Commit 81fbd9cc authored by Charles Plessy's avatar Charles Plessy

Imported Upstream version 0.5.8a

parent 9aae020c
------------------------------------------------------------------------
r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines
Changed paths:
M /branches/prog/bwa/bwtsw2_core.c
M /branches/prog/bwa/main.c
* bwa-r1440
* sorry, forget to remove a debugging line
------------------------------------------------------------------------
r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/bwtsw2_core.c
M /branches/prog/bwa/main.c
* bwa-r1439
* fixed a bug in bwasw caused by a recent modification
* throwing insane insert size when estimating isize
------------------------------------------------------------------------
r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines
Changed paths:
M /branches/prog/bwa/bwtsw2_core.c
M /branches/prog/bwa/bwtsw2_main.c
M /branches/prog/bwa/main.c
* bwa-0.5.7-7 (r1425)
* fixed a minor bug in bwasw command-line parsing
* When band-width is not large enough, bwasw may find two highly
overlapping but not completely overlapping alignments. The old
version will filter out one of them, which leads to false
negatives. The current outputs both. This solution is obviously not
ideal. The ideal one would be to increase the band-width and redo the
alignment.
------------------------------------------------------------------------
r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines
Changed paths:
M /branches/prog/bwa/ChangeLog
M /branches/prog/bwa/bwase.c
M /branches/prog/bwa/main.c
* bwa-0.5.7-6 (r1399)
* fixed a typo/bug (by Vaughn Iverson)
------------------------------------------------------------------------
r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/main.c
small correction
------------------------------------------------------------------------
r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/main.c
* bwa-0.5.7-4 (r1328)
* automatically adjust ap_prior based on alignment
------------------------------------------------------------------------
r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/main.c
M /branches/prog/bwa/stdaln.c
M /branches/prog/bwa/stdaln.h
* bwa-0.5.7-3 (r1327)
* evaluate hits obtained from SW alignment in a more proper way.
------------------------------------------------------------------------
r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines
Changed paths:
M /branches/prog/bwa/bwape.c
fixed a potential out-of-boundary error. Need more testing.
------------------------------------------------------------------------
r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines
Changed paths:
M /branches/prog/bwa/bwape.c
insert size is `weird' if the 3rd quatile larger than 100,000bp
------------------------------------------------------------------------
r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/bwtaln.h
M /branches/prog/bwa/main.c
* bwa-0.5.7-2 (r1318)
* in sampe, allow to disable insert size estimate
------------------------------------------------------------------------
r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/bwase.c
M /branches/prog/bwa/main.c
M /branches/prog/bwa/solid2fastq.pl
* bwa-0.5.7-1 (r1317)
* fixed a potential bug in solid2fastq.pl
* fixed a bug in calculating mapping quality (by Rodrigo Goya)
* fixed a very rare bug (if ever occur) about pairing
------------------------------------------------------------------------
r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines
Changed paths:
M /branches/prog/bwa/ChangeLog
M /branches/prog/bwa/NEWS
M /branches/prog/bwa/main.c
Release bwa-0.5.7
------------------------------------------------------------------------
r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
Changed paths:
......
Simply type `make' to compile and copy the resulting executable `bwa'
anywhere you want. You may also like to copy `solid2fastq.pl' and
`qualfa2fq.pl' for format conversion.
On 32-bit system, you should compile bwa with `make CFLAGS=-O2'.
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
## Makefile.am -- Process this file with automake to produce Makefile.in
ACLOCAL_AMFLAGS=-I m4
AM_CFLAGS = -Wall -m64 -fPIC
bin_PROGRAMS = bwa
noinst_LIBRARIES = libbwacore.a
libbwacore_a_SOURCES = utils.c bwt.c bwtio.c bwtaln.c bwtgap.c bntseq.c \
stdaln.c bwaseqio.c bwase.c kstring.c cs2nt.c
bwa_SOURCES = is.c bwtmisc.c bwtindex.c simple_dp.c bwape.c \
bwtsw2_core.c bwtsw2_main.c bwtsw2_aux.c bwt_lite.c bwtsw2_chain.c \
main.c
bwa_LDADD = bwt_gen/libbwtgen.a libbwacore.a
man_MANS= bwa.1
SUBDIRS= bwt_gen .
Beta Release 0.5.8 (8 June, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Notable changes in bwasw:
* Fixed an issue of missing alignments. This should happen rarely and
only when the contig/read alignment is multi-part. Very rarely, bwasw
may still miss a segment in a multi-part alignment. This is difficult
to fix, although possible.
Notable changes in bwa-short:
* Discard the SW alignment when the best single-end alignment is much
better. Such a SW alignment may caused by structural variations and
forcing it to be aligned leads to false alignment. This fix has not
been tested thoroughly. It would be great to receive more users
feedbacks on this issue.
* Fixed a typo/bug in sampe which leads to unnecessarily large memory
usage in some cases.
* Further reduced the chance of reporting `weird pairing'.
(0.5.8: 8 June 2010, r1442)
Beta Release 0.5.7 (1 March, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
#!/bin/sh
autoreconf -vi
.TH bwa 1 "10 Feburuary 2010" "bwa-0.5.6" "Bioinformatics tools"
.TH bwa 1 "8 June 2010" "bwa-0.5.8" "Bioinformatics tools"
.SH NAME
.PP
bwa - Burrows-Wheeler Alignment Tool
......
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......@@ -11,7 +11,7 @@
#include "utils.h"
#include "kstring.h"
static int g_log_n[256];
int g_log_n[256];
void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
{
......@@ -56,7 +56,7 @@ void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_ma
* simply output all hits, but the following samples "rest"
* number of random hits. */
rest = n_occ > n_multi + 1? n_multi + 1 : n_occ; // find one additional for ->sa
s->multi = calloc(rest, rest * sizeof(bwt_multi1_t));
s->multi = calloc(rest, sizeof(bwt_multi1_t));
for (k = 0; k < n_aln; ++k) {
const bwt_aln1_t *q = aln + k;
if (q->l - q->k + 1 <= rest) {
......
## Makefile.am -- Process this file with automake to produce Makefile.in
AM_CFLAGS = -g -Wall -O2 -m64
noinst_LIBRARIES = libbwtgen.a
libbwtgen_a_SOURCES = QSufSort.c bwt_gen.c
......@@ -100,7 +100,7 @@ typedef struct {
#define BWA_PET_SOLID 2
typedef struct {
int max_isize;
int max_isize, force_isize;
int max_occ;
int n_multi, N_multi;
int type, is_sw, is_preload;
......
......@@ -335,12 +335,19 @@ int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level)
if (p->G == 0) break;
for (j = 0; j < i; ++j) {
bsw2hit_t *q = b->hits + j;
int64_t tol = 0;
int qol, compatible = 0;
float fol;
if (q->G == 0) continue;
qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg);
if (qol < 0) qol = 0;
if ((float)qol / (p->end - p->beg) < mask_level
&& (float)qol / (q->end - q->beg) < mask_level) compatible = 1;
if (p->l == 0 && q->l == 0) {
tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
- (p->k > q->k? p->k : q->k);
if (tol < 0) tol = 0;
}
fol = (float)qol / (p->end - p->beg < q->end - q->beg? p->end - p->beg : q->end - q->beg);
if (fol < mask_level || (tol > 0 && qol < p->end - p->beg && qol < q->end - q->beg)) compatible = 1;
if (!compatible) {
if (q->G2 < p->G) q->G2 = p->G;
all_compatible = 0;
......
......@@ -16,7 +16,7 @@ int bwa_bwtsw2(int argc, char *argv[])
opt = bsw2_init_opt();
srand48(11);
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:y:s:c:N:H:f:")) >= 0) {
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:y:s:c:N:Hf:")) >= 0) {
switch (c) {
case 'q': opt->q = atoi(optarg); break;
case 'r': opt->r = atoi(optarg); break;
......
rm -fr autom4te.cache Makefile.in depcomp configure config.guess config.sub missing aclocal.m4 install-sh bwt_gen/Makefile.in
\ No newline at end of file
/* config.h.in. Generated from configure.in by autoheader. */
/* Define to 1 if you don't have `vprintf' but do have `_doprnt.' */
#undef HAVE_DOPRNT
/* Define to 1 if you have the <inttypes.h> header file. */
#undef HAVE_INTTYPES_H
/* Define to 1 if you have the `m' library (-lm). */
#undef HAVE_LIBM
/* Define to 1 if you have the `pthread' library (-lpthread). */
#undef HAVE_LIBPTHREAD
/* Define to 1 if you have the `z' library (-lz). */
#undef HAVE_LIBZ
/* Define to 1 if you have the <limits.h> header file. */
#undef HAVE_LIMITS_H
/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
to 0 otherwise. */
#undef HAVE_MALLOC
/* Define to 1 if you have the `memmove' function. */
#undef HAVE_MEMMOVE
/* Define to 1 if you have the <memory.h> header file. */
#undef HAVE_MEMORY_H
/* Define to 1 if you have the `memset' function. */
#undef HAVE_MEMSET
/* Define if you have POSIX threads libraries and header files. */
#undef HAVE_PTHREAD
/* Define to 1 if your system has a GNU libc compatible `realloc' function,
and to 0 otherwise. */
#undef HAVE_REALLOC
/* Define to 1 if you have the `sqrt' function. */
#undef HAVE_SQRT
/* Define to 1 if you have the <stdint.h> header file. */
#undef HAVE_STDINT_H
/* Define to 1 if you have the <stdlib.h> header file. */
#undef HAVE_STDLIB_H
/* Define to 1 if you have the `strdup' function. */
#undef HAVE_STRDUP
/* Define to 1 if you have the <strings.h> header file. */
#undef HAVE_STRINGS_H
/* Define to 1 if you have the <string.h> header file. */
#undef HAVE_STRING_H
/* Define to 1 if you have the `strstr' function. */
#undef HAVE_STRSTR
/* Define to 1 if you have the <sys/stat.h> header file. */
#undef HAVE_SYS_STAT_H
/* Define to 1 if you have the <sys/types.h> header file. */
#undef HAVE_SYS_TYPES_H
/* Define to 1 if you have the <unistd.h> header file. */
#undef HAVE_UNISTD_H
/* Define to 1 if you have the `vprintf' function. */
#undef HAVE_VPRINTF
/* Name of package */
#undef PACKAGE
/* Define to the address where bug reports for this package should be sent. */
#undef PACKAGE_BUGREPORT
/* Define to the full name of this package. */
#undef PACKAGE_NAME
/* Define to the full name and version of this package. */
#undef PACKAGE_STRING
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
/* Define to the version of this package. */
#undef PACKAGE_VERSION
/* Define to necessary symbol if this constant uses a non-standard name on
your system. */
#undef PTHREAD_CREATE_JOINABLE
/* Define to 1 if you have the ANSI C header files. */
#undef STDC_HEADERS
/* Version number of package */
#undef VERSION
/* Define for Solaris 2.5.1 so the uint32_t typedef from <sys/synch.h>,
<pthread.h>, or <semaphore.h> is not used. If the typedef was allowed, the
#define below would cause a syntax error. */
#undef _UINT32_T
/* Define for Solaris 2.5.1 so the uint64_t typedef from <sys/synch.h>,
<pthread.h>, or <semaphore.h> is not used. If the typedef was allowed, the
#define below would cause a syntax error. */
#undef _UINT64_T
/* Define for Solaris 2.5.1 so the uint8_t typedef from <sys/synch.h>,
<pthread.h>, or <semaphore.h> is not used. If the typedef was allowed, the
#define below would cause a syntax error. */
#undef _UINT8_T
/* Define to empty if `const' does not conform to ANSI C. */
#undef const
/* Define to `__inline__' or `__inline' if that's what the C compiler
calls it, or to nothing if 'inline' is not supported under any name. */
#ifndef __cplusplus
#undef inline
#endif
/* Define to the type of a signed integer type of width exactly 32 bits if
such a type exists and the standard includes do not define it. */
#undef int32_t
/* Define to the type of a signed integer type of width exactly 64 bits if
such a type exists and the standard includes do not define it. */
#undef int64_t
/* Define to rpl_malloc if the replacement function should be used. */
#undef malloc
/* Define to rpl_realloc if the replacement function should be used. */
#undef realloc
/* Define to `unsigned int' if <sys/types.h> does not define. */
#undef size_t
/* Define to the type of an unsigned integer type of width exactly 16 bits if
such a type exists and the standard includes do not define it. */
#undef uint16_t
/* Define to the type of an unsigned integer type of width exactly 32 bits if
such a type exists and the standard includes do not define it. */
#undef uint32_t
/* Define to the type of an unsigned integer type of width exactly 64 bits if
such a type exists and the standard includes do not define it. */
#undef uint64_t
/* Define to the type of an unsigned integer type of width exactly 8 bits if
such a type exists and the standard includes do not define it. */
#undef uint8_t
# -*- Autoconf -*-
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.61)
AC_INIT([bwa], [0.5.5])
AC_CONFIG_SRCDIR([bntseq.c])
AC_CONFIG_HEADER([config.h])
AC_CONFIG_MACRO_DIR([m4])
AM_INIT_AUTOMAKE()
# Checks for programs.
AC_PROG_CC([gcc])
AC_PROG_CXX([g++])
AC_PROG_INSTALL
AC_PROG_AWK
AC_PROG_MKDIR_P
AC_PROG_RANLIB
# Checks for libraries.
# Checks for header files.
AC_HEADER_STDC
AC_CHECK_HEADERS([limits.h stdint.h stdlib.h string.h unistd.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_C_CONST
AC_C_INLINE
AC_TYPE_INT32_T
AC_TYPE_INT64_T
AC_TYPE_SIZE_T
AC_TYPE_UINT16_T
AC_TYPE_UINT32_T
AC_TYPE_UINT64_T
AC_TYPE_UINT8_T
# Checks for library functions.
AC_FUNC_MALLOC
AC_FUNC_REALLOC
AC_FUNC_VPRINTF
AC_CHECK_FUNCS([memmove memset sqrt strdup strstr])
AC_CHECK_LIB([m],[log])
AC_CHECK_LIB([z],[gzopen])
AC_CHECK_LIB([pthread],[pthread_create])
ACX_PTHREAD
AC_CONFIG_FILES([Makefile
bwt_gen/Makefile])
AC_OUTPUT
This diff is collapsed.
......@@ -3,7 +3,7 @@
#include "main.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.5.7 (r1310)"
#define PACKAGE_VERSION "0.5.8 (r1442)"
#endif
static int usage()
......
......@@ -9,7 +9,7 @@ use warnings;
use Getopt::Std;
my %opts;
my $version = '0.1.3';
my $version = '0.1.4';
my $usage = qq{
Usage: solid2fastq.pl <in.title> <out.prefix>
......@@ -100,8 +100,8 @@ sub read1 {
tr/0123./ACGTN/;
my $s = $_;
$_ = <$fhq>;
s/^(\d+)\s*//;
s/-1\b/0/eg;
s/^(\d+)\s*//;
s/(\d+)\s*/chr($1+33)/eg;
$seq = qq/\@$name\n$s+\n$_\n/;
last;
......
......@@ -219,12 +219,20 @@ int aln_sm_blast[] = {
-2, -2, -2, -2, -2
};
int aln_sm_bwa[] = {
3, -9, -9, -9, -6,
-9, 3, -9, -9, -6,
-9, -9, 3, -9, -6,
-9, -9, -9, 3, -6,
-6, -6, -6, -6, -6
};
/********************/
/* START OF align.c */
/********************/
AlnParam aln_param_blast = { 5, 2, 2, aln_sm_blast, 5, 50 };
AlnParam aln_param_bwa = { 26, 9, 5, aln_sm_maq, 5, 50 };
AlnParam aln_param_bwa = { 13, 2, 2, aln_sm_bwa, 5, 50 }; /* e=1.21%; T=2.18 */
AlnParam aln_param_nt2nt = { 8, 2, 2, aln_sm_nt, 16, 75 };
AlnParam aln_param_rd2rd = { 1, 19, 19, aln_sm_read, 16, 75 };
AlnParam aln_param_aa2aa = { 10, 2, 2, aln_sm_blosum62, 22, 50 };
......
......@@ -148,7 +148,7 @@ extern AlnParam aln_param_aa2aa; /* = { 20, 19, 19, aln_sm_read, 16, 75 }; */
extern AlnParam aln_param_rd2rd; /* = { 12, 2, 2, aln_sm_blosum62, 22, 50 }; */
/* common nucleotide score matrix for 16 bases */
extern int aln_sm_nt[];
extern int aln_sm_nt[], aln_sm_bwa[];
/* BLOSUM62 and BLOSUM45 */
extern int aln_sm_blosum62[], aln_sm_blosum45[];
......
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