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Merge pull request #2 from RoelKluin/master 

Filter Casava 1.8 flagged sequences with bwa aln -Y
This commit is contained in:
Heng Li 2011-07-10 12:27:55 -07:00
parent d11674367d db59a605d1
commit 4f7734eb97
3 changed files with 11 additions and 1 deletions
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7
bwaseqio.c
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@ -157,6 +157,13 @@ bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int tri
n_seqs = 0; n_seqs = 0;
seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t)); seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
while ((l = kseq_read(seq)) >= 0) { while ((l = kseq_read(seq)) >= 0) {
if ((mode & BWA_MODE_CFY) && (seq->comment.l != 0)) {
// skip reads that are marked to be filtered by Casava
char *s = index(seq->comment.s, ':');
if (s && *(++s) == 'Y') {
continue;
}
}
if (is_64 && seq->qual.l) if (is_64 && seq->qual.l)
for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31; 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 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; gap_opt_t *opt;
opt = gap_init_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:b012IB:")) >= 0) { while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012IYB:")) >= 0) {
switch (c) { switch (c) {
case 'n': case 'n':
if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1; if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
@ -261,6 +261,7 @@ int bwa_aln(int argc, char *argv[])
case '1': opt->mode |= BWA_MODE_BAM_READ1; break; case '1': opt->mode |= BWA_MODE_BAM_READ1; break;
case '2': opt->mode |= BWA_MODE_BAM_READ2; break; case '2': opt->mode |= BWA_MODE_BAM_READ2; break;
case 'I': opt->mode |= BWA_MODE_IL13; 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; case 'B': opt->mode |= atoi(optarg) << 24; break;
default: return 1; default: return 1;
} }
@ -298,6 +299,7 @@ int bwa_aln(int argc, char *argv[])
fprintf(stderr, " -0 use single-end reads only (effective with -b)\n"); 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, " -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, " -2 use the 2nd read in a pair (effective with -b)\n");
fprintf(stderr, " -Y filter Casava-filtered sequences\n");
fprintf(stderr, "\n"); fprintf(stderr, "\n");
return 1; return 1;
} }

1
bwtaln.h
View File

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