X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=b562b94c7a2f150bd26b3b19b6343c1d8b09dbbc;hb=1bb8e1e608757f82c4c5e89fbe0912a7883e9890;hp=e3f73aaddd03a14343a82084ee060d9c41ba42d4;hpb=30004e9139b96449fa34831af2fd8e860567a29d;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index e3f73aa..b562b94 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -563,9 +563,10 @@ static int mplp_func(void *data, bam1_t *b)
 	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_core(b, ma->ref, 1);
 		if (has_ref && ma->capQ_thres > 10) {
@@ -849,7 +850,7 @@ 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;
@@ -858,7 +859,7 @@ int bam_mpileup(int argc, char *argv[])
 	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:o:e:h:I")) >= 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);
@@ -872,7 +873,6 @@ 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;
@@ -885,8 +885,10 @@ int bam_mpileup(int argc, char *argv[])
 		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");
@@ -902,6 +904,7 @@ int bam_mpileup(int argc, char *argv[])
 		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");