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allow to pac forward strand only

This commit is contained in:
Heng Li 2011-10-21 10:57:12 -04:00
parent 66629512d9
commit fe9da3c704
1 changed files with 15 additions and 7 deletions
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18
bntseq.c
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@ -211,7 +211,7 @@ static void add1(const kseq_t *seq, bntseq_t *bns, FILE *fp, uint8_t *buf, int *
bns->l_pac += seq->seq.l; bns->l_pac += seq->seq.l;
} }
int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix) int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only)
{ {
extern void seq_reverse(int len, ubyte_t *seq, int is_comp); // in bwaseqio.c extern void seq_reverse(int len, ubyte_t *seq, int is_comp); // in bwaseqio.c
kseq_t *seq; kseq_t *seq;
@ -241,9 +241,11 @@ int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix)
for (i = 0; i < seq->seq.l; ++i) // convert to 2-bit encoding for (i = 0; i < seq->seq.l; ++i) // convert to 2-bit encoding
seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]]; seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
add1(seq, bns, fp, buf, &l_buf, &m_seqs, &m_holes, &q); add1(seq, bns, fp, buf, &l_buf, &m_seqs, &m_holes, &q);
if (!for_only) {
seq_reverse(seq->seq.l, (uint8_t*)seq->seq.s, 1); seq_reverse(seq->seq.l, (uint8_t*)seq->seq.s, 1);
add1(seq, bns, fp, buf, &l_buf, &m_seqs, &m_holes, &q); add1(seq, bns, fp, buf, &l_buf, &m_seqs, &m_holes, &q);
} }
}
xassert(bns->l_pac, "zero length sequence."); xassert(bns->l_pac, "zero length sequence.");
ret = bns->l_pac; ret = bns->l_pac;
{ // finalize .pac file { // finalize .pac file
@ -267,13 +269,19 @@ int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix)
int bwa_fa2pac(int argc, char *argv[]) int bwa_fa2pac(int argc, char *argv[])
{ {
int c, for_only = 0;
gzFile fp; gzFile fp;
if (argc < 2) { while ((c = getopt(argc, argv, "f")) >= 0) {
fprintf(stderr, "Usage: bwa fa2pac <in.fasta> [<out.prefix>]\n"); switch (c) {
case 'f': for_only = 1; break;
}
}
if (argc == optind) {
fprintf(stderr, "Usage: bwa fa2pac [-f] <in.fasta> [<out.prefix>]\n");
return 1; return 1;
} }
fp = xzopen(argv[1], "r"); fp = xzopen(argv[optind], "r");
bns_fasta2bntseq(fp, (argc < 3)? argv[1] : argv[2]); bns_fasta2bntseq(fp, (optind+1 < argc)? argv[optind+1] : argv[optind], for_only);
gzclose(fp); gzclose(fp);
return 0; return 0;
} }