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Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa" 

This reverts commit 36cd4f9882.

The comment shouldn't be included in the sequence name.
This commit is contained in:
Roel Kluin 2011-07-10 16:40:42 +02:00
parent 36cd4f9882
commit 8f115a8e00
4 changed files with 2 additions and 24 deletions
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19
bwaseqio.c
View File

@ -157,25 +157,6 @@ bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int tri
n_seqs = 0;
seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
while ((l = kseq_read(seq)) >= 0) {
// skip reads that are marked to be filtered by Casava
if (mode & BWA_MODE_CFY) {
char *s = rindex(seq->name.s, ' ');
if (s) {
*s = '\0';
for(++s; *s != '\0'; ++s) {
if (*s == ':') {
++s;
break;
}
}
if (*s == 'Y')
continue;
}
if (!s || *s != 'N') {
fprintf(stderr, "No Casava filter character found.\n");
return 0;
}
}
if (is_64 && seq->qual.l)
for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31;
if (seq->seq.l <= l_bc) continue; // sequence length equals or smaller than the barcode length

4
bwtaln.c
View File

@ -233,7 +233,7 @@ int bwa_aln(int argc, char *argv[])
gap_opt_t *opt;
opt = gap_init_opt();
while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012IYB:")) >= 0) {
while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012IB:")) >= 0) {
switch (c) {
case 'n':
if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
@ -261,7 +261,6 @@ int bwa_aln(int argc, char *argv[])
case '1': opt->mode |= BWA_MODE_BAM_READ1; break;
case '2': opt->mode |= BWA_MODE_BAM_READ2; break;
case 'I': opt->mode |= BWA_MODE_IL13; break;
case 'Y': opt->mode |= BWA_MODE_CFY; break;
case 'B': opt->mode |= atoi(optarg) << 24; break;
default: return 1;
}
@ -299,7 +298,6 @@ int bwa_aln(int argc, char *argv[])
fprintf(stderr, " -0 use single-end reads only (effective with -b)\n");
fprintf(stderr, " -1 use the 1st read in a pair (effective with -b)\n");
fprintf(stderr, " -2 use the 2nd read in a pair (effective with -b)\n");
fprintf(stderr, " -Y filter Casava-filtered sequences\n");
fprintf(stderr, "\n");
return 1;
}

1
bwtaln.h
View File

@ -86,7 +86,6 @@ typedef struct {
#define BWA_MODE_GAPE 0x01
#define BWA_MODE_COMPREAD 0x02
#define BWA_MODE_LOGGAP 0x04
#define BWA_MODE_CFY 0x08
#define BWA_MODE_NONSTOP 0x10
#define BWA_MODE_BAM 0x20
#define BWA_MODE_BAM_SE 0x40

2
kseq.h
View File

@ -102,7 +102,7 @@ typedef struct __kstring_t {
if (ks->buf[i] == delimiter) break; \
} else { \
for (i = ks->begin; i < ks->end; ++i) \
if (isspace(ks->buf[i]) && (ks->buf[i] != ' ')) break; \
if (isspace(ks->buf[i])) break; \
} \
if (str->m - str->l < i - ks->begin + 1) { \
str->m = str->l + (i - ks->begin) + 1; \