effectively revert to the viterbi version. The forward realignment gives too many...

diff --git a/ChangeLog b/ChangeLog
index d43635f959b10163635da118160e55b0ed886f0e..a1beffd4dafdf3940ae567863815464117ba6dee 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,160 @@
+------------------------------------------------------------------------
+r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-9 (r810)
+ * use forward, instead of viterbi, for realignment
+ * realignment is now quality aware
+
+------------------------------------------------------------------------
+r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/kprobaln.c
+   M /trunk/samtools/kprobaln.h
+
+ * prepare to replace kaln with kprobaln in realignment
+
+------------------------------------------------------------------------
+r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+
+fixed a typo
+
+------------------------------------------------------------------------
+r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+
+use zlib for direct reading when BCF_LITE is in use
+
+------------------------------------------------------------------------
+r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+
+ * do not use reads containing too many mismatches for indel calling
+ * fixed a trivial bug in case of multi-allelic indels
+
+------------------------------------------------------------------------
+r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-8 (r809)
+ * fixed a bug in the indel caller
+
+------------------------------------------------------------------------
+r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+
+minor change to makefile
+
+------------------------------------------------------------------------
+r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * samtools-0.1.9-8 (r807)
+ * collect indel candidates only from specified platforms (@RG-PL)
+ * merge varFilter and filter4vcf in vcfutils.pl 
+
+------------------------------------------------------------------------
+r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+
+bcftools: compute equal-tail (Bayesian) credible interval
+
+------------------------------------------------------------------------
+r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+added a double-hit filter to avoid overestimated indel likelihood
+
+------------------------------------------------------------------------
+r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-7 (r804)
+ * fixed a bug in the gap caller
+
+------------------------------------------------------------------------
+r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/prob1.c
+
+ * samtools-0.1.9-6 (r803)
+ * mpileup: apply homopolymer correction when calculating GL, instead of before
+ * bcftools: apply a different prior to indels
+
+------------------------------------------------------------------------
+r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-5 (r802)
+ * relax tandem penalty. this will be made a command-line option in future.
+
+------------------------------------------------------------------------
+r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-4 (r801)
+ * fixed a minor issue in printing indel VCF
+
+------------------------------------------------------------------------
+r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+fixed another silly bug in mpileup's indel caller
+
+------------------------------------------------------------------------
+r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+
+fixed a silly bug in the indel caller
+
+------------------------------------------------------------------------
+r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/sam_view.c
+   M /trunk/samtools/samtools.1
+
+Incorporate patches by Marcel Martin for read counting.
+
 ------------------------------------------------------------------------
 r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
 Changed paths:

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index ab9b499b1afeb4acd7f180002f679fddb8f9eddc..2e0b04dfee68f01032665345ac7961ea7ba1a059 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -236,8 +236,9 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
        bca->indelreg = 0;
        for (t = 0; t < n_types; ++t) {
                int l, ir;
-               kpa_par_t ap = { 1e-4, 1e-2, 10 };
-               ap.bw = abs(types[t]) + 3;
+               kpa_par_t apf = { 1e-4, 1e-2, 10 };
+               ka_param2_t apv = ka_param2_qual;
+               apf.bw = apv.band_width = abs(types[t]) + 3;
                // compute indelreg
                if (types[t] == 0) ir = 0;
                else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
@@ -275,18 +276,25 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                // write the query sequence
                                for (l = qbeg; l < qend; ++l)
                                        query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
-                               { // do alignment; this is the bottleneck
+                               // do alignment; this is the bottleneck
+                               if (0) {
                                        const uint8_t *qual = bam1_qual(p->b), *bq;
                                        uint8_t *qq = 0;
                                        qq = calloc(qend - qbeg, 1);
                                        bq = (uint8_t*)bam_aux_get(p->b, "BQ");
                                        if (bq) ++bq;
-                                       for (l = qbeg; l < qend; ++l)
+                                       for (l = qbeg; l < qend; ++l) {
                                                qq[l - qbeg] = bq? qual[l] + (bq[l] - 33) : qual[l];
+                                               if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
+                                       }
                                        sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
-                                                                       (uint8_t*)query, qend - qbeg, qq, &ap, 0, 0);
+                                                                       (uint8_t*)query, qend - qbeg, qq, &apf, 0, 0);
                                        score[K*n_types + t] = sc;
                                        free(qq);
+                               } else {
+                                       sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+                                                                                (uint8_t*)query, qend - qbeg, &apv);
+                                       score[K*n_types + t] = -sc;
                                }
 /*
                                for (l = 0; l < tend - tbeg + abs(types[t]); ++l)