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code backup

This commit is contained in:
Heng Li 2013-02-16 10:09:30 -05:00
parent 5f8c6efbc3
commit fe2236f6fe
1 changed files with 22 additions and 1 deletions
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23
bwamem_pair.c
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@ -6,6 +6,7 @@
#include "bwamem.h"
#include "kvec.h"
#include "utils.h"
#include "ksw.h"
#define MIN_RATIO 0.8
#define MIN_DIR_CNT 10
@ -126,8 +127,28 @@ void mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const m
rb = (is_larger? a->rb + pes[r].low : a->rb - pes[r].high) - l_ms; // similarly on opposite strands
re = is_larger? a->rb + pes[r].high: a->rb - pes[r].low;
}
if (rb < 0) rb = 0;
if (re > l_pac) re = l_pac;
ref = bns_get_seq(l_pac, pac, rb, re, &len);
if (len == re - rb) {
if (len == re - rb) { // no funny things happening
kswr_t aln;
mem_alnreg_t b;
int tmp, xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250? KSW_XBYTE : 0) | opt->min_seed_len;
aln = ksw_align(l_ms, seq, len, ref, 5, opt->mat, opt->q, opt->r, xtra, 0);
memset(&b, 0, sizeof(mem_alnreg_t));
b.qb = aln.qb; b.qe = aln.qe + 1;
b.rb = rb + aln.tb;
b.re = rb + aln.te + 1;
b.score = aln.score;
b.csub = aln.score2;
b.secondary = -1;
kv_push(mem_alnreg_t, *ma, b); // make room for a new element
// move b s.t. ma is sorted
for (i = 0; i < ma->n - 1; ++i) // find the insertion point
if (ma->a[i].score < b.score) break;
tmp = i;
for (i = ma->n - 1; i > tmp; --i) ma->a[i] = ma->a[i-1];
ma->a[i] = b;
}
if (rev == 0) free(rev);
free(ref);