* samtools-0.1.4-12 (r347)

 * added `-S' to pileup, similar to `view -S'

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 46f078a99e715a89ccc4f73119192fe8d1ef280c..43e6cf572c19e5c05c93fe99bd29e10f7825cf30 100644 (file)
--- 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] <in.bam>|<in.sam>\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 27dde036773d9febec2ceacf95d9c97b1ac87582..79685ff0c94cf33ba356419057e571c4fe227767 100644 (file)
--- 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 e96afeefcdd4bc957f2879ad3ba3001a55ad57a8..02aee3c034cbc668b51295039d92a6adb1e74d51 100644 (file)
--- 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;
 }