X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=e45c8c8c81649630449f78d653cbd037e2046408;hb=6842e4470dcbd381d0893690b7d07344fd08e831;hp=07f0a4fe3afb9bc13da71aabced9881ba49085ce;hpb=183e4cb41c6136b9bff3dc83fcfa9f023e1d7629;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 07f0a4f..e45c8c8 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -72,6 +72,7 @@ static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, cons
 #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);
@@ -207,8 +208,17 @@ 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 %s: %s\n", __func__, fn[i], strerror(errno));
+            exit(1);
+        }
 		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);
@@ -217,11 +227,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			bam_index_t *idx;
 			idx = bam_index_load(fn[i]);
 			if (idx == 0) {
-				fprintf(stderr, "[%s] fail to load index for %d-th input.\n", __func__, i+1);
+				fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
 				exit(1);
 			}
 			if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
-				fprintf(stderr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
+				fprintf(stderr, "[%s] malformatted region or wrong seqname for %s\n", __func__, fn[i]);
 				exit(1);
 			}
 			if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
@@ -271,6 +281,7 @@ 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);
@@ -305,7 +316,7 @@ 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);
@@ -313,7 +324,7 @@ 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);
@@ -449,7 +460,7 @@ 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:o:e:h:Im:F:EG:6OsV")) >= 0) {
+	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 +470,7 @@ 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;
@@ -532,6 +544,7 @@ 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");