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Adding a flag to sampe (-d) to disable pair rescuing if too many rescue attempts are made. #12

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Adding a flag to sampe (-d) to disable pair rescuing if too many rescue attempts are made. #12

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250a88c
Adding a flag to sampe (-d) to disable pair rescuing, at runtime, if
drio Sep 30, 2012
757d100
Merge https://github.com/lh3/bwa
drio Mar 4, 2013
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19 changes: 16 additions & 3 deletions bwape.c
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,7 @@ pe_opt_t *bwa_init_pe_opt()
po->type = BWA_PET_STD;
po->is_sw = 1;
po->ap_prior = 1e-5;
po->cap_rescue = 0;
return po;
}
/*
Expand Down Expand Up @@ -478,7 +479,7 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
}
*_cnt = (uint32_t)n_mm<<16 | n_gapo<<8 | n_gape;
}

free(ref_seq); free(path);
return cigar;
}
Expand All @@ -499,6 +500,7 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,

// perform mate alignment
n_tot[0] = n_tot[1] = n_mapped[0] = n_mapped[1] = 0;
int n_attempts = 0; // number of rescue attempts
for (i = 0; i != n_seqs; ++i) {
bwa_seq_t *p[2];
p[0] = seqs[0] + i; p[1] = seqs[1] + i;
Expand All @@ -508,6 +510,15 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,
bwa_cigar_t *cigar[2];
uint32_t cnt[2];

if (popt->cap_rescue) {
// If we reached the cap for rescue attempts, stop rescuing
if (n_attempts > popt->cap_rescue) {
fprintf(stderr, "[bwa_paired_sw] Too many rescue attemps, disabling Smith-Waterman for unmapped mates.\n");
break;
}
++n_attempts;
}

/* In the following, _pref points to the reference read
* which must be aligned; _pmate points to its mate which is
* considered to be modified. */
Expand All @@ -525,7 +536,7 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,
if ((_a) < 0) (_a) = 0; \
if ((_b) > _pref->pos) (_b) = _pref->pos; \
} while (0)

#define __set_fixed(_pref, _pmate, _beg, _cnt) do { \
_pmate->type = BWA_TYPE_MATESW; \
_pmate->pos = _beg; \
Expand Down Expand Up @@ -720,7 +731,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
char *prefix, *rg_line = 0;

popt = bwa_init_pe_opt();
while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:")) >= 0) {
while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:d:")) >= 0) {
switch (c) {
case 'r':
if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
Expand All @@ -734,6 +745,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
case 'c': popt->ap_prior = atof(optarg); break;
case 'f': xreopen(optarg, "w", stdout); break;
case 'A': popt->force_isize = 1; break;
case 'd': popt->cap_rescue = atoi(optarg); break;
default: return 1;
}
}
Expand All @@ -750,6 +762,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
fprintf(stderr, " -r STR read group header line such as `@RG\\tID:foo\\tSM:bar' [null]\n");
fprintf(stderr, " -P preload index into memory (for base-space reads only)\n");
fprintf(stderr, " -s disable Smith-Waterman for the unmapped mate\n");
fprintf(stderr, " -d INT disable Smith-Waterman for the unmapped mate when cap is reached [%d]\n", popt->cap_rescue);
fprintf(stderr, " -A disable insert size estimate (force -s)\n\n");
fprintf(stderr, "Notes: 1. For SOLiD reads, <in1.fq> corresponds R3 reads and <in2.fq> to F3.\n");
fprintf(stderr, " 2. For reads shorter than 30bp, applying a smaller -o is recommended to\n");
Expand Down
2 changes: 1 addition & 1 deletion bwtaln.h
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Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,7 @@ typedef struct {
#define BWA_PET_STD 1

typedef struct {
int max_isize, force_isize;
int max_isize, force_isize, cap_rescue;
int max_occ;
int n_multi, N_multi;
int type, is_sw, is_preload;
Expand Down