\SK@citeauthor
|
||||||
|
\let\citefullauthor\SK@citefullauthor
|
||||||
|
\let\citeyear\SK@citeyear\fi
|
||||||
|
\fi}
|
||||||
|
\AtBeginDocument{\@ifpackageloaded{hyperref}{%
|
||||||
|
\ifnum\NAT@sort=2\def\NAT@sort{1}\fi}{}}
|
||||||
|
\newif\ifNAT@full\NAT@fullfalse
|
||||||
|
\newif\ifNAT@swa
|
||||||
|
\DeclareRobustCommand\citet
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@partrue
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\newcommand\NAT@citetp{\@ifnextchar[{\NAT@@citetp}{\NAT@@citetp[]}}
|
||||||
|
\newcommand\NAT@@citetp{}
|
||||||
|
\def\NAT@@citetp[#1]{\@ifnextchar[{\@citex[#1]}{\@citex[][#1]}}
|
||||||
|
\DeclareRobustCommand\citep
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@partrue
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\cite
|
||||||
|
{\begingroup\def\NAT@ctype{0}\NAT@partrue\NAT@swatrue
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@cites}{\NAT@fullfalse\NAT@cites}}
|
||||||
|
\newcommand\NAT@cites{\@ifnextchar [{\NAT@@citetp}{%
|
||||||
|
\ifNAT@numbers\else
|
||||||
|
\NAT@swafalse
|
||||||
|
\fi
|
||||||
|
\NAT@@citetp[]}}
|
||||||
|
\DeclareRobustCommand\citealt
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@parfalse
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\citealp
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@parfalse
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\citeauthor
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{1}\NAT@parfalse
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citet
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@partrue
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citep
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@partrue
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citealt
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@parfalse
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citealp
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@parfalse
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citeauthor
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{1}\NAT@parfalse
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\citeyear
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{2}\NAT@parfalse\NAT@citetp}
|
||||||
|
\DeclareRobustCommand\citeyearpar
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{2}\NAT@partrue\NAT@citetp}
|
||||||
|
\newcommand\citetext[1]{\NAT@open#1\NAT@close}
|
||||||
|
\DeclareRobustCommand\citefullauthor
|
||||||
|
{\citeauthor*}
|
||||||
|
\newcommand\defcitealias[2]{%
|
||||||
|
\@ifundefined{al@#1\@extra@b@citeb}{}
|
||||||
|
{\PackageWarning{natbib}{Overwriting existing alias for citation #1}}
|
||||||
|
\@namedef{al@#1\@extra@b@citeb}{#2}}
|
||||||
|
\DeclareRobustCommand\citetalias{\begingroup
|
||||||
|
\NAT@swafalse\def\NAT@ctype{3}\NAT@parfalse\NAT@citetp}
|
||||||
|
\DeclareRobustCommand\citepalias{\begingroup
|
||||||
|
\NAT@swatrue\def\NAT@ctype{3}\NAT@partrue\NAT@citetp}
|
||||||
|
\renewcommand\nocite[1]{\@bsphack
|
||||||
|
\@for\@citeb:=#1\do{%
|
||||||
|
\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi
|
||||||
|
\if*\@citeb\else
|
||||||
|
\@ifundefined{b@\@citeb\@extra@b@citeb}{%
|
||||||
|
\NAT@citeundefined \PackageWarning{natbib}%
|
||||||
|
{Citation `\@citeb' undefined}}{}\fi}%
|
||||||
|
\@esphack}
|
||||||
|
\newcommand\NAT@parse[1]{{%
|
||||||
|
\let\protect=\@unexpandable@protect\let~\relax
|
||||||
|
\let\active@prefix=\@gobble
|
||||||
|
\xdef\NAT@temp{\csname b@#1\@extra@b@citeb\endcsname}}%
|
||||||
|
\expandafter\NAT@split\NAT@temp
|
||||||
|
\expandafter\NAT@parse@date\NAT@date??????@@%
|
||||||
|
\ifciteindex\NAT@index\fi
|
||||||
|
}
|
||||||
|
\newcommand\NAT@split[4]{%
|
||||||
|
\gdef\NAT@num{#1}\gdef\NAT@name{#3}\gdef\NAT@date{#2}%
|
||||||
|
\gdef\NAT@all@names{#4}%
|
||||||
|
\ifx\NAT@noname\NAT@all@names \gdef\NAT@all@names{#3}\fi}
|
||||||
|
\newcommand\NAT@parse@date{}
|
||||||
|
\def\NAT@parse@date#1#2#3#4#5#6@@{%
|
||||||
|
\ifnum\the\catcode`#1=11\def\NAT@year{}\def\NAT@exlab{#1}\else
|
||||||
|
\ifnum\the\catcode`#2=11\def\NAT@year{#1}\def\NAT@exlab{#2}\else
|
||||||
|
\ifnum\the\catcode`#3=11\def\NAT@year{#1#2}\def\NAT@exlab{#3}\else
|
||||||
|
\ifnum\the\catcode`#4=11\def\NAT@year{#1#2#3}\def\NAT@exlab{#4}\else
|
||||||
|
\def\NAT@year{#1#2#3#4}\def\NAT@exlab{{#5}}\fi\fi\fi\fi}
|
||||||
|
\newcommand\NAT@index{}
|
||||||
|
\let\NAT@makeindex=\makeindex
|
||||||
|
\renewcommand\makeindex{\NAT@makeindex
|
||||||
|
\renewcommand\NAT@index{\@bsphack\begingroup
|
||||||
|
\def~{\string~}\@wrindex{\NAT@idxtxt}}}
|
||||||
|
\newcommand\NAT@idxtxt{\NAT@name\ \NAT@open\NAT@date\NAT@close}
|
||||||
|
\@ifundefined{@indexfile}{}{\let\NAT@makeindex\relax\makeindex}
|
||||||
|
\newif\ifciteindex \citeindexfalse
|
||||||
|
\newcommand\citeindextype{default}
|
||||||
|
\newcommand\NAT@index@alt{{\let\protect=\noexpand\let~\relax
|
||||||
|
\xdef\NAT@temp{\NAT@idxtxt}}\expandafter\NAT@exp\NAT@temp\@nil}
|
||||||
|
\newcommand\NAT@exp{}
|
||||||
|
\def\NAT@exp#1\@nil{\mbox{}\index[\citeindextype]{#1}}
|
||||||
|
|
||||||
|
\AtBeginDocument{%
|
||||||
|
\@ifpackageloaded{index}{\let\NAT@index=\NAT@index@alt}{}}
|
||||||
|
\newcommand\NAT@ifcmd{\futurelet\NAT@temp\NAT@ifxcmd}
|
||||||
|
\newcommand\NAT@ifxcmd{\ifx\NAT@temp\relax\else\expandafter\NAT@bare\fi}
|
||||||
|
\def\NAT@bare#1(#2)#3(@)#4\@nil#5{%
|
||||||
|
\if @#2
|
||||||
|
\expandafter\NAT@apalk#1, , \@nil{#5}\else
|
||||||
|
\stepcounter{NAT@ctr}%
|
||||||
|
\NAT@wrout{\arabic {NAT@ctr}}{#2}{#1}{#3}{#5}
|
||||||
|
\fi
|
||||||
|
}
|
||||||
|
\newcommand\NAT@wrout[5]{%
|
||||||
|
\if@filesw
|
||||||
|
{\let\protect\noexpand\let~\relax
|
||||||
|
\immediate
|
||||||
|
\write\@auxout{\string\bibcite{#5}{{#1}{#2}{{#3}}{{#4}}}}}\fi
|
||||||
|
\ignorespaces}
|
||||||
|
\def\NAT@noname{{}}
|
||||||
|
\renewcommand\bibitem{%
|
||||||
|
\@ifnextchar[{\@lbibitem}{%
|
||||||
|
\global\NAT@stdbsttrue
|
||||||
|
\stepcounter{NAT@ctr}\@lbibitem[\arabic{NAT@ctr}]}}
|
||||||
|
\def\@lbibitem[#1]#2{%
|
||||||
|
\if\relax\@extra@b@citeb\relax\else
|
||||||
|
\@ifundefined{br@#2\@extra@b@citeb}{}{%
|
||||||
|
\@namedef{br@#2}{\@nameuse{br@#2\@extra@b@citeb}}}\fi
|
||||||
|
\@ifundefined{b@#2\@extra@b@citeb}{\def\NAT@num{}}{\NAT@parse{#2}}%
|
||||||
|
\item[\hfil\hyper@natanchorstart{#2\@extra@b@citeb}\@biblabel{\NAT@num}%
|
||||||
|
\hyper@natanchorend]%
|
||||||
|
\NAT@ifcmd#1(@)(@)\@nil{#2}}
|
||||||
|
\ifx\SK@lbibitem\@undefined\else
|
||||||
|
\let\SK@lbibitem\@lbibitem
|
||||||
|
\def\@lbibitem[#1]#2{%
|
||||||
|
\SK@lbibitem[#1]{#2}\SK@\SK@@label{#2}\ignorespaces}\fi
|
||||||
|
\newif\ifNAT@stdbst \NAT@stdbstfalse
|
||||||
|
|
||||||
|
\AtEndDocument
|
||||||
|
{\ifNAT@stdbst\if@filesw\immediate\write\@auxout{\string
|
||||||
|
\global\string\NAT@numberstrue}\fi\fi
|
||||||
|
}
|
||||||
|
\providecommand\bibcite{}
|
||||||
|
\renewcommand\bibcite[2]{\@ifundefined{b@#1\@extra@binfo}\relax
|
||||||
|
{\NAT@citemultiple
|
||||||
|
\PackageWarningNoLine{natbib}{Citation `#1' multiply defined}}%
|
||||||
|
\global\@namedef{b@#1\@extra@binfo}{#2}}
|
||||||
|
\AtEndDocument{\NAT@swatrue\let\bibcite\NAT@testdef}
|
||||||
|
\newcommand\NAT@testdef[2]{%
|
||||||
|
\def\NAT@temp{#2}\expandafter \ifx \csname b@#1\@extra@binfo\endcsname
|
||||||
|
\NAT@temp \else \ifNAT@swa \NAT@swafalse
|
||||||
|
\PackageWarningNoLine{natbib}{Citation(s) may have
|
||||||
|
changed.\MessageBreak
|
||||||
|
Rerun to get citations correct}\fi\fi}
|
||||||
|
\newcommand\NAT@apalk{}
|
||||||
|
\def\NAT@apalk#1, #2, #3\@nil#4{\if\relax#2\relax
|
||||||
|
\global\NAT@stdbsttrue
|
||||||
|
\NAT@wrout{#1}{}{}{}{#4}\else
|
||||||
|
\stepcounter{NAT@ctr}%
|
||||||
|
\NAT@wrout{\arabic {NAT@ctr}}{#2}{#1}{}{#4}\fi}
|
||||||
|
\newcommand\citeauthoryear{}
|
||||||
|
\def\citeauthoryear#1#2#3(@)(@)\@nil#4{\stepcounter{NAT@ctr}\if\relax#3\relax
|
||||||
|
\NAT@wrout{\arabic {NAT@ctr}}{#2}{#1}{}{#4}\else
|
||||||
|
\NAT@wrout{\arabic {NAT@ctr}}{#3}{#2}{#1}{#4}\fi}
|
||||||
|
\newcommand\citestarts{\NAT@open}
|
||||||
|
\newcommand\citeends{\NAT@close}
|
||||||
|
\newcommand\betweenauthors{and}
|
||||||
|
\newcommand\astroncite{}
|
||||||
|
\def\astroncite#1#2(@)(@)\@nil#3{\stepcounter{NAT@ctr}\NAT@wrout{\arabic
|
||||||
|
{NAT@ctr}}{#2}{#1}{}{#3}}
|
||||||
|
\newcommand\citename{}
|
||||||
|
\def\citename#1#2(@)(@)\@nil#3{\expandafter\NAT@apalk#1#2, \@nil{#3}}
|
||||||
|
\newcommand\harvarditem[4][]%
|
||||||
|
{\if\relax#1\relax\bibitem[#2(#3)]{#4}\else
|
||||||
|
\bibitem[#1(#3)#2]{#4}\fi }
|
||||||
|
\newcommand\harvardleft{\NAT@open}
|
||||||
|
\newcommand\harvardright{\NAT@close}
|
||||||
|
\newcommand\harvardyearleft{\NAT@open}
|
||||||
|
\newcommand\harvardyearright{\NAT@close}
|
||||||
|
\AtBeginDocument{\providecommand{\harvardand}{and}}
|
||||||
|
\newcommand\harvardurl[1]{\textbf{URL:} \textit{#1}}
|
||||||
|
\providecommand\bibsection{}
|
||||||
|
\@ifundefined{chapter}%
|
||||||
|
{\renewcommand\bibsection{\section*{\refname
|
||||||
|
\@mkboth{\MakeUppercase{\refname}}{\MakeUppercase{\refname}}}}}
|
||||||
|
{\@ifundefined{NAT@sectionbib}%
|
||||||
|
{\renewcommand\bibsection{\chapter*{\bibname
|
||||||
|
\@mkboth{\MakeUppercase{\bibname}}{\MakeUppercase{\bibname}}}}}
|
||||||
|
{\renewcommand\bibsection{\section*{\bibname
|
||||||
|
\ifx\@mkboth\@gobbletwo\else\markright{\MakeUppercase{\bibname}}\fi}}}}
|
||||||
|
\@ifclassloaded{amsart}%
|
||||||
|
{\renewcommand\bibsection{\section*{\refname}}}{}
|
||||||
|
\@ifclassloaded{amsbook}%
|
||||||
|
{\renewcommand\bibsection{\chapter*{\bibname}}}{}
|
||||||
|
\@ifundefined{bib@heading}{}{\let\bibsection\bib@heading}
|
||||||
|
\newcounter{NAT@ctr}
|
||||||
|
\renewenvironment{thebibliography}[1]{%
|
||||||
|
\bibsection
|
||||||
|
\vspace{1\p@}\parindent \z@\bibpreamble\bibfont\list
|
||||||
|
{\@biblabel{\arabic{NAT@ctr}}}{\@bibsetup{#1}%
|
||||||
|
\setcounter{NAT@ctr}{0}}%
|
||||||
|
\ifNAT@openbib
|
||||||
|
\renewcommand\newblock{\par}
|
||||||
|
\else
|
||||||
|
\renewcommand\newblock{\hskip .11em \@plus.33em \@minus.07em}%
|
||||||
|
\fi
|
||||||
|
\sloppy\clubpenalty4000\widowpenalty4000
|
||||||
|
\sfcode`\.=1000\relax
|
||||||
|
\let\citeN\cite \let\shortcite\cite
|
||||||
|
\let\citeasnoun\cite\fontsize{7}{9}\selectfont
|
||||||
|
}{\def\@noitemerr{%
|
||||||
|
\PackageWarning{natbib}
|
||||||
|
{Empty `thebibliography' environment}}%
|
||||||
|
\endlist\vskip-\lastskip}
|
||||||
|
\let\bibfont\relax
|
||||||
|
\let\bibpreamble\relax
|
||||||
|
\providecommand\reset@font{\relax}
|
||||||
|
\providecommand\bibname{Bibliography}
|
||||||
|
\providecommand\refname{References}
|
||||||
|
\newcommand\NAT@citeundefined{\gdef \NAT@undefined {%
|
||||||
|
\PackageWarningNoLine{natbib}{There were undefined citations}}}
|
||||||
|
\let \NAT@undefined \relax
|
||||||
|
\newcommand\NAT@citemultiple{\gdef \NAT@multiple {%
|
||||||
|
\PackageWarningNoLine{natbib}{There were multiply defined citations}}}
|
||||||
|
\let \NAT@multiple \relax
|
||||||
|
\AtEndDocument{\NAT@undefined\NAT@multiple}
|
||||||
|
\providecommand\@mkboth[2]{}
|
||||||
|
\providecommand\MakeUppercase{\uppercase}
|
||||||
|
\providecommand{\@extra@b@citeb}{}
|
||||||
|
\gdef\@extra@binfo{}
|
||||||
|
\providecommand\hyper@natanchorstart[1]{}
|
||||||
|
\providecommand\hyper@natanchorend{}
|
||||||
|
\providecommand\hyper@natlinkstart[1]{}
|
||||||
|
\providecommand\hyper@natlinkend{}
|
||||||
|
\providecommand\hyper@natlinkbreak[2]{#1}
|
||||||
|
\@ifundefined{bbl@redefine}{}{%
|
||||||
|
\bbl@redefine\nocite#1{%
|
||||||
|
\@safe@activestrue\org@nocite{#1}\@safe@activesfalse}%
|
||||||
|
\bbl@redefine\@lbibitem[#1]#2{%
|
||||||
|
\@safe@activestrue\org@@lbibitem[#1]{#2}\@safe@activesfalse}%
|
||||||
|
}
|
||||||
|
\AtBeginDocument{\@ifundefined{bbl@redefine}{}{%
|
||||||
|
\bbl@redefine\@citex[#1][#2]#3{%
|
||||||
|
\@safe@activestrue\org@@citex[#1][#2]{#3}\@safe@activesfalse}%
|
||||||
|
\bbl@redefine\NAT@testdef#1#2{%
|
||||||
|
\@safe@activestrue\org@NAT@testdef{#1}{#2}\@safe@activesfalse}%
|
||||||
|
\@ifundefined{org@@lbibitem}{%
|
||||||
|
\bbl@redefine\@lbibitem[#1]#2{%
|
||||||
|
\@safe@activestrue\org@@lbibitem[#1]{#2}\@safe@activesfalse}}{}%
|
||||||
|
}}
|
||||||
|
\ifnum\NAT@sort>0
|
||||||
|
\newcommand\NAT@sort@cites[1]{%
|
||||||
|
\@tempcntb\m@ne
|
||||||
|
\let\@celt\delimiter
|
||||||
|
\def\NAT@num@list{}%
|
||||||
|
\def\NAT@cite@list{}%
|
||||||
|
\def\NAT@nonsort@list{}%
|
||||||
|
\@for \@citeb:=#1\do{\NAT@make@cite@list}%
|
||||||
|
\edef\NAT@cite@list{\NAT@cite@list\NAT@nonsort@list}%
|
||||||
|
\edef\NAT@cite@list{\expandafter\NAT@xcom\NAT@cite@list @@}}
|
||||||
|
\begingroup \catcode`\_=8
|
||||||
|
\gdef\NAT@make@cite@list{%
|
||||||
|
\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\@ifundefined{b@\@citeb\@extra@b@citeb}{\def\NAT@num{A}}%
|
||||||
|
{\NAT@parse{\@citeb}}%
|
||||||
|
\ifcat _\ifnum\z@<0\NAT@num _\else A\fi
|
||||||
|
\@tempcnta\NAT@num \relax
|
||||||
|
\ifnum \@tempcnta>\@tempcntb
|
||||||
|
\edef\NAT@num@list{\NAT@num@list \@celt{\NAT@num}}%
|
||||||
|
\edef\NAT@cite@list{\NAT@cite@list\@citeb,}%
|
||||||
|
\@tempcntb\@tempcnta
|
||||||
|
\else
|
||||||
|
\let\NAT@@cite@list=\NAT@cite@list \def\NAT@cite@list{}%
|
||||||
|
\edef\NAT@num@list{\expandafter\NAT@num@celt \NAT@num@list \@gobble @}%
|
||||||
|
{\let\@celt=\NAT@celt\NAT@num@list}%
|
||||||
|
\fi
|
||||||
|
\else
|
||||||
|
\edef\NAT@nonsort@list{\NAT@nonsort@list\@citeb,}%
|
||||||
|
\fi}
|
||||||
|
\endgroup
|
||||||
|
\def\NAT@celt#1{\ifnum #1<\@tempcnta
|
||||||
|
\xdef\NAT@cite@list{\NAT@cite@list\expandafter\NAT@nextc\NAT@@cite@list @@}%
|
||||||
|
\xdef\NAT@@cite@list{\expandafter\NAT@restc\NAT@@cite@list}%
|
||||||
|
\else
|
||||||
|
\xdef\NAT@cite@list{\NAT@cite@list\@citeb,\NAT@@cite@list}\let\@celt\@gobble%
|
||||||
|
\fi}
|
||||||
|
\def\NAT@num@celt#1#2{\ifx \@celt #1%
|
||||||
|
\ifnum #2<\@tempcnta
|
||||||
|
\@celt{#2}%
|
||||||
|
\expandafter\expandafter\expandafter\NAT@num@celt
|
||||||
|
\else
|
||||||
|
\@celt{\number\@tempcnta}\@celt{#2}%
|
||||||
|
\fi\fi}
|
||||||
|
\def\NAT@nextc#1,#2@@{#1,}
|
||||||
|
\def\NAT@restc#1,#2{#2}
|
||||||
|
\def\NAT@xcom#1,@@{#1}
|
||||||
|
\else
|
||||||
|
\newcommand\NAT@sort@cites[1]{\edef\NAT@cite@list{#1}}\fi
|
||||||
|
\InputIfFileExists{natbib.cfg}
|
||||||
|
{\typeout{Local config file natbib.cfg used}}{}
|
||||||
|
%%
|
||||||
|
%% <<<<< End of generated file <<<<<<
|
||||||
|
%%
|
||||||
|
%% End of file `natbib.sty'.
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
Q 60 23616 0 0.000000000
|
||||||
|
Q 45 3520 1 0.000036851
|
||||||
|
Q 41 1840 1 0.000069023
|
||||||
|
Q 37 328 2 0.000136500
|
||||||
|
Q 36 276 1 0.000169033
|
||||||
|
Q 35 480 1 0.000199601
|
||||||
|
Q 33 375 2 0.000262855
|
||||||
|
Q 31 178 2 0.000326659
|
||||||
|
Q 30 153 5 0.000487551
|
||||||
|
Q 29 200 1 0.000516696
|
||||||
|
Q 27 100 3 0.000611601
|
||||||
|
Q 26 93 3 0.000706056
|
||||||
|
Q 25 75 2 0.000768393
|
||||||
|
Q 24 82 1 0.000798314
|
||||||
|
Q 23 80 6 0.000987387
|
||||||
|
Q 22 71 6 0.001175835
|
||||||
|
Q 21 76 7 0.001394921
|
||||||
|
Q 20 63 9 0.001676897
|
||||||
|
Q 19 55 4 0.001800322
|
||||||
|
Q 18 62 8 0.002048987
|
||||||
|
Q 17 55 7 0.002265718
|
||||||
|
Q 16 60 10 0.002575539
|
||||||
|
Q 15 82 9 0.002850877
|
||||||
|
Q 14 67 7 0.003063745
|
||||||
|
Q 13 62 11 0.003401042
|
||||||
|
Q 12 64 13 0.003799084
|
||||||
|
Q 11 56 5 0.003947900
|
||||||
|
Q 10 58 17 0.004468303
|
||||||
|
Q 9 70 22 0.005139796
|
||||||
|
Q 8 23 9 0.005414604
|
||||||
|
Q 7 41 17 0.005933068
|
||||||
|
Q 6 42 18 0.006480881
|
||||||
|
Q 5 33 9 0.006751757
|
||||||
|
Q 4 29 9 0.007022948
|
||||||
|
Q 3 27 15 0.007478764
|
||||||
|
Q 2 23 10 0.007781024
|
||||||
|
Q 1 9 2 0.007840364
|
||||||
|
Q 0 13 8 0.008083105
|
||||||
|
|
@ -0,0 +1,52 @@
|
||||||
|
set t po eps enh co so "Helvetica,26"
|
||||||
|
|
||||||
|
set style line 1 lt 1 pt 1 lc rgb "#e41a1c" lw 2;
|
||||||
|
set style line 2 lt 1 pt 2 lc rgb "#377eb8" lw 2;
|
||||||
|
set style line 3 lt 1 pt 3 lc rgb "#4daf4a" lw 2;
|
||||||
|
set style line 4 lt 1 pt 4 lc rgb "#984ea3" lw 2;
|
||||||
|
set style line 5 lt 1 pt 6 lc rgb "#ff7f00" lw 2;
|
||||||
|
set style line 6 lt 1 pt 8 lc rgb "#f781bf" lw 2;
|
||||||
|
|
||||||
|
set out "roc-color.eps"
|
||||||
|
|
||||||
|
set pointsize 2.0
|
||||||
|
set size 1.59,1.04
|
||||||
|
set multiplot layout 1,2
|
||||||
|
|
||||||
|
set label "(a)" at graph -0.245,1.06 font "Helvetica-bold,40"
|
||||||
|
set xlab "Error rate of mapped reads"
|
||||||
|
set ylab "Fraction of mapped reads" off +1.8
|
||||||
|
set ytics 0.02
|
||||||
|
set yran [0.9:1]
|
||||||
|
|
||||||
|
set size 0.8,1
|
||||||
|
set log x
|
||||||
|
set format x "10^{%L}"
|
||||||
|
set key bot right
|
||||||
|
plot "<./eval2roc.pl blasr-mc.eval" u 2:3 t "blasr-mc" w lp ls 4, \
|
||||||
|
"<./eval2roc.pl bwa.eval" u 2:3 t "bwa-mem" w lp ls 2, \
|
||||||
|
"<./eval2roc.pl graphmap.eval" u 2:3 t "graphmap" w lp ls 3, \
|
||||||
|
"<./eval2roc.pl minialign.eval" u 2:3 t "minialign" w lp ls 1, \
|
||||||
|
"<./eval2roc.pl mm2.eval" u 2:3 t "minimap2" w lp ls 6, \
|
||||||
|
"<./eval2roc.pl ngmlr.eval" u 2:3 t "ngm-lr" w lp ls 5
|
||||||
|
unset label
|
||||||
|
|
||||||
|
set origin 0.8,0
|
||||||
|
set size 0.79,1
|
||||||
|
set label "(b)" at graph -0.245,1.06 font "Helvetica-bold,40"
|
||||||
|
unset log
|
||||||
|
unset format
|
||||||
|
unset key
|
||||||
|
set log y
|
||||||
|
set ylab "Accumulative mapping error rate" off +0
|
||||||
|
set xlab "Mapping quality"
|
||||||
|
set yran [1e-5:0.1]
|
||||||
|
set ytics 1e-5,0.1
|
||||||
|
set format y "10^{%L}"
|
||||||
|
set xran [60:0] reverse
|
||||||
|
plot "<./eval2roc.pl blasr-mc.eval" u 1:2 w lp ls 4, \
|
||||||
|
"<./eval2roc.pl bwa.eval" u 1:2 t "bwa-mem" w lp ls 2, \
|
||||||
|
"<./eval2roc.pl graphmap.eval" u 1:2 t "graphmap" w lp ls 3, \
|
||||||
|
"<./eval2roc.pl minialign.eval" u 1:2 t "minialign" w lp ls 1, \
|
||||||
|
"<./eval2roc.pl mm2.eval" u 1:2 t "minimap2" w lp ls 6, \
|
||||||
|
"<./eval2roc.pl ngmlr.eval" u 1:2 t "ngm-lr" w lp ls 5
|
||||||
Loading…
Reference in New Issue