Optionally output "DP", the individual read depth

diff --git a/bam2bcf.c b/bam2bcf.c
index e55212ca98cbb28041fb6a6dfc46619ff595ee09..88222e76954634e1e7b7e6a5b41941b9107b1723 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -154,8 +154,9 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
        return 0;
 }
 
-int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
+int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr)
 {
+       extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
        kstring_t s;
        int i;
        b->n_smpl = bc->n;
@@ -178,9 +179,19 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
        }
        kputc('\0', &s);
        // FMT
-       kputs("PL", &s); kputc('\0', &s);
+       kputs("PL", &s);
+       if (bcr) {
+               kputs(":DP", &s);
+       }
+       kputc('\0', &s);
        b->m_str = s.m; b->str = s.s; b->l_str = s.l;
        bcf_sync(b);
        memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
+       if (bcr) {
+               uint16_t *dp = (uint16_t*)b->gi[1].data;
+               for (i = 0; i < bc->n; ++i) {
+                       dp[i] = bcr[i].depth < 0xffff? bcr[i].depth : 0xffff;
+               }
+       }
        return 0;
 }

diff --git a/bam2bcf.h b/bam2bcf.h
index 0dddb924dcf62fee4f1352a9a20eecb7001da450..f96a7e33719b08d003513d03e857df38ddb4dbf5 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -28,7 +28,7 @@ extern "C" {
        void bcf_call_destroy(bcf_callaux_t *bca);
        int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r);
        int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
-       int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b);
+       int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr);
 
 #ifdef __cplusplus
 }

diff --git a/bam_plcmd.c b/bam_plcmd.c
index dca85181f99bf1c7343650846039153a019e7ea9..75f5691c7815184b43d29e9c9072df5856ddff5e 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -528,6 +528,7 @@ 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
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ, capQ_thres;
@@ -714,7 +715,7 @@ 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);
+                       bcf_call2bcf(tid, pos, &bc, b, (conf->flag&MPLP_SAMINFO)? bcr : 0);
                        bcf_write(bp, bh, b);
                        bcf_destroy(b);
                } else {
@@ -770,7 +771,7 @@ 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:B")) >= 0) {
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BI")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -784,6 +785,7 @@ 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 'C': mplp.capQ_thres = atoi(optarg); break;
                case 'M': mplp.max_mq = atoi(optarg); break;
                case 'q': mplp.min_mq = atoi(optarg); break;
@@ -802,6 +804,7 @@ 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, "\n");
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
                return 1;

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 9044b93b0b514fd9566f037a705f8769f60ecc54..035eddc70386bd011f710970026e50358a502be4 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -134,7 +134,9 @@ int bcf_sync(bcf1_t *b)
                        b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
                } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
                        b->gi[i].len = 2;
-               } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
+               } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
+                                  || b->gi[i].fmt == bcf_str2int("ST", 2))
+               {
                        b->gi[i].len = 1;
                } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
                        b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
@@ -236,7 +238,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
                                }
                        } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
                                kputw(((uint16_t*)b->gi[i].data)[j], s);
-                       } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
+                       } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("ST", 2)) {
                                kputw(((uint8_t*)b->gi[i].data)[j], s);
                        } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
                                int y = ((uint8_t*)b->gi[i].data)[j];