From d5f9862ca91b1b3915c6ecc5142e7c10668593a6 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 13 Jun 2009 20:20:49 +0000 Subject: [PATCH] * samtools-0.1.4-12 (r347) * added `-S' to pileup, similar to `view -S' --- bam_plcmd.c | 9 ++++++--- bamtk.c | 2 +- sam_view.c | 3 +++ 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/bam_plcmd.c b/bam_plcmd.c index 46f078a..43e6cf5 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -274,13 +274,13 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p int bam_pileup(int argc, char *argv[]) { - int c; + int c, is_SAM = 0; char *fn_list = 0, *fn_fa = 0, *fn_pos = 0; pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t)); d->tid = -1; d->mask = BAM_DEF_MASK; d->c = bam_maqcns_init(); d->ido = bam_maqindel_opt_init(); - while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:")) >= 0) { + while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S")) >= 0) { switch (c) { case 's': d->format |= BAM_PLF_SIMPLE; break; case 't': fn_list = strdup(optarg); break; @@ -297,13 +297,16 @@ int bam_pileup(int argc, char *argv[]) case 'g': d->format |= BAM_PLF_GLF; break; case 'I': d->ido->q_indel = atoi(optarg); break; case 'G': d->ido->r_indel = atof(optarg); break; + case 'S': is_SAM = 1; break; default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1; } } + if (fn_list) is_SAM = 1; if (optind == argc) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools pileup [options] |\n\n"); fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n"); + fprintf(stderr, " -S the input is in SAM\n"); fprintf(stderr, " -i only show lines/consensus with indels\n"); fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask); fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ); @@ -335,7 +338,7 @@ int bam_pileup(int argc, char *argv[]) fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n"); { samfile_t *fp; - fp = fn_list? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0); + fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0); if (fp == 0 || fp->header == 0) { fprintf(stderr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n"); return 1; diff --git a/bamtk.c b/bamtk.c index 27dde03..79685ff 100644 --- a/bamtk.c +++ b/bamtk.c @@ -3,7 +3,7 @@ #include "bam.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.4-11 (r346)" +#define PACKAGE_VERSION "0.1.4-12 (r347)" #endif int bam_taf2baf(int argc, char *argv[]); diff --git a/sam_view.c b/sam_view.c index e96afee..02aee3c 100644 --- a/sam_view.c +++ b/sam_view.c @@ -148,6 +148,9 @@ Notes:\n\ 4. A region should be presented in one of the following formats:\n\ `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\ specified, the input alignment file must be an indexed BAM file.\n\ +\n\ + 5. Option `-u' is preferred over `-b' when the output is piped to\n\ + another samtools command.\n\ \n"); return 1; } -- 2.39.5