* samtools-0.1.9-8 (r807)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 54b8f91722b2f16ade955231e075764b3161d2d5..0fbc9303c25744ebde8d1b0e269c539d5c4f5325 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -535,7 +535,7 @@ int bam_pileup(int argc, char *argv[])
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
-       char *reg, *fn_pos;
+       char *reg, *fn_pos, *pl_list;
        faidx_t *fai;
        kh_64_t *hash;
 } mplp_conf_t;
@@ -602,6 +602,8 @@ static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
 
 static int mpileup(mplp_conf_t *conf, int n, char **fn)
 {
+       extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
+       extern void bcf_call_del_rghash(void *rghash);
        mplp_aux_t **data;
        int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth;
        const bam_pileup1_t **plp;
@@ -609,6 +611,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        bam_header_t *h = 0;
        char *ref;
        khash_t(64) *hash = 0;
+       void *rghash = 0;
 
        bcf_callaux_t *bca = 0;
        bcf_callret1_t *bcr = 0;
@@ -638,6 +641,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
                h_tmp = bam_header_read(data[i]->fp);
                bam_smpl_add(sm, fn[i], h_tmp->text);
+               rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
                if (conf->reg) {
                        int beg, end;
                        bam_index_t *idx;
@@ -693,6 +697,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                bcf_hdr_write(bp, bh);
                bca = bcf_call_init(-1., conf->min_baseQ);
                bcr = calloc(sm->n, sizeof(bcf_callret1_t));
+               bca->rghash = rghash;
        }
        ref_tid = -1; ref = 0;
        iter = bam_mplp_init(n, mplp_func, (void**)data);
@@ -731,7 +736,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        bcf_write(bp, bh, b);
                        bcf_destroy(b);
                        // call indels
-                       if (bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref) >= 0) {
+                       if (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);
                                bcf_call_combine(gplp.n, bcr, -1, &bc);
@@ -767,6 +772,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        bam_smpl_destroy(sm); free(buf.s);
        for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
        free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
+       bcf_call_del_rghash(rghash);
        if (hash) { // free the hash table
                khint_t k;
                for (k = kh_begin(hash); k < kh_end(hash); ++k)
@@ -847,7 +853,7 @@ int bam_mpileup(int argc, char *argv[])
        mplp.capQ_thres = 0;
        mplp.max_depth = 250;
        mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
-       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:")) >= 0) {
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:P:")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -856,6 +862,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'd': mplp.max_depth = atoi(optarg); break;
                case 'r': mplp.reg = strdup(optarg); break;
                case 'l': mplp.fn_pos = strdup(optarg); break;
+               case 'P': mplp.pl_list = strdup(optarg); break;
                case 'g': mplp.flag |= MPLP_GLF; break;
                case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
@@ -882,6 +889,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -Q INT      min base quality [%d]\n", mplp.min_baseQ);
                fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "         -d INT      max per-sample depth [%d]\n", mplp.max_depth);
+               fprintf(stderr, "         -P STR      comma separated list of platforms for indels [all]\n");
                fprintf(stderr, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");
                fprintf(stderr, "         -B          disable BAQ computation\n");
@@ -900,7 +908,7 @@ int bam_mpileup(int argc, char *argv[])
     }
     else
            mpileup(&mplp, argc - optind, argv + optind);
-       free(mplp.reg);
+       free(mplp.reg); free(mplp.pl_list);
        if (mplp.fai) fai_destroy(mplp.fai);
        return 0;
 }