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Several trivial Debian patches 

[Andreas Tille]
Check exact number of arguments of bwtupdate
Fix spelling

[Fabian Klötzl]
change printing as size_t is unsigned
This commit is contained in:
Andreas Tille 2015-07-12 14:59:23 +02:00 committed by John Marshall
parent 690649872b
commit c56c2e4677
3 changed files with 6 additions and 6 deletions
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2
bwtindex.c
View File

@ -175,7 +175,7 @@ void bwt_bwtupdate_core(bwt_t *bwt)
int bwa_bwtupdate(int argc, char *argv[]) // the "bwtupdate" command int bwa_bwtupdate(int argc, char *argv[]) // the "bwtupdate" command
{ {
bwt_t *bwt; bwt_t *bwt;
if (argc < 2) { if (argc != 2) {
fprintf(stderr, "Usage: bwa bwtupdate <the.bwt>\n"); fprintf(stderr, "Usage: bwa bwtupdate <the.bwt>\n");
return 1; return 1;
} }

2
fastmap.c
View File

@ -258,7 +258,7 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [%d,%d]\n", opt->e_del, opt->e_ins); fprintf(stderr, " -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [%d,%d]\n", opt->e_del, opt->e_ins);
fprintf(stderr, " -L INT[,INT] penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3); fprintf(stderr, " -L INT[,INT] penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3);
fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n\n", opt->pen_unpaired); fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n\n", opt->pen_unpaired);
fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n"); fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overridden [null]\n");
fprintf(stderr, " pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref)\n"); fprintf(stderr, " pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref)\n");
fprintf(stderr, " ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref)\n"); fprintf(stderr, " ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref)\n");
fprintf(stderr, " intractg: -B9 -O16 -L5 (intra-species contigs to ref)\n"); fprintf(stderr, " intractg: -B9 -O16 -L5 (intra-species contigs to ref)\n");

8
malloc_wrap.c
View File

@ -13,7 +13,7 @@ void *wrap_calloc(size_t nmemb, size_t size,
void *p = calloc(nmemb, size); void *p = calloc(nmemb, size);
if (NULL == p) { if (NULL == p) {
fprintf(stderr, fprintf(stderr,
"[%s] Failed to allocate %zd bytes at %s line %u: %s\n", "[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
func, nmemb * size, file, line, strerror(errno)); func, nmemb * size, file, line, strerror(errno));
exit(EXIT_FAILURE); exit(EXIT_FAILURE);
} }
@ -25,7 +25,7 @@ void *wrap_malloc(size_t size,
void *p = malloc(size); void *p = malloc(size);
if (NULL == p) { if (NULL == p) {
fprintf(stderr, fprintf(stderr,
"[%s] Failed to allocate %zd bytes at %s line %u: %s\n", "[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
func, size, file, line, strerror(errno)); func, size, file, line, strerror(errno));
exit(EXIT_FAILURE); exit(EXIT_FAILURE);
} }
@ -37,7 +37,7 @@ void *wrap_realloc(void *ptr, size_t size,
void *p = realloc(ptr, size); void *p = realloc(ptr, size);
if (NULL == p) { if (NULL == p) {
fprintf(stderr, fprintf(stderr,
"[%s] Failed to allocate %zd bytes at %s line %u: %s\n", "[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
func, size, file, line, strerror(errno)); func, size, file, line, strerror(errno));
exit(EXIT_FAILURE); exit(EXIT_FAILURE);
} }
@ -49,7 +49,7 @@ char *wrap_strdup(const char *s,
char *p = strdup(s); char *p = strdup(s);
if (NULL == p) { if (NULL == p) {
fprintf(stderr, fprintf(stderr,
"[%s] Failed to allocate %zd bytes at %s line %u: %s\n", "[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
func, strlen(s), file, line, strerror(errno)); func, strlen(s), file, line, strerror(errno));
exit(EXIT_FAILURE); exit(EXIT_FAILURE);
} }