New -p switch for increased sensititivy of indel-calling. Here -m and -F are used...

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 07f0a4fe3afb9bc13da71aabced9881ba49085ce..ed00d2e80202fde96d5c5aecfc28aa8ff39e5bd6 100644 (file)
--- 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);
@@ -271,6 +272,7 @@ 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);
@@ -449,7 +451,7 @@ 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 +461,7 @@ 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 +535,7 @@ 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");