The indel stats (IS) annotation splitted into two: IDV and IMF

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 852e9ee4c0203c7febb1a4d498eb96ad7a18bf98..31e3017dcca25be269bd7cb393ae9da83f93c279 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -5,9 +5,11 @@
 #include <string.h>
 #include <errno.h>
 #include <sys/stat.h>
+#include <getopt.h>
 #include "sam.h"
 #include "faidx.h"
 #include "kstring.h"
+#include "sam_header.h"
 
 static inline int printw(int c, FILE *fp)
 {
@@ -81,9 +83,10 @@ int bed_overlap(const void *_h, const char *chr, int beg, int end);
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
+    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;
@@ -118,6 +121,8 @@ static int mplp_func(void *data, bam1_t *b)
                        skip = 1;
                        continue;
                }
+        if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
+        if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
                if (ma->conf->bed) { // test overlap
                        skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
                        if (skip) continue;
@@ -204,6 +209,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        n_plp = calloc(n, sizeof(int*));
        sm = bam_smpl_init();
 
+    if (n == 0) {
+        fprintf(stderr,"[%s] no input file/data given\n", __func__);
+        exit(1);
+    }
+
        // read the header and initialize data
        for (i = 0; i < n; ++i) {
                bam_header_t *h_tmp;
@@ -216,6 +226,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         }
                data[i]->conf = conf;
                h_tmp = bam_header_read(data[i]->fp);
+        if ( !h_tmp ) {
+            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+            exit(1);
+        }
                data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
                bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
                rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
@@ -267,9 +281,24 @@ 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);
@@ -313,7 +342,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        ref16 = bam_nt16_table[_ref0];
                        for (i = 0; i < gplp.n; ++i)
                                bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
-                       bcf_call_combine(gplp.n, bcr, ref16, &bc);
+                       bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
                        bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, 0, 0);
                        bcf_write(bp, bh, b);
                        bcf_destroy(b);
@@ -321,7 +350,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
                                for (i = 0; i < gplp.n; ++i)
                                        bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
-                               if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
+                               if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
                                        b = calloc(1, sizeof(bcf1_t));
                                        bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, bca, ref);
                                        bcf_write(bp, bh, b);
@@ -394,7 +423,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 }
 
 #define MAX_PATH_LEN 1024
-static int read_file_list(const char *file_list,int *n,char **argv[])
+int read_file_list(const char *file_list,int *n,char **argv[])
 {
     char buf[MAX_PATH_LEN];
     int len, nfiles = 0;
@@ -466,11 +495,20 @@ 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;
-       while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV")) >= 0) {
+    static struct option lopts[] = 
+    {
+        {"rf",1,0,1},   // require flag
+        {"ff",1,0,2},   // filter 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) {
                switch (c) {
+        case  1 : mplp.rflag_require = strtol(optarg,0,0); break;
+        case  2 : mplp.rflag_filter  = strtol(optarg,0,0); break;
                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;
@@ -535,6 +573,8 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "       -R           ignore RG tags\n");
                fprintf(stderr, "       -q INT       skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "       -Q INT       skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
+               fprintf(stderr, "       --rf INT     required flags: skip reads with mask bits unset []\n");
+               fprintf(stderr, "       --ff INT     filter flags: skip reads with mask bits set []\n");
                fprintf(stderr, "\nOutput options:\n\n");
                fprintf(stderr, "       -D           output per-sample DP in BCF (require -g/-u)\n");
                fprintf(stderr, "       -g           generate BCF output (genotype likelihoods)\n");