* samtools-0.1.12-6 (r887)

 * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.

diff --git a/bam_md.c b/bam_md.c
index 44d46a492438beecae74fc648c9564a566565be7..1fa903e8a401ea960d8ea48f6d7289b157e2eea5 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -162,14 +162,14 @@ int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
        return (int)(t + .499);
 }
 
-int bam_prob_realn_core(bam1_t *b, const char *ref, int apply_baq)
+int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
 {
-       int k, i, bw, x, y, yb, ye, xb, xe;
+       int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1;
        uint32_t *cigar = bam1_cigar(b);
        bam1_core_t *c = &b->core;
        kpa_par_t conf = kpa_par_def;
        uint8_t *bq = 0, *zq = 0, *qual = bam1_qual(b);
-       if (c->flag & BAM_FUNMAP) return -1; // do nothing
+       if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0) return -1; // do nothing
        // test if BQ or ZQ is present
        if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
        if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
@@ -226,18 +226,40 @@ int bam_prob_realn_core(bam1_t *b, const char *ref, int apply_baq)
                state = calloc(c->l_qseq, sizeof(int));
                q = calloc(c->l_qseq, 1);
                kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
-               for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
-                       int op = cigar[k]&0xf, l = cigar[k]>>4;
-                       if (op == BAM_CMATCH) {
-                               for (i = y; i < y + l; ++i) {
-                                       if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
-                                       else bq[i] = bq[i] < q[i]? bq[i] : q[i];
-                               }
-                               x += l; y += l;
-                       } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
-                       else if (op == BAM_CDEL) x += l;
+               if (!extend_baq) { // in this block, bq[] is capped by base quality qual[]
+                       for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
+                               int op = cigar[k]&0xf, l = cigar[k]>>4;
+                               if (op == BAM_CMATCH) {
+                                       for (i = y; i < y + l; ++i) {
+                                               if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
+                                               else bq[i] = bq[i] < q[i]? bq[i] : q[i];
+                                       }
+                                       x += l; y += l;
+                               } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+                               else if (op == BAM_CDEL) x += l;
+                       }
+                       for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
+               } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!)
+                       uint8_t *left, *rght;
+                       left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
+                       for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
+                               int op = cigar[k]&0xf, l = cigar[k]>>4;
+                               if (op == BAM_CMATCH) {
+                                       for (i = y; i < y + l; ++i)
+                                               bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i];
+                                       for (left[y] = bq[y], i = y + 1; i < y + l; ++i)
+                                               left[i] = bq[i] > left[i-1]? bq[i] : left[i-1];
+                                       for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i)
+                                               rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1];
+                                       for (i = y; i < y + l; ++i)
+                                               bq[i] = left[i] < rght[i]? left[i] : rght[i];
+                                       x += l; y += l;
+                               } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+                               else if (op == BAM_CDEL) x += l;
+                       }
+                       for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ
+                       free(left); free(rght);
                }
-               for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
                if (apply_baq) {
                        for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual
                        bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq);
@@ -254,16 +276,16 @@ int bam_prob_realn(bam1_t *b, const char *ref)
 
 int bam_fillmd(int argc, char *argv[])
 {
-       int c, is_equal, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, apply_baq;
+       int c, is_equal, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag;
        samfile_t *fp, *fpout = 0;
        faidx_t *fai;
        char *ref = 0, mode_w[8], mode_r[8];
        bam1_t *b;
 
-       is_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = apply_baq = capQ = 0;
+       is_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0;
        mode_w[0] = mode_r[0] = 0;
        strcpy(mode_r, "r"); strcpy(mode_w, "w");
-       while ((c = getopt(argc, argv, "reubSC:n:A")) >= 0) {
+       while ((c = getopt(argc, argv, "EreubSC:n:A")) >= 0) {
                switch (c) {
                case 'r': is_realn = 1; break;
                case 'e': is_equal = 1; break;
@@ -272,7 +294,8 @@ int bam_fillmd(int argc, char *argv[])
                case 'S': is_sam_in = 1; break;
                case 'n': max_nm = atoi(optarg); break;
                case 'C': capQ = atoi(optarg); break;
-               case 'A': apply_baq = 1; break;
+               case 'A': baq_flag |= 1; break;
+               case 'E': baq_flag |= 2; break;
                default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
                }
        }
@@ -311,7 +334,7 @@ int bam_fillmd(int argc, char *argv[])
                                        fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
                                                        fp->header->target_name[tid]);
                        }
-                       if (is_realn) bam_prob_realn_core(b, ref, apply_baq);
+                       if (is_realn) bam_prob_realn_core(b, ref, baq_flag);
                        if (capQ > 10) {
                                int q = bam_cap_mapQ(b, ref, capQ);
                                if (b->core.qual > q) b->core.qual = q;

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 1aa93614f35db8891e7bbe1fd955e1100efdbed0..27f67629337b89385080e1904deb80e4dd313d50 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -533,6 +533,7 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_FMT_DP 0x100
 #define MPLP_FMT_SP 0x200
 #define MPLP_NO_INDEL 0x400
+#define MPLP_EXT_BAQ 0x800
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
@@ -569,7 +570,7 @@ static int mplp_func(void *data, bam1_t *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->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->flag & MPLP_EXT_BAQ)? 3 : 1);
                if (has_ref && ma->capQ_thres > 10) {
                        int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
                        if (q < 0) skip = 1;
@@ -863,7 +864,7 @@ 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:b:P:o:e:h:Im:F:")) >= 0) {
+       while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:b:P:o:e:h:Im:F:E")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -881,6 +882,7 @@ int bam_mpileup(int argc, char *argv[])
                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 'E': mplp.flag |= MPLP_EXT_BAQ; 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;

diff --git a/bamtk.c b/bamtk.c
index 41ebcbc9e9d0b3688a4a9132118fb1d2089aabf4..9706069828948c274db15ffe99c2717c83ca9fe0 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.12-5 (r886)"
+#define PACKAGE_VERSION "0.1.12-6 (r887)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);