From: Heng Li <lh3@live.co.uk>
Date: Fri, 12 Nov 2010 18:04:53 +0000 (+0000)
Subject: * samtools-r818
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=bf8b35cc189c6c846f01752f9e9500a3c08cd9b1;p=samtools.git
* samtools-r818
* for indel calling, do two rounds of probabilistic realignments
---
diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 5f4d893..ad13eb3 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -113,7 +113,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
const void *rghash)
{
extern void ks_introsort_uint32_t(int, uint32_t*);
- int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score, N, K, l_run, ref_type, n_alt;
+ int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2;
+ int N, K, l_run, ref_type, n_alt;
char *inscns = 0, *ref2, *query;
khash_t(rg) *hash = (khash_t(rg)*)rghash;
if (ref == 0 || bca == 0) return -1;
@@ -238,13 +239,13 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
// compute the likelihood given each type of indel for each read
ref2 = calloc(right - left + max_ins + 2, 1);
query = calloc(right - left + max_rd_len + max_ins + 2, 1);
- score = calloc(N * n_types, sizeof(int));
+ score1 = calloc(N * n_types, sizeof(int));
+ score2 = calloc(N * n_types, sizeof(int));
bca->indelreg = 0;
for (t = 0; t < n_types; ++t) {
int l, ir;
- 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;
+ kpa_par_t apf1 = { 1e-4, 1e-2, 10 }, apf2 = { 1e-6, 1e-3, 10 };
+ apf1.bw = apf2.bw = 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]);
@@ -282,26 +283,26 @@ 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
- if (1) {
+ { // do realignment; this is the bottleneck
const uint8_t *qual = bam1_qual(p->b), *bq;
- uint8_t *qq = 0;
+ uint8_t *qq;
qq = calloc(qend - qbeg, 1);
bq = (uint8_t*)bam_aux_get(p->b, "BQ");
- if (bq) ++bq;
+ if (bq) ++bq; // skip type
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;
if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
}
sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
- (uint8_t*)query, qend - qbeg, qq, &apf, 0, 0);
- score[K*n_types + t] = sc;
+ (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0);
+ score1[K*n_types + t] = score2[K*n_types + t] = sc;
+ if (sc > 5) { // I do not know why, but a long exact match always has sc==5
+ sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+ (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0);
+ score2[K*n_types + t] = sc;
+ }
free(qq);
- } else { // the following block is for testing only
- 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)
@@ -323,7 +324,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
for (s = K = 0; s < n; ++s) {
for (i = 0; i < n_plp[s]; ++i, ++K) {
bam_pileup1_t *p = plp[s] + i;
- int *sct = &score[K*n_types], indelQ, seqQ;
+ int *sct = &score1[K*n_types], indelQ1, indelQ2, seqQ, indelQ;
for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
for (t = 1; t < n_types; ++t) // insertion sort
for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
@@ -335,14 +336,27 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
* compromise for multi-allelic indels.
*/
if ((sc[0]&0x3f) == ref_type) {
- indelQ = (sc[1]>>6) - (sc[0]>>6);
+ indelQ1 = (sc[1]>>6) - (sc[0]>>6);
seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run);
} else {
for (t = 0; t < n_types; ++t) // look for the reference type
if ((sc[t]&0x3f) == ref_type) break;
- indelQ = (sc[t]>>6) - (sc[0]>>6);
+ indelQ1 = (sc[t]>>6) - (sc[0]>>6);
seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
}
+ sct = &score2[K*n_types];
+ for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
+ for (t = 1; t < n_types; ++t) // insertion sort
+ for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
+ tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+ if ((sc[0]&0x3f) == ref_type) {
+ indelQ2 = (sc[1]>>6) - (sc[0]>>6);
+ } else {
+ for (t = 0; t < n_types; ++t) // look for the reference type
+ if ((sc[t]&0x3f) == ref_type) break;
+ indelQ2 = (sc[t]>>6) - (sc[0]>>6);
+ }
+ indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
if (sc[0]>>6 > MAX_SCORE) indelQ = 0; // too many mismatches; something bad possibly happened
p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ;
sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
@@ -382,7 +396,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
}
}
}
- free(score);
+ free(score1); free(score2);
// free
free(types); free(inscns);
return n_alt > 0? 0 : -1;
diff --git a/bamtk.c b/bamtk.c
index da29ed7..428e9ed 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.9-11 (r817)"
+#define PACKAGE_VERSION "0.1.9-12 (r818)"
#endif
int bam_taf2baf(int argc, char *argv[]);