Generate binary VCF

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index bea91692de426eb0daf5150b5d7b190fa74155ff..8affabfd078f0a18452e65c29d60a39b0071e0ba 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -6,6 +6,7 @@
 #include "faidx.h"
 #include "bam_maqcns.h"
 #include "bam_mcns.h"
+#include "bam2bcf.h"
 #include "khash.h"
 #include "glf.h"
 #include "kstring.h"
@@ -452,6 +453,7 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_VCF   0x1
 #define MPLP_VAR   0x2
 #define MPLP_AFALL 0x8
+#define MPLP_GLF   0x10
 
 #define MPLP_AFS_BLOCK 0x10000
 
@@ -482,7 +484,6 @@ static int mplp_func(void *data, bam1_t *b)
 static int mpileup(mplp_conf_t *conf, int n, char **fn)
 {
        mplp_aux_t **data;
-       mc_aux_t *ma = 0;
        int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid;
        const bam_pileup1_t **plp;
        bam_mplp_t iter;
@@ -490,10 +491,19 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        uint64_t N = 0;
        char *ref;
        khash_t(64) *hash = 0;
-       // allocate
+
+       mc_aux_t *ma = 0;
+
+       bcf_callaux_t *bca = 0;
+       bcf_callret1_t *bcr = 0;
+       bcf_call_t bc;
+       bcf_t *bp = 0;
+
+       memset(&bc, 0, sizeof(bcf_call_t));
        data = calloc(n, sizeof(void*));
        plp = calloc(n, sizeof(void*));
        n_plp = calloc(n, sizeof(int*));
+
        // read the header and initialize data
        for (i = 0; i < n; ++i) {
                bam_header_t *h_tmp;
@@ -525,7 +535,33 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        }
        if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
        // write the VCF header
-       if (conf->flag & MPLP_VCF) {
+       if (conf->flag & MPLP_GLF) {
+               kstring_t s;
+               s.l = s.m = 0; s.s = 0;
+               bp = bcf_open("-", "w");
+               for (i = 0; i < h->n_targets; ++i) {
+                       kputs(h->target_name[i], &s);
+                       kputc('\0', &s);
+               }
+               bp->h.l_nm = s.l;
+               bp->h.name = malloc(s.l);
+               memcpy(bp->h.name, s.s, s.l);
+               s.l = 0;
+               for (i = 0; i < n; ++i) {
+                       const char *p;
+                       if ((p = strstr(fn[i], ".bam")) != 0)
+                               kputsn(fn[i], p - fn[i], &s);
+                       else kputs(fn[i], &s);
+                       kputc('\0', &s);
+               }
+               bp->h.l_smpl = s.l;
+               bp->h.sname = malloc(s.l);
+               memcpy(bp->h.sname, s.s, s.l);
+               bp->h.l_txt = 0;
+               free(s.s);
+               bcf_hdr_sync(&bp->h);
+               bcf_hdr_write(bp);
+       } else if (conf->flag & MPLP_VCF) {
                kstring_t s;
                s.l = s.m = 0; s.s = 0;
                puts("##fileformat=VCFv4.0");
@@ -546,7 +582,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                free(s.s);
        }
        // mpileup
-       if (conf->flag & MPLP_VCF) {
+       if (conf->flag & MPLP_GLF) {
+               bca = bcf_call_init(-1.);
+               bcr = calloc(n, sizeof(bcf_callret1_t));
+       } else if (conf->flag & MPLP_VCF) {
                ma = mc_init(n);
                mc_init_prior(ma, conf->prior_type, conf->theta);
        }
@@ -564,7 +603,19 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
                        ref_tid = tid;
                }
-               if (conf->flag & MPLP_VCF) {
+               if (conf->flag & MPLP_GLF) {
+                       int _ref0, ref16;
+                       bcf1_t *b = calloc(1, sizeof(bcf1_t));
+                       _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+                       ref16 = bam_nt16_table[_ref0];
+                       for (i = 0; i < n; ++i)
+                               bcf_call_glfgen(n_plp[i], plp[i], ref16, bca, bcr + i);
+                       bcf_call_combine(n, bcr, ref16, &bc);
+                       bcf_call2bcf(tid, pos, &bc, b);
+                       bcf_write(bp, b);
+                       //fprintf(stderr, "%d,%d,%d\n", b->tid, b->pos, b->l_str);
+                       bcf_destroy(b);
+               } else if (conf->flag & MPLP_VCF) {
                        mc_rst_t r;
                        int j, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0, level = 2, tot;
                        uint64_t sqr_sum;
@@ -636,6 +687,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        putchar('\n');
                }
        }
+       bcf_close(bp);
        if (conf->flag&MPLP_VCF) mc_dump_afs(ma);
        if (hash) { // free the hash table
                khint_t k;
@@ -643,6 +695,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        if (kh_exist(hash, k)) free(kh_val(hash, k));
                kh_destroy(64, hash);
        }
+       bcf_call_destroy(bca); free(bc.PL); free(bcr);
        mc_destroy(ma);
        bam_mplp_destroy(iter);
        bam_header_destroy(h);
@@ -663,7 +716,7 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.prior_type = MC_PTYPE_FULL;
        mplp.theta = 1e-3;
-       while ((c = getopt(argc, argv, "vVcFSP:f:r:l:VM:q:t:")) >= 0) {
+       while ((c = getopt(argc, argv, "gvVcFSP:f:r:l:VM:q:t:")) >= 0) {
                switch (c) {
                case 't': mplp.theta = atof(optarg); break;
                case 'P':
@@ -681,6 +734,7 @@ int bam_mpileup(int argc, char *argv[])
                        break;
                case 'r': mplp.reg = strdup(optarg); break;
                case 'l': mplp.fn_pos = strdup(optarg); break;
+               case 'g': mplp.flag |= MPLP_GLF; break;
                case 'V':
                case 'c': mplp.flag |= MPLP_VCF; break;
                case 'F': mplp.flag |= MPLP_AFALL; break;
@@ -689,6 +743,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'q': mplp.min_mq = atoi(optarg); break;
                }
        }
+       if (mplp.flag&MPLP_GLF) mplp.flag &= ~MPLP_VCF;
        if (argc == 1) {
                fprintf(stderr, "\n");
                fprintf(stderr, "Usage:   samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
@@ -700,6 +755,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -t FLOAT    scaled mutation rate [%lg]\n", mplp.theta);
                fprintf(stderr, "         -P STR      prior: full, flat, cond2 [full]\n");
                fprintf(stderr, "         -c          generate VCF output (consensus calling)\n");
+               fprintf(stderr, "         -g          generate GLF output\n");
                fprintf(stderr, "         -v          show variant sites only\n");
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");