Commit 9aae020c authored by Charles Plessy's avatar Charles Plessy

Imported Upstream version 0.5.7

parent 723987e1
r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/bwtaln.c
M /branches/prog/bwa/main.c
* bwa-0.5.6-2 (r1309)
* fixed an unfixed bug (by Carol Scott)
* fixed some tiny formatting
r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/bwase.c
M /branches/prog/bwa/bwtaln.c
M /branches/prog/bwa/bwtsw2_main.c
M /branches/prog/bwa/main.c
* bwa-0.5.6-1 (r1304)
* optionally write output to a file (by Tim Fennel)
r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
Changed paths:
M /branches/prog/bwa/ChangeLog
M /branches/prog/bwa/NEWS
M /branches/prog/bwa/bwa.1
M /branches/prog/bwa/bwtsw2_main.c
M /branches/prog/bwa/main.c
Release bwa-0.5.6
r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
Changed paths:
Installation Instructions
Simply type `make' to compile and copy the resulting executable `bwa'
anywhere you want. You may also like to copy `' and
`' for format conversion.
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
2006 Free Software Foundation, Inc.
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Running `configure' might take a while. While running, it prints
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an Autoconf bug. Until the bug is fixed you can use this workaround:
CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
`configure' Invocation
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`configure' can determine that directory automatically.
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`configure --help' for more details.
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The GNU building system is also supported, which is necessary for
building Java binding. Nonetheless, directly runing `make' is
recommended in most other cases.
\ No newline at end of file
Beta Release 0.5.7 (1 March, 2010)
This release only has an effect on paired-end data with fat insert-size
distribution. Users are still recommended to update as the new release
improves the robustness to poor data.
* The fix for `weird pairing' was not working in version 0.5.6, pointed
out by Carol Scott. It should work now.
* Optionally output to a normal file rather than to stdout (by Tim
(0.5.7: 1 March 2010, r1310)
Beta Release 0.5.6 (10 Feburary, 2010)
......@@ -88,7 +88,7 @@ static double ierfc(double x) // inverse erfc(); iphi(x) = M_SQRT2 *ierfc(2 * x)
static int infer_isize(int n_seqs, bwa_seq_t *seqs[2], isize_info_t *ii, double ap_prior, int64_t L)
uint64_t x, *isizes;
int n, i, tot, p25, p75, p50;
int n, i, tot, p25, p75, p50, max_len = 1, tmp;
double skewness = 0.0, kurtosis = 0.0, y;
ii->avg = ii->std = -1.0;
......@@ -99,6 +99,8 @@ static int infer_isize(int n_seqs, bwa_seq_t *seqs[2], isize_info_t *ii, double
p[0] = seqs[0] + i; p[1] = seqs[1] + i;
if (p[0]->mapQ >= 20 && p[1]->mapQ >= 20)
isizes[tot++] = (p[0]->pos < p[1]->pos)? p[1]->pos + p[1]->len - p[0]->pos : p[0]->pos + p[0]->len - p[1]->pos;
if (p[0]->len > max_len) max_len = p[0]->len;
if (p[1]->len > max_len) max_len = p[1]->len;
if (tot < 20) {
fprintf(stderr, "[infer_isize] fail to infer insert size: too few good pairs\n");
......@@ -109,7 +111,8 @@ static int infer_isize(int n_seqs, bwa_seq_t *seqs[2], isize_info_t *ii, double
p25 = isizes[(int)(tot*0.25 + 0.5)];
p50 = isizes[(int)(tot*0.50 + 0.5)];
p75 = isizes[(int)(tot*0.75 + 0.5)];
ii->low = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
tmp = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
ii->low = tmp > max_len? tmp : max_len; // ii->low is unsigned
ii->high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
for (i = 0, x = n = 0; i < tot; ++i)
if (isizes[i] >= ii->low && isizes[i] <= ii->high)
......@@ -135,7 +138,6 @@ static int infer_isize(int n_seqs, bwa_seq_t *seqs[2], isize_info_t *ii, double
for (y = 1.0; y < 10.0; y += 0.01)
if (.5 * erfc(y / M_SQRT2) < ap_prior / L * (y * ii->std + ii->avg)) break;
ii->high_bayesian = (bwtint_t)(y * ii->std + ii->avg + .499);
if (ii->low < 0) ii->low = 35;
fprintf(stderr, "[infer_isize] (25, 50, 75) percentile: (%d, %d, %d)\n", p25, p50, p75);
fprintf(stderr, "[infer_isize] low and high boundaries: %d and %d for estimating avg and std\n", ii->low, ii->high);
fprintf(stderr, "[infer_isize] inferred external isize from %d pairs: %.3lf +/- %.3lf\n", n, ii->avg, ii->std);
......@@ -663,7 +665,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
fprintf(stderr, "[bwa_sai2sam_pe_core] convert to sequence coordinate... \n");
cnt_chg = bwa_cal_pac_pos_pe(prefix, bwt, n_seqs, seqs, fp_sa, &ii, popt, &opt, &last_ii);
fprintf(stderr, "[bwa_sai2sam_pe_core] time elapses: %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
fprintf(stderr, "[bwa_sai2sam_pe_core] change of coordinates in %d alignments.\n", cnt_chg);
fprintf(stderr, "[bwa_sai2sam_pe_core] changing coordinates of %d alignments.\n", cnt_chg);
fprintf(stderr, "[bwa_sai2sam_pe_core] align unmapped mate...\n");
pacseq = bwa_paired_sw(bns, pac, n_seqs, seqs, popt, &ii);
......@@ -708,7 +710,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
int c;
pe_opt_t *popt;
popt = bwa_init_pe_opt();
while ((c = getopt(argc, argv, "a:o:sPn:N:c:")) >= 0) {
while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:")) >= 0) {
switch (c) {
case 'a': popt->max_isize = atoi(optarg); break;
case 'o': popt->max_occ = atoi(optarg); break;
......@@ -717,6 +719,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
case 'n': popt->n_multi = atoi(optarg); break;
case 'N': popt->N_multi = atoi(optarg); break;
case 'c': popt->ap_prior = atof(optarg); break;
case 'f': freopen(optarg, "w", stdout); break;
default: return 1;
......@@ -730,8 +733,9 @@ int bwa_sai2sam_pe(int argc, char *argv[])
fprintf(stderr, " -N INT maximum hits to output for discordant pairs [%d]\n", popt->N_multi);
fprintf(stderr, " -c FLOAT prior of chimeric rate [%.1le]\n", popt->ap_prior);
fprintf(stderr, " -P preload index into memory (for base-space reads only)\n");
fprintf(stderr, " -s disable Smith-Waterman for the unmapped mate\n\n");
fprintf(stderr, "Notes: 1. For SOLiD read, <in1.fq> corresponds R3 reads and <in2.fq> to F3.\n");
fprintf(stderr, " -s disable Smith-Waterman for the unmapped mate\n");
fprintf(stderr, " -f FILE sam file to output results to instead of stdout\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");
fprintf(stderr, " to get a sensible speed at the cost of pairing accuracy.\n");
fprintf(stderr, "\n");
......@@ -612,16 +612,17 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
int bwa_sai2sam_se(int argc, char *argv[])
int c, n_occ = 3;
while ((c = getopt(argc, argv, "hn:")) >= 0) {
while ((c = getopt(argc, argv, "hn:f:")) >= 0) {
switch (c) {
case 'h': break;
case 'n': n_occ = atoi(optarg); break;
case 'f': freopen(optarg, "w", stdout); break;
default: return 1;
if (optind + 3 > argc) {
fprintf(stderr, "Usage: bwa samse [-n max_occ] <prefix> <in.sai> <in.fq>\n");
fprintf(stderr, "Usage: bwa samse [-n max_occ] [-f out.sam] <prefix> <in.sai> <in.fq>\n");
return 1;
bwa_sai2sam_se_core(argv[optind], argv[optind+1], argv[optind+2], n_occ);
......@@ -230,7 +230,7 @@ int bwa_aln(int argc, char *argv[])
gap_opt_t *opt;
opt = gap_init_opt();
while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:")) >= 0) {
while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:")) >= 0) {
switch (c) {
case 'n':
if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
......@@ -252,6 +252,7 @@ int bwa_aln(int argc, char *argv[])
case 'q': opt->trim_qual = atoi(optarg); break;
case 'c': opt->mode &= ~BWA_MODE_COMPREAD; break;
case 'N': opt->mode |= BWA_MODE_NONSTOP; opt->max_top2 = 0x7fffffff; break;
case 'f': freopen(optarg, "wb", stdout); break;
default: return 1;
......@@ -281,6 +282,7 @@ int bwa_aln(int argc, char *argv[])
fprintf(stderr, " -c input sequences are in the color space\n");
fprintf(stderr, " -L log-scaled gap penalty for long deletions\n");
fprintf(stderr, " -N non-iterative mode: search for all n-difference hits (slooow)\n");
fprintf(stderr, " -f FILE file to write output to instead of stdout\n");
fprintf(stderr, "\n");
return 1;
......@@ -16,7 +16,7 @@ int bwa_bwtsw2(int argc, char *argv[])
opt = bsw2_init_opt();
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:y:s:c:N:H")) >= 0) {
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:y:s:c:N:H:f:")) >= 0) {
switch (c) {
case 'q': opt->q = atoi(optarg); break;
case 'r': opt->r = atoi(optarg); break;
......@@ -32,6 +32,7 @@ int bwa_bwtsw2(int argc, char *argv[])
case 'c': opt->coef = atof(optarg); break;
case 'N': opt->t_seeds = atoi(optarg); break;
case 'H': opt->hard_clip = 1; break;
case 'f': freopen(optarg, "w", stdout);
opt->qr = opt->q + opt->r;
......@@ -57,6 +58,7 @@ int bwa_bwtsw2(int argc, char *argv[])
fprintf(stderr, " -N INT # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
fprintf(stderr, " -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
fprintf(stderr, " -H in SAM output, use hard clipping rather than soft\n");
fprintf(stderr, " -f FILE file to output results to instead of stdout\n");
fprintf(stderr, "\n");
rm -fr autom4te.cache depcomp configure config.guess config.sub missing aclocal.m4 install-sh bwt_gen/
\ No newline at end of file
......@@ -3,7 +3,7 @@
#include "main.h"
#define PACKAGE_VERSION "0.5.6 (r1303)"
#define PACKAGE_VERSION "0.5.7 (r1310)"
static int usage()
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