applied patches from Alec Wysoker
This commit is contained in:
Heng Li
parent
4d064c69ce
commit
243e735431
68
bwase.c
68
bwase.c
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@ -437,15 +437,15 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
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if (mate->strand) flag |= SAM_FMR;
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} else flag |= SAM_FMU;
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}
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printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
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printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
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err_printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
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err_printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
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// print CIGAR
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if (p->cigar) {
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for (j = 0; j != p->n_cigar; ++j)
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printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
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} else if (p->type == BWA_TYPE_NO_MATCH) printf("*");
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else printf("%dM", p->len);
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err_printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
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} else if (p->type == BWA_TYPE_NO_MATCH) err_printf("*");
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else err_printf("%dM", p->len);
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// print mate coordinate
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if (mate && mate->type != BWA_TYPE_NO_MATCH) {
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@ -454,12 +454,12 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
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am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
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// redundant calculation here, but should not matter too much
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m_is_N = bns_coor_pac2real(bns, mate->pos, mate->len, &m_seqid);
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printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
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err_printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
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isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
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if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
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printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
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} else if (mate) printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
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else printf("\t*\t0\t0\t");
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err_printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
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} else if (mate) err_printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
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else err_printf("\t*\t0\t0\t");
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// print sequence and quality
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if (p->strand == 0)
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@ -468,42 +468,42 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
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putchar('\t');
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if (p->qual) {
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if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
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printf("%s", p->qual);
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} else printf("*");
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err_printf("%s", p->qual);
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} else err_printf("*");
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if (bwa_rg_id) printf("\tRG:Z:%s", bwa_rg_id);
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if (p->bc[0]) printf("\tBC:Z:%s", p->bc);
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if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
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if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
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if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
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if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
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if (p->type != BWA_TYPE_NO_MATCH) {
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int i;
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// calculate XT tag
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XT = "NURM"[p->type];
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if (nn > 10) XT = 'N';
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// print tags
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printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
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if (nn) printf("\tXN:i:%d", nn);
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if (mate) printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
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err_printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
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if (nn) err_printf("\tXN:i:%d", nn);
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if (mate) err_printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
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if (p->type != BWA_TYPE_MATESW) { // X0 and X1 are not available for this type of alignment
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printf("\tX0:i:%d", p->c1);
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if (p->c1 <= max_top2) printf("\tX1:i:%d", p->c2);
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err_printf("\tX0:i:%d", p->c1);
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if (p->c1 <= max_top2) err_printf("\tX1:i:%d", p->c2);
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}
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printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
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if (p->md) printf("\tMD:Z:%s", p->md);
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err_printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
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if (p->md) err_printf("\tMD:Z:%s", p->md);
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// print multiple hits
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if (p->n_multi) {
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printf("\tXA:Z:");
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err_printf("\tXA:Z:");
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for (i = 0; i < p->n_multi; ++i) {
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bwt_multi1_t *q = p->multi + i;
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int k;
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j = pos_end_multi(q, p->len) - q->pos;
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nn = bns_coor_pac2real(bns, q->pos, j, &seqid);
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printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
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err_printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
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(int)(q->pos - bns->anns[seqid].offset + 1));
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if (q->cigar) {
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for (k = 0; k < q->n_cigar; ++k)
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printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
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} else printf("%dM", p->len);
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printf(",%d;", q->gap + q->mm);
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err_printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
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} else err_printf("%dM", p->len);
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err_printf(",%d;", q->gap + q->mm);
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}
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}
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}
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@ -512,16 +512,16 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
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ubyte_t *s = p->strand? p->rseq : p->seq;
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int flag = p->extra_flag | SAM_FSU;
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if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
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printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
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err_printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
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for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
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putchar('\t');
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if (p->qual) {
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if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
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printf("%s", p->qual);
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} else printf("*");
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if (bwa_rg_id) printf("\tRG:Z:%s", bwa_rg_id);
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if (p->bc[0]) printf("\tBC:Z:%s", p->bc);
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if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
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err_printf("%s", p->qual);
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} else err_printf("*");
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if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
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if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
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if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
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putchar('\n');
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}
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}
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@ -541,8 +541,8 @@ void bwa_print_sam_SQ(const bntseq_t *bns)
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{
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int i;
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for (i = 0; i < bns->n_seqs; ++i)
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printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
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if (bwa_rg_line) printf("%s\n", bwa_rg_line);
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err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
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if (bwa_rg_line) err_printf("%s\n", bwa_rg_line);
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}
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void bwase_initialize()
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6
bwtaln.c
6
bwtaln.c
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@ -176,7 +176,7 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
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}
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// core loop
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fwrite(opt, sizeof(gap_opt_t), 1, stdout);
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err_fwrite(opt, sizeof(gap_opt_t), 1, stdout);
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while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode, opt->trim_qual)) != 0) {
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tot_seqs += n_seqs;
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t = clock();
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@ -213,8 +213,8 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
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fprintf(stderr, "[bwa_aln_core] write to the disk... ");
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for (i = 0; i < n_seqs; ++i) {
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bwa_seq_t *p = seqs + i;
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fwrite(&p->n_aln, 4, 1, stdout);
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if (p->n_aln) fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
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err_fwrite(&p->n_aln, 4, 1, stdout);
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if (p->n_aln) err_fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
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}
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fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
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5
main.c
5
main.c
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@ -1,9 +1,10 @@
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#include <stdio.h>
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#include <string.h>
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#include "main.h"
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#include "utils.h"
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#ifndef PACKAGE_VERSION
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#define PACKAGE_VERSION "0.5.9-r16"
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#define PACKAGE_VERSION "0.5.9-r18-dev"
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#endif
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static int usage()
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@ -59,5 +60,7 @@ int main(int argc, char *argv[])
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fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
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return 1;
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}
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err_fflush(stdout);
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err_fclose(stdout);
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return 0;
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}
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66
utils.c
66
utils.c
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@ -30,6 +30,7 @@
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#include <stdlib.h>
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#include <string.h>
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#include <zlib.h>
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#include <errno.h>
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#include "utils.h"
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FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
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@ -80,3 +81,68 @@ void err_fatal_simple_core(const char *func, const char *msg)
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fprintf(stderr, "[%s] %s Abort!\n", func, msg);
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abort();
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}
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size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream)
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{
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size_t ret = fwrite(ptr, size, nmemb, stream);
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if (ret != nmemb)
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{
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err_fatal_simple_core("fwrite", strerror(errno));
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}
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return ret;
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}
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int err_printf(const char *format, ...)
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{
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va_list arg;
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int done;
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va_start(arg, format);
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done = vfprintf(stdout, format, arg);
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int saveErrno = errno;
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va_end(arg);
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if (done < 0)
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{
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err_fatal_simple_core("vfprintf(stdout)", strerror(saveErrno));
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}
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return done;
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}
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int err_fprintf(FILE *stream, const char *format, ...)
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{
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va_list arg;
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int done;
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va_start(arg, format);
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done = vfprintf(stream, format, arg);
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int saveErrno = errno;
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va_end(arg);
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if (done < 0)
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{
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err_fatal_simple_core("vfprintf", strerror(saveErrno));
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}
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return done;
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}
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int err_fflush(FILE *stream)
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{
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int ret = fflush(stream);
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if (ret != 0)
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{
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err_fatal_simple_core("fflush", strerror(errno));
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}
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return ret;
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}
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int err_fclose(FILE *stream)
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{
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int ret = fclose(stream);
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if (ret != 0)
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{
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err_fatal_simple_core("fclose", strerror(errno));
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}
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return ret;
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}
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16
utils.h
16
utils.h
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@ -31,6 +31,15 @@
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#include <stdio.h>
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#include <zlib.h>
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#ifdef __GNUC__
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// Tell GCC to validate printf format string and args
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#define ATTRIBUTE(list) __attribute__ (list)
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#else
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#define ATTRIBUTE(list)
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#endif
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#define err_fatal_simple(msg) err_fatal_simple_core(__func__, msg)
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#define xopen(fn, mode) err_xopen_core(__func__, fn, mode)
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#define xreopen(fn, mode, fp) err_xreopen_core(__func__, fn, mode, fp)
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@ -46,6 +55,13 @@ extern "C" {
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FILE *err_xopen_core(const char *func, const char *fn, const char *mode);
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FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp);
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gzFile err_xzopen_core(const char *func, const char *fn, const char *mode);
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size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream);
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int err_fprintf(FILE *stream, const char *format, ...)
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ATTRIBUTE((format(printf, 2, 3)));
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int err_printf(const char *format, ...)
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ATTRIBUTE((format(printf, 1, 2)));
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int err_fflush(FILE *stream);
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int err_fclose(FILE *stream);
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#ifdef __cplusplus
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}
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