X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=b562b94c7a2f150bd26b3b19b6343c1d8b09dbbc;hb=1bb8e1e608757f82c4c5e89fbe0912a7883e9890;hp=1dc819a6d8870782dd94eb5d446821c4622d4b94;hpb=1a1147a5aef19776be078f3be4bd4cc7b9aa8ceb;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 1dc819a..b562b94 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -532,9 +532,11 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_REALN   0x80
 #define MPLP_FMT_DP 0x100
 #define MPLP_FMT_SP 0x200
+#define MPLP_NO_INDEL 0x400
 
 typedef struct {
 	int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
+	int openQ, extQ, tandemQ;
 	char *reg, *fn_pos, *pl_list;
 	faidx_t *fai;
 	kh_64_t *hash;
@@ -556,16 +558,17 @@ typedef struct {
 static int mplp_func(void *data, bam1_t *b)
 {
 	extern int bam_realn(bam1_t *b, const char *ref);
-	extern int bam_prob_realn(bam1_t *b, const char *ref);
+	extern int bam_prob_realn_core(bam1_t *b, const char *ref, int);
 	extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
 	mplp_aux_t *ma = (mplp_aux_t*)data;
 	int ret, skip = 0;
 	do {
-		int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
+		int has_ref;
 		ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
 		if (ret < 0) break;
+		has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
 		skip = 0;
-		if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn(b, ma->ref);
+		if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
 		if (has_ref && ma->capQ_thres > 10) {
 			int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
 			if (q < 0) skip = 1;
@@ -698,6 +701,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 		bca = bcf_call_init(-1., conf->min_baseQ);
 		bcr = calloc(sm->n, sizeof(bcf_callret1_t));
 		bca->rghash = rghash;
+		bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
 	}
 	ref_tid = -1; ref = 0;
 	iter = bam_mplp_init(n, mplp_func, (void**)data);
@@ -736,7 +740,7 @@ 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, rghash) >= 0) {
+			if (!(conf->flag&MPLP_NO_INDEL) && 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) {
@@ -846,15 +850,16 @@ int bam_mpileup(int argc, char *argv[])
 	int c;
     const char *file_list = NULL;
     char **fn = NULL;
-    int nfiles = 0;
+    int nfiles = 0, use_orphan = 0;
 	mplp_conf_t mplp;
 	memset(&mplp, 0, sizeof(mplp_conf_t));
 	mplp.max_mq = 60;
 	mplp.min_baseQ = 13;
 	mplp.capQ_thres = 0;
 	mplp.max_depth = 250;
+	mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
 	mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
-	while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:P:")) >= 0) {
+	while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:b:P:o:e:h:I")) >= 0) {
 		switch (c) {
 		case 'f':
 			mplp.fai = fai_load(optarg);
@@ -868,17 +873,22 @@ int bam_mpileup(int argc, char *argv[])
 		case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
 		case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
 		case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
-		case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
 		case 'R': mplp.flag |= MPLP_REALN; break;
 		case 'D': mplp.flag |= MPLP_FMT_DP; break;
 		case 'S': mplp.flag |= MPLP_FMT_SP; break;
+		case 'I': mplp.flag |= MPLP_NO_INDEL; break;
 		case 'C': mplp.capQ_thres = atoi(optarg); break;
 		case 'M': mplp.max_mq = atoi(optarg); break;
 		case 'q': mplp.min_mq = atoi(optarg); break;
 		case 'Q': mplp.min_baseQ = atoi(optarg); break;
         case 'b': file_list = optarg; break;
+		case 'o': mplp.openQ = atoi(optarg); break;
+		case 'e': mplp.extQ = atoi(optarg); break;
+		case 'h': mplp.tandemQ = atoi(optarg); break;
+		case 'A': use_orphan = 1; break;
 		}
 	}
+	if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
 	if (argc == 1) {
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Usage:   samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
@@ -891,11 +901,16 @@ int bam_mpileup(int argc, char *argv[])
 		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, "         -o INT      Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
+		fprintf(stderr, "         -e INT      Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
+		fprintf(stderr, "         -h INT      coefficient for homopolyer errors [%d]\n", mplp.tandemQ);
+		fprintf(stderr, "         -A          use anomalous read pairs in SNP/INDEL calling\n");
 		fprintf(stderr, "         -g          generate BCF output\n");
 		fprintf(stderr, "         -u          do not compress BCF output\n");
 		fprintf(stderr, "         -B          disable BAQ computation\n");
 		fprintf(stderr, "         -D          output per-sample DP\n");
 		fprintf(stderr, "         -S          output per-sample SP (strand bias P-value, slow)\n");
+		fprintf(stderr, "         -I          do not perform indel calling\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
 		return 1;