Complain when BAM cannot be open. Severe bug fixed in -m haploid calling.

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index be2c87d0e5d8f52f7913bf720c54ce9e3ab9ea24..f77be0467e6442c12145a35ebb97259e237d5625 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -67,11 +67,12 @@ static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, cons
 #define MPLP_NO_ORPHAN 0x40
 #define MPLP_REALN   0x80
 #define MPLP_NO_INDEL 0x400
-#define MPLP_EXT_BAQ 0x800
+#define MPLP_REDO_BAQ 0x800
 #define MPLP_ILLUMINA13 0x1000
 #define MPLP_IGNORE_RG 0x2000
 #define MPLP_PRINT_POS 0x4000
 #define MPLP_PRINT_MAPQ 0x8000
+#define MPLP_PER_SAMPLE 0x10000
 
 void *bed_read(const char *fn);
 void bed_destroy(void *_h);
@@ -133,7 +134,7 @@ static int mplp_func(void *data, bam1_t *b)
                }
                has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
                skip = 0;
-               if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
+               if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
                if (has_ref && ma->conf->capQ_thres > 10) {
                        int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres);
                        if (q < 0) skip = 1;
@@ -207,6 +208,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                bam_header_t *h_tmp;
                data[i] = calloc(1, sizeof(mplp_aux_t));
                data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
+        if ( !data[i]->fp )
+        {
+            fprintf(stderr, "[%s] failed to open %d-th input.\n", __func__, i+1);
+            exit(1);
+        }
                data[i]->conf = conf;
                h_tmp = bam_header_read(data[i]->fp);
                data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
@@ -271,6 +277,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
                bca->min_frac = conf->min_frac;
                bca->min_support = conf->min_support;
+        bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
        }
        if (tid0 >= 0 && conf->fai) { // region is set
                ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
@@ -448,8 +455,8 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_depth = 250; mplp.max_indel_depth = 250;
        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 | MPLP_EXT_BAQ;
-       while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6OsV")) >= 0) {
+       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) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -459,6 +466,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'r': mplp.reg = strdup(optarg); break;
                case 'l': mplp.bed = bed_read(optarg); break;
                case 'P': mplp.pl_list = strdup(optarg); break;
+               case 'p': mplp.flag |= MPLP_PER_SAMPLE; 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;
@@ -467,7 +475,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'S': mplp.fmt_flag |= B2B_FMT_SP; break;
                case 'V': mplp.fmt_flag |= B2B_FMT_DV; break;
                case 'I': mplp.flag |= MPLP_NO_INDEL; break;
-               case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
+               case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
                case '6': mplp.flag |= MPLP_ILLUMINA13; break;
                case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
                case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
@@ -508,7 +516,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "       -b FILE      list of input BAM files [null]\n");
                fprintf(stderr, "       -C INT       parameter for adjusting mapQ; 0 to disable [0]\n");
                fprintf(stderr, "       -d INT       max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
-//             fprintf(stderr, "       -E           extended BAQ for higher sensitivity but lower specificity\n");
+               fprintf(stderr, "       -E           recalculate extended BAQ on the fly thus ignoring existing BQs\n");
                fprintf(stderr, "       -f FILE      faidx indexed reference sequence file [null]\n");
                fprintf(stderr, "       -G FILE      exclude read groups listed in FILE [null]\n");
                fprintf(stderr, "       -l FILE      list of positions (chr pos) or regions (BED) [null]\n");
@@ -532,6 +540,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "       -L INT       max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
                fprintf(stderr, "       -m INT       minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
                fprintf(stderr, "       -o INT       Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
+               fprintf(stderr, "       -p           apply -m and -F per-sample to increase sensitivity\n");
                fprintf(stderr, "       -P STR       comma separated list of platforms for indels [all]\n");
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");