mpileup: New HWE, QBD, RPS annotations. Modified VDB (beware: this version of VDB...

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 9c4f273dcbfe2c3576e9c6ea0e2d7661839bbb85..54a4597a702d441dc15bfa4070fae16d3905a990 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -9,6 +9,7 @@
 #include "sam.h"
 #include "faidx.h"
 #include "kstring.h"
+#include "sam_header.h"
 
 static inline int printw(int c, FILE *fp)
 {
@@ -85,7 +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;
+       char *reg, *pl_list, *fai_fname;
        faidx_t *fai;
        void *bed, *rghash;
 } mplp_conf_t;
@@ -275,9 +276,24 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                bh->l_smpl = s.l;
                bh->sname = malloc(s.l);
                memcpy(bh->sname, s.s, s.l);
-               bh->txt = malloc(strlen(BAM_VERSION) + 64);
-               bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
-               free(s.s);
+        s.l = 0;
+        ksprintf(&s, "##samtoolsVersion=%s\n", BAM_VERSION);
+        if (conf->fai_fname) ksprintf(&s, "##reference=file://%s\n", conf->fai_fname);
+        h->dict = sam_header_parse2(h->text);
+        int nseq;
+        const char *tags[] = {"SN","LN","UR","M5",NULL};
+        char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &nseq);
+        for (i=0; i<nseq; i++)
+        {
+            ksprintf(&s, "##contig=<ID=%s", tbl[4*i]);
+            if ( tbl[4*i+1] ) ksprintf(&s, ",length=%s", tbl[4*i+1]);
+            if ( tbl[4*i+2] ) ksprintf(&s, ",URL=%s", tbl[4*i+2]);
+            if ( tbl[4*i+3] ) ksprintf(&s, ",md5=%s", tbl[4*i+3]);
+            kputs(">\n", &s);
+        }
+        if (tbl) free(tbl);
+               bh->txt = s.s;
+               bh->l_txt = 1 + s.l;
                bcf_hdr_sync(bh);
                bcf_hdr_write(bp, bh);
                bca = bcf_call_init(-1., conf->min_baseQ);
@@ -487,6 +503,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'f':
                        mplp.fai = fai_load(optarg);
                        if (mplp.fai == 0) return 1;
+            mplp.fai_fname = optarg;
                        break;
                case 'd': mplp.max_depth = atoi(optarg); break;
                case 'r': mplp.reg = strdup(optarg); break;