X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=c23726ec51272658f1c7b876d0822085a57ea2b7;hb=896d270d34b71e0422ddca4a0d62136cb2e537be;hp=75f5691c7815184b43d29e9c9072df5856ddff5e;hpb=f221655a2515b417a545caece40b6985e927fb83;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 75f5691..c23726e 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -528,7 +528,8 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_NO_COMP 0x20
 #define MPLP_NO_ORPHAN 0x40
 #define MPLP_REALN   0x80
-#define MPLP_SAMINFO 0x100
+#define MPLP_FMT_DP 0x100
+#define MPLP_FMT_SP 0x200
 
 typedef struct {
 	int max_mq, min_mq, flag, min_baseQ, capQ_thres;
@@ -715,7 +716,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			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_call2bcf(tid, pos, &bc, b, (conf->flag&MPLP_SAMINFO)? bcr : 0);
+			bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP));
 			bcf_write(bp, bh, b);
 			bcf_destroy(b);
 		} else {
@@ -771,7 +772,7 @@ int bam_mpileup(int argc, char *argv[])
 	mplp.min_baseQ = 13;
 	mplp.capQ_thres = 0;
 	mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
-	while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BI")) >= 0) {
+	while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDS")) >= 0) {
 		switch (c) {
 		case 'f':
 			mplp.fai = fai_load(optarg);
@@ -785,7 +786,8 @@ int bam_mpileup(int argc, char *argv[])
 		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 'I': mplp.flag |= MPLP_SAMINFO; break;
+		case 'D': mplp.flag |= MPLP_FMT_DP; break;
+		case 'S': mplp.flag |= MPLP_FMT_SP; 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;
@@ -804,7 +806,8 @@ int bam_mpileup(int argc, char *argv[])
 		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, "         -I          additional individual information (DP and ST)\n");
+		fprintf(stderr, "         -D          output per-sample DP\n");
+		fprintf(stderr, "         -S          output per-sample SP (strand bias P-value, slow)\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
 		return 1;