* samtools-0.1.8-11 (r672)

 * collect more stats for allele balance test in bcftools (not yet)

diff --git a/bam2bcf.c b/bam2bcf.c
index e64e3357c04d5cd61bc7ecdc3e6af6d0fd859182..5ad81c05641935ffd4c7f2b6082acc9d341214b2 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -5,6 +5,8 @@
 #include "bam2bcf.h"
 #include "bcftools/bcf.h"
 
+#define MAX_END_DIST 30
+
 extern void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 
 #define CALL_ETA 0.03f
@@ -71,11 +73,12 @@ typedef struct {
  */
 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 i, j, k, c, n;
+       int i, j, k, c, n, ref4;
        float *p = r->p;
        auxaux_t aux;
 
        memset(r, 0, sizeof(bcf_callret1_t));
+       ref4 = bam_nt16_nt4_table[ref_base];
        if (_n == 0) return -1;
 
        // enlarge the aux array if necessary
@@ -88,6 +91,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
        for (i = n = 0; i < _n; ++i) {
                const bam_pileup1_t *p = pl + i;
                uint32_t q, x = 0, qq;
+               int min_dist;
                if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases
                q = (uint32_t)bam1_qual(p->b)[p->qpos]; // base quality
                if (q < bca->min_baseQ) continue;
@@ -97,8 +101,17 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
                qq = bam1_seqi(bam1_seq(p->b), p->qpos); // base
                q = bam_nt16_nt4_table[qq? qq : ref_base]; // q is the 2-bit base
                if (q < 4) x |= 1 << 21 | q << 16;
-               
+               k = (ref4 < 4 && q == ref4)? 0 : 1;
+               k = k<<1 | bam1_strand(p->b);
+               ++r->d[k];
                bca->info[n++] = x;
+               // calculate min_dist
+               min_dist = p->b->core.l_qseq - 1 - p->qpos;
+               if (min_dist > p->qpos) min_dist = p->qpos;
+               if (min_dist > MAX_END_DIST) min_dist = MAX_END_DIST;
+               k >>= 1;
+               r->dsum[k]  += min_dist;
+               r->d2sum[k] += min_dist * min_dist;
        }
        ks_introsort_uint32_t(n, bca->info);
        r->depth = n;
@@ -204,10 +217,26 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
                }
                call->shift = (int)(sum_min + .499);
        }
+       memset(call->d, 0, 4 * sizeof(int));
+       call->davg[0] = call->davg[1] = call->dstd[0] = call->dstd[1] = 0.;
        for (i = call->depth = 0, tmp = 0; i < n; ++i) {
                call->depth += calls[i].depth;
+               for (j = 0; j < 4; ++j) call->d[j] += calls[i].d[j];
+               for (j = 0; j < 2; ++j) {
+                       call->davg[j] += calls[i].dsum[j];
+                       call->dstd[j] += calls[i].d2sum[j];
+               }
                tmp += calls[i].sum_Q2;
        }
+       for (j = 0; j < 2; ++j) {
+               int x = call->d[j*2] + call->d[j*2+1];
+               if (x == 0) {
+                       call->davg[j] = call->dstd[j] = 0.;
+               } else {
+                       call->davg[j] /= x;
+                       call->dstd[j] = sqrt(call->dstd[j] / x - call->davg[j] * call->davg[j]);
+               }
+       }
        call->rmsQ = (int)(sqrt((double)tmp / call->depth) + .499);
        return 0;
 }
@@ -228,7 +257,17 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
        }
        kputc('\0', &s);
        kputc('\0', &s);
-       kputs("MQ=", &s); kputw(bc->rmsQ, &s); kputs(";DP=", &s); kputw(bc->depth, &s); kputc('\0', &s);
+       // INFO
+       kputs("MQ=", &s); kputw(bc->rmsQ, &s); // kputs(";DP=", &s); kputw(bc->depth, &s);
+       kputs(";DP4=", &s);
+       for (i = 0; i < 4; ++i) {
+               if (i) kputc(',', &s);
+               kputw(bc->d[i], &s);
+       }
+       if (bc->d[2] + bc->d[3] > 1)
+               ksprintf(&s, ";MED=%.1lf,%.1lf,%.1lf,%.1lf", bc->davg[0], bc->dstd[0], bc->davg[1], bc->dstd[1]);
+       kputc('\0', &s);
+       // FMT
        kputs("PL", &s); kputc('\0', &s);
        b->m_str = s.m; b->str = s.s; b->l_str = s.l;
        bcf_sync(bc->n, b);

diff --git a/bam2bcf.h b/bam2bcf.h
index 655174f585f663b54c0e10327df45eddb8942616..73624c0a6bdc789d892aa4dc9d89ac07f7adcc38 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -8,7 +8,8 @@ struct __bcf_callaux_t;
 typedef struct __bcf_callaux_t bcf_callaux_t;
 
 typedef struct {
-       int depth;
+       int depth, d[4];
+       int dsum[2], d2sum[2];
        uint64_t sum_Q2;
        float p[25], esum[5];
 } bcf_callret1_t;
@@ -16,7 +17,8 @@ typedef struct {
 typedef struct {
        int a[5]; // alleles: ref, alt, alt2, alt3
        int n, n_alleles, shift, ori_ref, unseen;
-       int depth, rmsQ;
+       int d[4], depth, rmsQ;
+       double davg[2], dstd[2];
        uint8_t *PL;
 } bcf_call_t;
 

diff --git a/bamtk.c b/bamtk.c
index 863ba33e0e0b345db99bb33387289dab856c72a2..480f7468a12d0342cf2acf746fb17f34929372a5 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-10 (r658)"
+#define PACKAGE_VERSION "0.1.8-11 (r672)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/examples/Makefile b/examples/Makefile
index b12f882e1fd3cb9fd92dbd9909df11167943716c..96a4e7ed96d14ebf38013ff60216d6cda25bfa49 100644 (file)
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -45,4 +45,4 @@ calDepth:../libbam.a calDepth.c
 clean:
                rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf
 
-# ../samtools pileup ex1.bam|perl -ape '$_=$F[4];s/\^.//g;$x=tr/A-Z/X/;$y=tr/a-z/x/;s/(\d+)(X)/$x-=$1,$2/eg;s/(\d+)(x)/$y-=$1,$2/eg;$_=join("\t",@F[0,1],$x,$y)."\n"'
\ No newline at end of file
+# ../samtools pileup ex1.bam|perl -ape '$_=$F[4];s/(\d+)(??{".{$1}"})|\^.//g;@_=(tr/A-Z//,tr/a-z//);$_=join("\t",@F[0,1],@_)."\n"'
\ No newline at end of file