Merge remote branch 'remotes/master/master' into fb-annots

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index eb584987d4c4a23b1c8fcab33332e701536dd149..18805a03e7b76ab8db3040cc6e9d87a5e16dadaa 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -328,6 +328,9 @@ int bcfview(int argc, char *argv[])
        extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
        extern int bcf_pair_call(const bcf1_t *b);
        extern int bcf_min_diff(const bcf1_t *b);
+       extern int bcf_p1_get_M(bcf_p1aux_t *b);
+
+       extern gzFile bcf_p1_fp_lk;
 
        bcf_t *bp, *bout = 0;
        bcf1_t *b, *blast;
@@ -343,10 +346,10 @@ int bcfview(int argc, char *argv[])
        memset(&vc, 0, sizeof(viewconf_t));
        vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1; vc.min_ma_lrt = -1;
        memset(qcnt, 0, 8 * 256);
-       while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:")) >= 0) {
+       while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
                switch (c) {
                case '1': vc.n1 = atoi(optarg); break;
-               case 'l': vc.bed = bed_read(optarg); break;
+               case 'l': vc.bed = bed_read(optarg); if (!vc.bed) fprintf(stderr,"Could not read \"%s\"\n", optarg); return 1; break;
                case 'D': vc.fn_dict = strdup(optarg); break;
                case 'F': vc.flag |= VC_FIX_PL; break;
                case 'N': vc.flag |= VC_ACGT_ONLY; break;
@@ -373,6 +376,7 @@ int bcfview(int argc, char *argv[])
                case 'C': vc.min_lrt = atof(optarg); break;
                case 'X': vc.min_perm_p = atof(optarg); break;
                case 'd': vc.min_smpl_frac = atof(optarg); break;
+               case 'K': bcf_p1_fp_lk = gzopen(optarg, "w"); break;
                case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
                        vc.ploidy = calloc(vc.n_sub + 1, 1);
                        for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
@@ -462,7 +466,7 @@ int bcfview(int argc, char *argv[])
                        vc.sublist = calloc(vc.n_sub, sizeof(int));
                        hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
                }
-               if (vc.flag & VC_CALL) write_header(hout);
+               write_header(hout); // always print the header
                vcf_hdr_write(bout, hout);
        }
        if (vc.flag & VC_CALL) {
@@ -496,6 +500,10 @@ int bcfview(int argc, char *argv[])
                        }
                }
        }
+       if (bcf_p1_fp_lk && p1) {
+               int32_t M = bcf_p1_get_M(p1);
+               gzwrite(bcf_p1_fp_lk, &M, 4);
+       }
        while (vcf_read(bp, hin, b) > 0) {
                int is_indel, cons_llr = -1;
                int64_t cons_gt = -1;
@@ -544,7 +552,7 @@ int bcfview(int argc, char *argv[])
                        int i;
                        for (i = 0; i < 9; ++i) em[i] = -1.;
                }
-        if ( !(vc.flag&VC_KEEPALT) && vc.flag&VC_CALL && vc.min_ma_lrt>=0 )
+        if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 )
         {
             bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
             int gts = call_multiallelic_gt(b, p1, vc.min_ma_lrt, vc.flag&VC_VARONLY);
@@ -552,7 +560,11 @@ int bcfview(int argc, char *argv[])
         }
                else if (vc.flag & VC_CALL) { // call variants
                        bcf_p1rst_t pr;
-                       int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
+                       int calret;
+                       gzwrite(bcf_p1_fp_lk, &b->tid, 4);
+                       gzwrite(bcf_p1_fp_lk, &b->pos, 4);
+                       gzwrite(bcf_p1_fp_lk, &em[0], sizeof(double));
+                       calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
                        if (n_processed % 100000 == 0) {
                                fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
                                bcf_p1_dump_afs(p1);
@@ -597,6 +609,8 @@ int bcfview(int argc, char *argv[])
                } else bcf_fix_gt(b);
                vcf_write(bout, hout, b);
        }
+
+       if (bcf_p1_fp_lk) gzclose(bcf_p1_fp_lk);
        if (vc.prior_file) free(vc.prior_file);
        if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
        if (hin != hout) bcf_hdr_destroy(hout);