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r875: warn given incorrect FASTA/Q 

resolves #252
resolves #255
This commit is contained in:
Heng Li 2018-11-05 10:02:44 -05:00
parent 24df95e4b8
commit fd64dd26f6
2 changed files with 7 additions and 2 deletions
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7
bseq.c
View File

@ -65,6 +65,8 @@ static inline char *kstrdup(const kstring_t *s)
static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual, int with_comment) static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual, int with_comment)
{ {
int i; int i;
if (ks->name.l == 0)
fprintf(stderr, "[WARNING]\033[1;31m empty sequence name in the input.\033[0m\n");
s->name = kstrdup(&ks->name); s->name = kstrdup(&ks->name);
s->seq = kstrdup(&ks->seq); s->seq = kstrdup(&ks->seq);
for (i = 0; i < (int)ks->seq.l; ++i) // convert U to T for (i = 0; i < (int)ks->seq.l; ++i) // convert U to T
@ -78,6 +80,7 @@ static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual, int with_
mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int chunk_size, int with_qual, int with_comment, int frag_mode, int *n_) mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int chunk_size, int with_qual, int with_comment, int frag_mode, int *n_)
{ {
int64_t size = 0; int64_t size = 0;
int ret;
kvec_t(mm_bseq1_t) a = {0,0,0}; kvec_t(mm_bseq1_t) a = {0,0,0};
kseq_t *ks = fp->ks; kseq_t *ks = fp->ks;
*n_ = 0; *n_ = 0;
@ -87,7 +90,7 @@ mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int chunk_size, int with_qual, int
size = fp->s.l_seq; size = fp->s.l_seq;
memset(&fp->s, 0, sizeof(mm_bseq1_t)); memset(&fp->s, 0, sizeof(mm_bseq1_t));
} }
while (kseq_read(ks) >= 0) { while ((ret = kseq_read(ks)) >= 0) {
mm_bseq1_t *s; mm_bseq1_t *s;
assert(ks->seq.l <= INT32_MAX); assert(ks->seq.l <= INT32_MAX);
if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256); if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
@ -107,6 +110,8 @@ mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int chunk_size, int with_qual, int
break; break;
} }
} }
if (ret != -1)
fprintf(stderr, "[WARNING]\033[1;31m wrong FASTA/FASTQ record. Continue anyway.\033[0m\n");
*n_ = a.n; *n_ = a.n;
return a.a; return a.a;
} }

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.13-r874-dirty" #define MM_VERSION "2.13-r875-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>