add --output,-c option to mpileup

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 31e3017dcca25be269bd7cb393ae9da83f93c279..15b65d2a1d31ea66dc36daee4c0a322253e60242 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -86,7 +86,7 @@ typedef struct {
     int rflag_require, rflag_filter;
        int openQ, extQ, tandemQ, min_support; // for indels
        double min_frac; // for indels
-       char *reg, *pl_list, *fai_fname;
+       char *reg, *pl_list, *fai_fname, *bcf_fname;
        faidx_t *fai;
        void *bed, *rghash;
 } mplp_conf_t;
@@ -266,7 +266,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                kstring_t s;
                bh = calloc(1, sizeof(bcf_hdr_t));
                s.l = s.m = 0; s.s = 0;
-               bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
+               bp = bcf_open(conf->bcf_fname, (conf->flag&MPLP_NO_COMP)? "wu" : "w");
                for (i = 0; i < h->n_targets; ++i) {
                        kputs(h->target_name[i], &s);
                        kputc('\0', &s);
@@ -495,13 +495,15 @@ int bam_mpileup(int argc, char *argv[])
        mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
        mplp.min_frac = 0.002; mplp.min_support = 1;
        mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
+    mplp.bcf_fname="-";
     static struct option lopts[] = 
     {
         {"rf",1,0,1},   // require flag
         {"ff",1,0,2},   // filter flag
+        {"output",1,0,(int)'c'}, // output flag
         {0,0,0,0}
     };
-       while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:",lopts,NULL)) >= 0) {
+       while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:c:",lopts,NULL)) >= 0) {
                switch (c) {
         case  1 : mplp.rflag_require = strtol(optarg,0,0); break;
         case  2 : mplp.rflag_filter  = strtol(optarg,0,0); break;
@@ -528,6 +530,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
                case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
                case 'O': mplp.flag |= MPLP_PRINT_POS; break;
+               case 'c': mplp.bcf_fname = strdup(optarg); break;
                case 'C': mplp.capQ_thres = atoi(optarg); break;
                case 'M': mplp.max_mq = atoi(optarg); break;
                case 'q': mplp.min_mq = atoi(optarg); break;
@@ -582,6 +585,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "       -s           output mapping quality (disabled by -g/-u)\n");
                fprintf(stderr, "       -S           output per-sample strand bias P-value in BCF (require -g/-u)\n");
                fprintf(stderr, "       -u           generate uncompress BCF output\n");
+               fprintf(stderr, "       -c, --output=FILE output filename [stdout]\n");
                fprintf(stderr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
                fprintf(stderr, "       -e INT       Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
                fprintf(stderr, "       -F FLOAT     minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);

diff --git a/samtools.1 b/samtools.1
index 5923abd52608ee9003cbe17c49e93755f67a647f..2762563646802321108dc811b86934de99412199 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -186,6 +186,8 @@ samtools mpileup
 .IR minBaseQ ]
 .RB [ \-q
 .IR minMapQ ]
+.RB [ \-c
+.IR Output file [stdout] ]
 .I in.bam
 .RI [ in2.bam
 .RI [ ... ]]
@@ -285,6 +287,9 @@ Output per-sample Phred-scaled strand bias P-value
 Similar to
 .B -g
 except that the output is uncompressed BCF, which is preferred for piping.
+.TP
+.BR \-c ", " \-\-output =\fIFILE\fR
+File to output bcf (vcf with \fB\-g\fR) to; default is stdout.
 
 .TP
 .B Options for Genotype Likelihood Computation (for -g or -u):