Commit 83bd9a53 authored by Charles Plessy's avatar Charles Plessy

Imported Upstream version 0.5.8c

parent 81fbd9cc
------------------------------------------------------------------------
r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines
Changed paths:
M /branches/prog/bwa/bwape.c
M /branches/prog/bwa/main.c
M /branches/prog/bwa/stdaln.c
* fixed a bug in the scoring matrix
* release bwa-0.5.8c (r1536)
------------------------------------------------------------------------
r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines
Changed paths:
M /branches/prog/bwa/bwa.1
version change
------------------------------------------------------------------------
r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines
Changed paths:
M /branches/prog/bwa/main.c
M /branches/prog/bwa/stdaln.c
* bwa-0.5.8b (r1450)
* fixed a bug in scoring matrix
------------------------------------------------------------------------
r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines
Changed paths:
M /branches/prog/bwa/bwa.1
M /branches/prog/bwa/bwape.c
fixed a serious bug
------------------------------------------------------------------------
r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines
Changed paths:
M /branches/prog/bwa/ChangeLog
M /branches/prog/bwa/NEWS
M /branches/prog/bwa/main.c
Release bwa-0.5.8 (r1442)
------------------------------------------------------------------------
r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 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 .
#!/bin/sh
autoreconf -vi
.TH bwa 1 "8 June 2010" "bwa-0.5.8" "Bioinformatics tools"
.TH bwa 1 "16 October 2010" "bwa-0.5.8c" "Bioinformatics tools"
.SH NAME
.PP
bwa - Burrows-Wheeler Alignment Tool
......
This diff is collapsed.
......@@ -141,6 +141,7 @@ static int infer_isize(int n_seqs, bwa_seq_t *seqs[2], isize_info_t *ii, double
ii->ap_prior = .01 * (n_ap + .01) / tot;
if (ii->ap_prior < ap_prior) ii->ap_prior = ap_prior;
free(isizes);
fprintf(stderr, "[infer_isize] (25, 50, 75) percentile: (%d, %d, %d)\n", p25, p50, p75);
if (isnan(ii->std) || p75 > 100000) {
ii->low = ii->high = ii->high_bayesian = 0; ii->avg = ii->std = -1.0;
fprintf(stderr, "[infer_isize] fail to infer insert size: weird pairing\n");
......@@ -149,7 +150,6 @@ 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);
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);
fprintf(stderr, "[infer_isize] skewness: %.3lf; kurtosis: %.3lf; ap_prior: %.2e\n", skewness, kurtosis, ii->ap_prior);
......
## 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
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 "0.5.8 (r1442)"
#define PACKAGE_VERSION "0.5.8c (r1536)"
#endif
static int usage()
......
#!/usr/bin/perl -w
use strict;
use warnings;
die("Usage: sracsfq2fq.pl <in.sra.fasta>\n") if (@ARGV == 0 && -t STDIN);
while (<>) {
print;
$_ = <>; $_ = substr($_, 2);
tr/0123./ACGTN/;
print;
$_ = <>; print $_;
$_ = <>; print substr($_, 2);
}
......@@ -219,20 +219,12 @@ 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 = { 13, 2, 2, aln_sm_bwa, 5, 50 }; /* e=1.21%; T=2.18 */
AlnParam aln_param_bwa = { 26, 9, 5, aln_sm_maq, 5, 50 };
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 };
......
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