[med-svn] [tophat] 01/05: Imported Upstream version 2.0.13
Andreas Tille
tille at debian.org
Sat Oct 4 19:33:18 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository tophat.
commit 9a58423841ee7399a6d9197d1477ddb5913bac19
Author: Andreas Tille <tille at debian.org>
Date: Sat Oct 4 21:29:53 2014 +0200
Imported Upstream version 2.0.13
---
AUTHORS | 33 +-
COPYING | 1 -
Makefile.am | 1 -
Makefile.in | 14 +-
README | 25 +-
ax_bam.m4 | 203 -
ax_boost_thread.m4 | 246 +-
build-aux/config.guess => config.guess | 0
config.h.in | 6 +-
build-aux/config.sub => config.sub | 0
configure | 2943 ++++++++-------
configure.ac | 45 +-
build-aux/depcomp => depcomp | 0
build-aux/install-sh => install-sh | 0
build-aux/missing => missing | 0
src/GBase.cpp | 49 +-
src/GBase.h | 2 +-
src/Makefile.am | 126 +-
src/Makefile.in | 209 +-
src/align_status.h | 2 +-
src/bam2fastx.cpp | 4 +-
src/bed_to_juncs | 7 +-
src/bwt_map.h | 10 +-
src/common.cpp | 2 +-
src/common.h | 4 +-
src/map2gtf.h | 4 +-
src/samtools-0.1.18/AUTHORS | 20 +
src/samtools-0.1.18/COPYING | 21 +
src/samtools-0.1.18/ChangeLog | 5948 ++++++++++++++++++++++++++++++
src/samtools-0.1.18/INSTALL | 30 +
src/samtools-0.1.18/Makefile | 93 +
src/samtools-0.1.18/Makefile.mingw | 63 +
src/samtools-0.1.18/NEWS | 806 ++++
src/samtools-0.1.18/bam.c | 362 ++
src/samtools-0.1.18/bam.h | 763 ++++
src/samtools-0.1.18/bam2bcf.c | 351 ++
src/samtools-0.1.18/bam2bcf.h | 57 +
src/samtools-0.1.18/bam2bcf_indel.c | 475 +++
src/samtools-0.1.18/bam2depth.c | 112 +
src/samtools-0.1.18/bam_aux.c | 213 ++
src/samtools-0.1.18/bam_cat.c | 184 +
src/samtools-0.1.18/bam_color.c | 127 +
src/samtools-0.1.18/bam_endian.h | 42 +
src/samtools-0.1.18/bam_import.c | 485 +++
src/samtools-0.1.18/bam_index.c | 719 ++++
src/samtools-0.1.18/bam_lpileup.c | 198 +
src/samtools-0.1.18/bam_mate.c | 70 +
src/samtools-0.1.18/bam_md.c | 384 ++
src/samtools-0.1.18/bam_pileup.c | 437 +++
src/samtools-0.1.18/bam_plcmd.c | 546 +++
src/samtools-0.1.18/bam_reheader.c | 61 +
src/samtools-0.1.18/bam_rmdup.c | 206 ++
src/samtools-0.1.18/bam_rmdupse.c | 159 +
src/samtools-0.1.18/bam_sort.c | 438 +++
src/samtools-0.1.18/bam_stat.c | 77 +
src/samtools-0.1.18/bam_tview.c | 440 +++
src/samtools-0.1.18/bamtk.c | 109 +
src/samtools-0.1.18/bcftools/Makefile | 51 +
src/samtools-0.1.18/bcftools/README | 36 +
src/samtools-0.1.18/bcftools/bcf.c | 328 ++
src/samtools-0.1.18/bcftools/bcf.h | 190 +
src/samtools-0.1.18/bcftools/bcf.tex | 77 +
src/samtools-0.1.18/bcftools/bcf2qcall.c | 91 +
src/samtools-0.1.18/bcftools/bcfutils.c | 390 ++
src/samtools-0.1.18/bcftools/call1.c | 586 +++
src/samtools-0.1.18/bcftools/em.c | 310 ++
src/samtools-0.1.18/bcftools/fet.c | 112 +
src/samtools-0.1.18/bcftools/index.c | 335 ++
src/samtools-0.1.18/bcftools/kfunc.c | 162 +
src/samtools-0.1.18/bcftools/kmin.c | 209 ++
src/samtools-0.1.18/bcftools/kmin.h | 46 +
src/samtools-0.1.18/bcftools/main.c | 190 +
src/samtools-0.1.18/bcftools/mut.c | 127 +
src/samtools-0.1.18/bcftools/prob1.c | 554 +++
src/samtools-0.1.18/bcftools/prob1.h | 42 +
src/samtools-0.1.18/bcftools/vcf.c | 244 ++
src/samtools-0.1.18/bcftools/vcfutils.pl | 567 +++
src/samtools-0.1.18/bedidx.c | 162 +
src/samtools-0.1.18/bgzf.c | 714 ++++
src/samtools-0.1.18/bgzf.h | 157 +
src/samtools-0.1.18/bgzip.c | 206 ++
src/samtools-0.1.18/cut_target.c | 193 +
src/samtools-0.1.18/errmod.c | 130 +
src/samtools-0.1.18/errmod.h | 24 +
src/samtools-0.1.18/faidx.c | 432 +++
src/samtools-0.1.18/faidx.h | 103 +
src/samtools-0.1.18/kaln.c | 486 +++
src/samtools-0.1.18/kaln.h | 67 +
src/samtools-0.1.18/khash.h | 528 +++
src/samtools-0.1.18/klist.h | 96 +
src/samtools-0.1.18/knetfile.c | 632 ++++
src/samtools-0.1.18/knetfile.h | 75 +
src/samtools-0.1.18/kprobaln.c | 278 ++
src/samtools-0.1.18/kprobaln.h | 49 +
src/samtools-0.1.18/kseq.h | 224 ++
src/samtools-0.1.18/ksort.h | 281 ++
src/samtools-0.1.18/kstring.c | 212 ++
src/samtools-0.1.18/kstring.h | 117 +
src/samtools-0.1.18/phase.c | 687 ++++
src/samtools-0.1.18/razf.c | 853 +++++
src/samtools-0.1.18/razf.h | 134 +
src/samtools-0.1.18/razip.c | 141 +
src/samtools-0.1.18/sam.c | 179 +
src/samtools-0.1.18/sam.h | 98 +
src/samtools-0.1.18/sam_header.c | 736 ++++
src/samtools-0.1.18/sam_header.h | 24 +
src/samtools-0.1.18/sam_view.c | 406 ++
src/samtools-0.1.18/sample.c | 107 +
src/samtools-0.1.18/sample.h | 17 +
src/samtools-0.1.18/samtools.1 | 994 +++++
src/segment_juncs.cpp | 143 +-
src/tophat-fusion-post | 2 +-
src/tophat.py | 21 +-
src/tophat_reports.cpp | 8 +-
114 files changed, 30194 insertions(+), 2101 deletions(-)
diff --git a/AUTHORS b/AUTHORS
index 4d05852..5b5292e 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,15 +1,24 @@
-TopHat authors
-Primary contact <cole at cs.umd.edu>
+TopHat Authors
-Cole Trapnell wrote TopHat. TopHat is built on Bowtie, which was written by
-Ben Langmead and Cole Trapnell. Daehwan Kim and Geo Pertea added support
-for SOLiD reads, Bowtie 2 and other features and improvements. The SeqAn-1.2 library is used
-in TopHat and Bowtie and some of its sources are included in TopHat source releases; its
-authors are Andreas Doring, David Weese, Tobias Rausch, and Knut Reinert.
+Contact:
+ tophat.cufflinks at gmail.com
+
+Cole Trapnell wrote the original TopHat program. TopHat is built on Bowtie,
+ which was written by Ben Langmead and Cole Trapnell.
+Daehwan Kim and Geo Pertea added support for SOLiD reads, Bowtie 2 and many
+ other features and improvements leading to the release of TopHat2, of which
+ they are the current maintainers.
-Websites:
- TopHat: http://tophat.cbcb.umd.edu
- Bowtie: http://bowtie-bio.sf.net
- SeqAn: http://www.seqan.de
+SAMtools version 0.1.18 is used in TopHat2 and its sources are included in
+ TopHat2's source release starting with version 2.0.13; SAMtools 0.1.18 was
+ written primarily by Heng Li and Bob Handsaker.
+
+The SeqAn-1.3 library is used in TopHat and some of its sources are included
+ in TopHat source releases; its authors are Andreas Doring, David Weese,
+ Tobias Rausch, and Knut Reinert.
-October 2010
+Websites:
+ TopHat: http://ccb.jhu.edu/software/tophat
+ Bowtie: http://bowtie-bio.sourceforge.net/bowtie2
+ Samtools: http://samtools.sourceforge.net
+ SeqAn: http://www.seqan.de
diff --git a/COPYING b/COPYING
index 7cb8b7b..31a6350 100644
--- a/COPYING
+++ b/COPYING
@@ -111,4 +111,3 @@ The End
This license is approved by the Open Source Initiative
(www.opensource.org) for certifying software as OSI Certified Open
Source.
-
diff --git a/Makefile.am b/Makefile.am
index 83cb1b8..a319a05 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,4 +1,3 @@
-
ALWAYS_BUILT = src
SUBDIRS = $(ALWAYS_BUILT)
DIST_SUBDIRS = $(ALWAYS_BUILT)
diff --git a/Makefile.in b/Makefile.in
index 45231eb..bcd296a 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -38,13 +38,11 @@ host_triplet = @host@
DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
$(srcdir)/Makefile.in $(srcdir)/config.h.in \
$(top_srcdir)/configure AUTHORS COPYING ChangeLog INSTALL NEWS \
- THANKS build-aux/config.guess build-aux/config.sub \
- build-aux/depcomp build-aux/install-sh build-aux/missing
+ THANKS config.guess config.sub depcomp install-sh missing
subdir = .
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/ax_boost_base.m4 \
- $(top_srcdir)/ax_boost_thread.m4 $(top_srcdir)/ax_bam.m4 \
- $(top_srcdir)/configure.ac
+ $(top_srcdir)/ax_boost_thread.m4 $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
@@ -86,14 +84,13 @@ BAM_LDFLAGS = @BAM_LDFLAGS@
BAM_LIB = @BAM_LIB@
BOOST_CPPFLAGS = @BOOST_CPPFLAGS@
BOOST_LDFLAGS = @BOOST_LDFLAGS@
-BOOST_SYSTEM_LIB = @BOOST_SYSTEM_LIB@
-BOOST_THREAD_LIB = @BOOST_THREAD_LIB@
+BOOST_THREAD_LIBS = @BOOST_THREAD_LIBS@
CC = @CC@
CCDEPMODE = @CCDEPMODE@
CFLAGS = @CFLAGS@
-CPP = @CPP@
CPPFLAGS = @CPPFLAGS@
CXX = @CXX@
+CXXCPP = @CXXCPP@
CXXDEPMODE = @CXXDEPMODE@
CXXFLAGS = @CXXFLAGS@
CYGPATH_W = @CYGPATH_W@
@@ -371,7 +368,6 @@ distclean-tags:
distdir: $(DISTFILES)
$(am__remove_distdir)
mkdir $(distdir)
- $(mkdir_p) $(distdir)/build-aux
@srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
list='$(DISTFILES)'; for file in $$list; do \
@@ -459,7 +455,7 @@ distcheck: dist
*.zip*) \
unzip $(distdir).zip ;;\
esac
- chmod -R a-w $(distdir); chmod a+w $(distdir)
+ chmod -R a-w $(distdir); chmod u+w $(distdir)
mkdir $(distdir)/_build
mkdir $(distdir)/_inst
chmod a-w $(distdir)
diff --git a/README b/README
index f7ce76a..58a8e9f 100644
--- a/README
+++ b/README
@@ -8,25 +8,12 @@ Johns Hopkins University, the Department of Mathematics at the University of
California, Berkeley, and the Department of Stem Cell and Regenerative Biology
at Harvard University.
-See http://tophat.cbcb.umd.edu for more information.
+Please see http://ccb.jhu.edu/software/tophat for more information.
-Notes on compiling the package from source:
--------------------------------------------
-TopHat requires the Samtools package (http://samtools.sourceforge.net/)
-in order to generate and handle the compressed, binary alignment files (BAM).
-The --with-bam=<bam_prefix> option of the configure script expects the
-following subdirectories and files:
-
-<bam_prefix>/include/bam/*.h (all the header files from Samtools)
-<bam_prefix>/lib/libbam.a (obtained by compiling Samtools)
-At the time of this writing the Samtools package does not have an
-install routine the user will have to explicitly create the above
-directory structure (./include/bam/ and ./lib) and copy the required
-Samtools files as indicated (the header files and libbam.a)
-
-TopHat also requires the Boost libraries (http://www.boost.org).
-Please refer to the TopHat webpage for installation information.
+Note on compiling the package from source:
+-------------------------------------------
-Note TopHat uses the SeqAn library that comes with the TopHat2 source code distribution.
-It is not necessary for the SeqAn library to be installed separately in order to run TopHat.
+TopHat requires the Boost libraries (http://www.boost.org).
+Please see http://ccb.jhu.edu/software/tophat/tutorial.shtml#boost
+for documentation about building TopHat2 from source
diff --git a/ax_bam.m4 b/ax_bam.m4
deleted file mode 100644
index 23bcc5c..0000000
--- a/ax_bam.m4
+++ /dev/null
@@ -1,203 +0,0 @@
-# SYNOPSIS
-#
-# AX_BAM
-#
-# DESCRIPTION
-#
-# Test for the BAM libraries of a particular version (or newer)
-#
-# If no path to the installed bam library is given the macro searchs
-# under /usr, /usr/local, /opt and /opt/local and evaluates the
-# $BAM_ROOT environment variable.
-# Adapted from AX_BOOST_BASE
-#
-# This macro calls:
-#
-# AC_SUBST(BAM_CPPFLAGS) / AC_SUBST(BAM_LDFLAGS)
-#
-# And sets:
-#
-# HAVE_BAM
-#
-# LICENSE
-#
-# Copyright (c) 2010 Cole Trapnell <cole at cs.umd.edu>
-#
-# Copying and distribution of this file, with or without modification, are
-# permitted in any medium without royalty provided the copyright notice
-# and this notice are preserved.
-
-AC_DEFUN([AX_BAM],
-[
-AC_ARG_WITH([bam],
- AS_HELP_STRING([--with-bam@<:@=DIR@:>@], [use BAM libraries (default is yes) - it is possible to specify the root directory for BAM (optional)]),
- [
- if test "$withval" = "no"; then
- want_bam="no"
- elif test "$withval" = "yes"; then
- want_bam="yes"
- ac_bam_path=""
- else
- want_bam="yes"
- ac_bam_path="$withval"
- fi
- ],
- [want_bam="yes"])
-
-
-AC_ARG_WITH([bam-libdir],
- AS_HELP_STRING([--with-bam-libdir=LIB_DIR],
- [Force given directory for bam libraries. Note that this will overwrite library path detection, so use this parameter only if default library detection fails and you know exactly where your bam libraries are located.]),
- [
- if test -d $withval
- then
- ac_bam_lib_path="$withval"
- else
- AC_MSG_ERROR(--with-bam-libdir expected directory name)
- fi
- ],
- [ac_bam_lib_path=""]
-)
-
-if test "x$want_bam" = "xyes"; then
-# bam_lib_version_req=ifelse([$1], ,1.20.0,$1)
-# bam_lib_version_req_shorten=`expr $bam_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
-# bam_lib_version_req_major=`expr $bam_lib_version_req : '\([[0-9]]*\)'`
-# bam_lib_version_req_minor=`expr $bam_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
-# bam_lib_version_req_sub_minor=`expr $bam_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
-# if test "x$bam_lib_version_req_sub_minor" = "x" ; then
-# bam_lib_version_req_sub_minor="0"
-# fi
-# WANT_BAM_VERSION=`expr $bam_lib_version_req_major \* 100000 \+ $bam_lib_version_req_minor \* 100 \+ $bam_lib_version_req_sub_minor`
- AC_MSG_CHECKING(for bamlib)
- succeeded=no
-
- dnl first we check the system location for bam libraries
- if test "$ac_bam_path" != ""; then
- BAM_LDFLAGS="-L$ac_bam_path/lib"
- BAM_CPPFLAGS="-I$ac_bam_path/include"
- else
- for ac_bam_path_tmp in /usr /usr/local /opt /opt/local ; do
- if test -d "$ac_bam_path_tmp/include/bam" && test -r "$ac_bam_path_tmp/include/bam"; then
- BAM_LDFLAGS="-L$ac_bam_path_tmp/lib"
- BAM_CPPFLAGS="-I$ac_bam_path_tmp/include"
- break;
- fi
- done
- fi
-
- dnl overwrite ld flags if we have required special directory with
- dnl --with-bam-libdir parameter
- if test "$ac_bam_lib_path" != ""; then
- BAM_LDFLAGS="-L$ac_bam_lib_path"
- fi
-
- CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BAM_CPPFLAGS"
- export CPPFLAGS
-
- LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BAM_LDFLAGS"
- export LDFLAGS
-
- AC_LANG_PUSH(C++)
- AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <bam/bam.h>
- ]], [[
- ]])],[
- AC_MSG_RESULT(yes)
- succeeded=yes
- found_system=yes
- ],[
- ])
- AC_LANG_POP([C++])
-
- dnl if we found no bam with system layout we search for bam libraries
- dnl built and installed without the --layout=system option or for a staged(not installed) version
- if test "x$succeeded" != "xyes"; then
- _version=0
- if test "$ac_bam_path" != ""; then
- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
- for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
- _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
- V_CHECK=`expr $_version_tmp \> $_version`
- if test "$V_CHECK" = "1" ; then
- _version=$_version_tmp
- fi
- VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
- BAM_CPPFLAGS="-I$ac_bam_path/include/bam-$VERSION_UNDERSCORE"
- done
- fi
- else
- for ac_bam_path in /usr /usr/local /opt /opt/local ; do
- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
- for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
- _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
- V_CHECK=`expr $_version_tmp \> $_version`
- if test "$V_CHECK" = "1" ; then
- _version=$_version_tmp
- best_path=$ac_bam_path
- fi
- done
- fi
- done
-
- VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
- BAM_CPPFLAGS="-I$best_path/include/bam-$VERSION_UNDERSCORE"
- if test "$ac_bam_lib_path" = ""
- then
- BAM_LDFLAGS="-L$best_path/lib"
- fi
-
- if test "x$BAM_ROOT" != "x"; then
- if test -d "$BAM_ROOT" && test -r "$BAM_ROOT" && test -d "$BAM_ROOT/stage/lib" && test -r "$BAM_ROOT/stage/lib"; then
- version_dir=`expr //$BAM_ROOT : '.*/\(.*\)'`
- stage_version=`echo $version_dir | sed 's/bam_//' | sed 's/_/./g'`
- stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
- V_CHECK=`expr $stage_version_shorten \>\= $_version`
- if test "$V_CHECK" = "1" -a "$ac_bam_lib_path" = "" ; then
- AC_MSG_NOTICE(We will use a staged bam library from $BAM_ROOT)
- BAM_CPPFLAGS="-I$BAM_ROOT"
- BAM_LDFLAGS="-L$BAM_ROOT/stage/lib"
- fi
- fi
- fi
- fi
-
- CPPFLAGS="$CPPFLAGS $BAM_CPPFLAGS"
- export CPPFLAGS
- LDFLAGS="$LDFLAGS $BAM_LDFLAGS"
- export LDFLAGS
-
- AC_LANG_PUSH(C++)
- AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <bam/version.hpp>
- ]], [[
- ]])],[
- AC_MSG_RESULT(yes)
- succeeded=yes
- found_system=yes
- ],[
- ])
- AC_LANG_POP([C++])
- fi
-
- if test "$succeeded" != "yes" ; then
- if test "$_version" = "0" ; then
- AC_MSG_ERROR([[We could not detect the bam libraries (version $bam_lib_version_req_shorten or higher). If you have a staged bam library (still not installed) please specify \$BAM_ROOT in your environment and do not give a PATH to --with-bam option.]])
- else
- AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
- fi
- else
- BAM_LIB="-lbam"
- AC_SUBST(BAM_CPPFLAGS)
- AC_SUBST(BAM_LDFLAGS)
- AC_SUBST(BAM_LIB)
- AC_DEFINE(HAVE_BAM,,[define if the BAM library is available])
- fi
-
- CPPFLAGS="$CPPFLAGS_SAVED"
- LDFLAGS="$LDFLAGS_SAVED"
-fi
-
-])
diff --git a/ax_boost_thread.m4 b/ax_boost_thread.m4
index 9a3a36e..30cc340 100644
--- a/ax_boost_thread.m4
+++ b/ax_boost_thread.m4
@@ -1,169 +1,97 @@
-# ===========================================================================
-# http://autoconf-archive.cryp.to/ax_boost_thread.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-# AX_BOOST_THREAD
-#
-# DESCRIPTION
-#
-# Test for Thread library from the Boost C++ libraries. The macro requires
-# a preceding call to AX_BOOST_BASE. Further documentation is available at
-# <http://randspringer.de/boost/index.html>.
-#
-# This macro calls:
-#
-# AC_SUBST(BOOST_THREAD_LIB)
-# AC_SUBST(BOOST_SYSTEM_LIB)
-#
-# And sets:
-#
-# HAVE_BOOST_THREAD
-#
-# LICENSE
-#
-# Copyright (c) 2009 Thomas Porschberg <thomas at randspringer.de>
-# Copyright (c) 2009 Michael Tindal
-#
-# Copying and distribution of this file, with or without modification, are
-# permitted in any medium without royalty provided the copyright notice
-# and this notice are preserved.
+dnl @synopsis AX_BOOST_THREAD
+dnl
+dnl This macro checks to see if the Boost.Thread library is installed.
+dnl It also attempts to guess the currect library name using several
+dnl attempts. It tries to build the library name using a user supplied
+dnl name or suffix and then just the raw library.
+dnl
+dnl If the library is found, HAVE_BOOST_THREAD is defined and
+dnl BOOST_THREAD_LIBS is set to the name of the library.
+dnl
+dnl This macro calls AC_SUBST(BOOST_THREAD_LIBS).
+dnl
+dnl @category InstalledPackages
+dnl @author Michael Tindal <mtindal at paradoxpoint.com>
+dnl @version 2004-09-20
+dnl @license GPLWithACException
AC_DEFUN([AX_BOOST_THREAD],
-[
- AC_ARG_WITH([boost-thread],
- AS_HELP_STRING([--with-boost-thread@<:@=special-lib@:>@],
- [use the Thread library from boost - it is possible to specify a certain library for the linker
- e.g. --with-boost-thread=boost_thread-gcc-mt ]),
- [
- if test "$withval" = "no"; then
- want_boost="no"
- elif test "$withval" = "yes"; then
- want_boost="yes"
- ax_boost_user_thread_lib=""
- ax_booth_user_system_lib=""
- else
- want_boost="yes"
- echo "using $withval"
- ax_boost_user_thread_lib="$withval"
- fi
- ],
- [want_boost="yes"]
- )
-
- if test "x$want_boost" = "xyes"; then
- AC_REQUIRE([AC_PROG_CC])
- AC_REQUIRE([AC_CANONICAL_BUILD])
- CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
- export CPPFLAGS
-
- LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
- export LDFLAGS
-
- AC_CACHE_CHECK(whether the Boost::Thread library is available,
- ax_cv_boost_thread,
- [AC_LANG_PUSH([C++])
- CXXFLAGS_SAVE=$CXXFLAGS
-
- if test "x$build_os" = "xsolaris" ; then
- CXXFLAGS="-pthreads $CXXFLAGS"
- elif test "x$build_os" = "xming32" ; then
- CXXFLAGS="-mthreads $CXXFLAGS"
- else
- CXXFLAGS="-pthread $CXXFLAGS"
- fi
- AC_COMPILE_IFELSE(AC_LANG_PROGRAM([[@%:@include <boost/thread/thread.hpp>]],
- [[boost::thread_group thrds;
- return 0;]]),
- ax_cv_boost_thread=yes, ax_cv_boost_thread=no)
- CXXFLAGS=$CXXFLAGS_SAVE
- AC_LANG_POP([C++])
- ])
- if test "x$ax_cv_boost_thread" = "xyes"; then
- if test "x$build_os" = "xsolaris" ; then
- BOOST_CPPFLAGS="-pthreads $BOOST_CPPFLAGS"
- elif test "x$build_os" = "xming32" ; then
- BOOST_CPPFLAGS="-mthreads $BOOST_CPPFLAGS"
- else
- BOOST_CPPFLAGS="-pthread $BOOST_CPPFLAGS"
- fi
-
- AC_SUBST(BOOST_CPPFLAGS)
+[AC_CACHE_CHECK(whether the compiler implements namespaces,
+ac_cv_cxx_namespaces,
+[AC_LANG_SAVE
+ AC_LANG_CPLUSPLUS
+ AC_TRY_COMPILE([namespace Outer { namespace Inner { int i = 0; }}],
+ [using namespace Outer::Inner; return i;],
+ ac_cv_cxx_namespaces=yes, ac_cv_cxx_namespaces=no)
+ AC_LANG_RESTORE
+])
+if test "$ac_cv_cxx_namespaces" = yes; then
+ AC_DEFINE(HAVE_NAMESPACES,,[define if the compiler implements namespaces])
+fi
- AC_DEFINE(HAVE_BOOST_THREAD,,[define if the Boost::Thread library is available])
- BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/@<:@^\/@:>@*//'`
+AC_LANG_SAVE
+AC_LANG_CPLUSPLUS
+CXXFLAGS_SAVE=$CXXFLAGS
+LIBS_SAVE=$LIBS
+dnl FIXME: need to include a generic way to check for the flag
+dnl to turn on threading support.
- LDFLAGS_SAVE=$LDFLAGS
- case "x$build_os" in
- *bsd* )
- LDFLAGS="-pthread $LDFLAGS"
- break;
- ;;
- esac
- if test "x$ax_boost_user_thread_lib" = "x"; then
- for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- AC_CHECK_LIB($ax_lib, exit,
- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
- [link_thread="no"])
- done
- if test "x$link_thread" != "xyes"; then
- for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do
- ax_lib=${libextension}
- AC_CHECK_LIB($ax_lib, exit,
- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
- [link_thread="no"])
- done
- fi
+CPPFLAGS_SAVED="$CPPFLAGS"
+CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+export CPPFLAGS
+LDFLAGS_SAVED="$LDFLAGS"
+LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+export LDFLAGS
- else
- BOOST_THREAD_LIB="$ax_boost_user_thread_lib";
- AC_SUBST(BOOST_THREAD_LIB)
- link_thread="yes";
-
+CXXFLAGS="-pthread $CXXFLAGS"
- fi
- if test "x$link_thread" = "xno"; then
- AC_MSG_ERROR(Could not link against $ax_lib !)
- else
- case "x$build_os" in
- *bsd* )
- BOOST_LDFLAGS="-pthread $BOOST_LDFLAGS"
- break;
- ;;
- esac
+AC_CACHE_CHECK(whether the Boost::Thread library is available,
+ax_cv_boost_thread,
+[AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <boost/thread/thread.hpp>]],
+ [[boost::thread_group thrds; return 0;]])],
+ ax_cv_boost_thread=yes, ax_cv_boost_thread=no)
+])
- fi
-
- if test "x$ax_boost_user_system_lib" = "x"; then
- for libextension in `ls $BOOSTLIBDIR/libboost_system*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- AC_CHECK_LIB($ax_lib, exit,
- [BOOST_SYSTEM_LIB="-l$ax_lib"; AC_SUBST(BOOST_SYSTEM_LIB) link_system="yes"; break],
- [link_system="no"])
- done
- if test "x$link_system" != "xyes"; then
- for libextension in `ls $BOOSTLIBDIR/boost_system*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.a*$;\1;'` ; do
- ax_lib=${libextension}
- AC_CHECK_LIB($ax_lib, exit,
- [BOOST_SYSTEM_LIB="-l$ax_lib"; AC_SUBST(BOOST_SYSTEM_LIB) link_system="yes"; break],
- [link_system="no"])
- done
- fi
+if test "$ax_cv_boost_thread" = yes; then
- else
- BOOST_SYSTEM_LIB="$ax_boost_user_system_lib";
- AC_SUBST(BOOST_SYSTEM_LIB)
- link_system="yes";
-
+ BOOST_CPPFLAGS="-pthread $BOOST_CPPFLAGS"
+ AC_SUBST(BOOST_CPPFLAGS)
+
+ AC_DEFINE(HAVE_BOOST_THREAD,,[define if the Boost::Thread library is available])
+ dnl Now determine the appropriate file names
+ AC_ARG_WITH([boost-thread],AS_HELP_STRING([--with-boost-thread],
+ [specify the boost thread library suffix to use]),
+ [if test "x$with_boost_thread" != "xno"; then
+ ax_boost_thread_lib=boost_thread$with_boost_thread
+ fi])
+ for ax_lib in $ax_boost_thread_lib boost_thread boost_thread-mt; do
+ AC_CHECK_LIB($ax_lib, main, [BOOST_THREAD_LIBS=-l$ax_lib; break])
+ done
- fi
- fi
+ # in recent Boost versions, boost::thread depends on boost::system
+ AC_CACHE_CHECK(whether Boost::Thread needs Boost::System library,
+ ax_cv_boost_thread_system,
+ [LIBS="$LIBS $BOOST_THREAD_LIBS"
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <boost/thread/thread.hpp>]],
+ [[boost::thread_group thrds; return 0;]])],
+ [ax_cv_boost_thread_system=no],
+ [LIBS="$LIBS $BOOST_THREAD_LIBS -lboost_system$with_boost_thread"
+ AC_LINK_IFELSE([
+ AC_LANG_PROGRAM([[#include <boost/thread/thread.hpp>]],
+ [[boost::thread_group thrds; return 0;]])
+ ],
+ [BOOST_THREAD_LIBS="$BOOST_THREAD_LIBS -lboost_system$with_boost_thread"
+ ax_cv_boost_thread_system=yes],
+ [AC_ERROR([Cannot use Boost::Thread])]
+ )])
+ ])
+
+ CXXFLAGS=$CXXFLAGS_SAVE
+ LIBS=$LIBS_SAVE
+ AC_LANG_RESTORE
- CPPFLAGS="$CPPFLAGS_SAVED"
- LDFLAGS="$LDFLAGS_SAVED"
- fi
-])
+ AC_SUBST(BOOST_THREAD_LIBS)
+fi
+CPPFLAGS="$CPPFLAGS_SAVED"
+LDFLAGS="$LDFLAGS_SAVED"
+])dnl
diff --git a/build-aux/config.guess b/config.guess
similarity index 100%
rename from build-aux/config.guess
rename to config.guess
diff --git a/config.h.in b/config.h.in
index 0fd4ad4..693eccf 100644
--- a/config.h.in
+++ b/config.h.in
@@ -1,8 +1,5 @@
/* config.h.in. Generated from configure.ac by autoheader. */
-/* define if the BAM library is available */
-#undef HAVE_BAM
-
/* define if the Boost library is available */
#undef HAVE_BOOST
@@ -25,6 +22,9 @@
/* Define to 1 if you have the `memset' function. */
#undef HAVE_MEMSET
+/* define if the compiler implements namespaces */
+#undef HAVE_NAMESPACES
+
/* Define to 1 if the system has the type `ptrdiff_t'. */
#undef HAVE_PTRDIFF_T
diff --git a/build-aux/config.sub b/config.sub
similarity index 100%
rename from build-aux/config.sub
rename to config.sub
diff --git a/configure b/configure
index 05fb885..9cb7b48 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.59 for tophat 2.0.12.
+# Generated by GNU Autoconf 2.59 for tophat 2.0.13.
#
# Report bugs to <tophat.cufflinks at gmail.com>.
#
@@ -269,8 +269,8 @@ SHELL=${CONFIG_SHELL-/bin/sh}
# Identity of this package.
PACKAGE_NAME='tophat'
PACKAGE_TARNAME='tophat'
-PACKAGE_VERSION='2.0.12'
-PACKAGE_STRING='tophat 2.0.12'
+PACKAGE_VERSION='2.0.13'
+PACKAGE_STRING='tophat 2.0.13'
PACKAGE_BUGREPORT='tophat.cufflinks at gmail.com'
ac_unique_file="config.h.in"
@@ -311,7 +311,7 @@ ac_includes_default="\
# include <unistd.h>
#endif"
-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INS [...]
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INS [...]
ac_subst_files=''
# Initialize some variables set by options.
@@ -780,10 +780,10 @@ ac_env_CFLAGS_set=${CFLAGS+set}
ac_env_CFLAGS_value=$CFLAGS
ac_cv_env_CFLAGS_set=${CFLAGS+set}
ac_cv_env_CFLAGS_value=$CFLAGS
-ac_env_CPP_set=${CPP+set}
-ac_env_CPP_value=$CPP
-ac_cv_env_CPP_set=${CPP+set}
-ac_cv_env_CPP_value=$CPP
+ac_env_CXXCPP_set=${CXXCPP+set}
+ac_env_CXXCPP_value=$CXXCPP
+ac_cv_env_CXXCPP_set=${CXXCPP+set}
+ac_cv_env_CXXCPP_value=$CXXCPP
#
# Report the --help message.
@@ -792,7 +792,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures tophat 2.0.12 to adapt to many kinds of systems.
+\`configure' configures tophat 2.0.13 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -858,7 +858,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of tophat 2.0.12:";;
+ short | recursive ) echo "Configuration of tophat 2.0.13:";;
esac
cat <<\_ACEOF
@@ -885,18 +885,7 @@ Optional Packages:
this parameter only if default library detection
fails and you know exactly where your boost
libraries are located.
- --with-bam[=DIR] use BAM libraries (default is yes) - it is possible
- to specify the root directory for BAM (optional)
- --with-bam-libdir=LIB_DIR
- Force given directory for bam libraries. Note that
- this will overwrite library path detection, so use
- this parameter only if default library detection
- fails and you know exactly where your bam libraries
- are located.
- --with-boost-thread[=special-lib]
- use the Thread library from boost - it is possible
- to specify a certain library for the linker e.g.
- --with-boost-thread=boost_thread-gcc-mt
+ --with-boost-thread specify the boost thread library suffix to use
Some influential environment variables:
PYTHON python program
@@ -908,7 +897,7 @@ Some influential environment variables:
headers in a nonstandard directory <include dir>
CC C compiler command
CFLAGS C compiler flags
- CPP C preprocessor
+ CXXCPP C++ preprocessor
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
@@ -1009,7 +998,7 @@ fi
test -n "$ac_init_help" && exit 0
if $ac_init_version; then
cat <<\_ACEOF
-tophat configure 2.0.12
+tophat configure 2.0.13
generated by GNU Autoconf 2.59
Copyright (C) 2003 Free Software Foundation, Inc.
@@ -1023,7 +1012,7 @@ cat >&5 <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by tophat $as_me 2.0.12, which was
+It was created by tophat $as_me 2.0.13, which was
generated by GNU Autoconf 2.59. Invocation command line was
$ $0 $@
@@ -1361,15 +1350,17 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
cat >>confdefs.h <<\_ACEOF
-#define SVN_REVISION "4238:4275M"
+#define SVN_REVISION "4306M"
_ACEOF
ac_config_headers="$ac_config_headers config.h"
+# AC_CONFIG_AUX_DIR([build-aux])
+am__api_version="1.9"
ac_aux_dir=
-for ac_dir in build-aux $srcdir/build-aux; do
+for ac_dir in $srcdir $srcdir/.. $srcdir/../..; do
if test -f $ac_dir/install-sh; then
ac_aux_dir=$ac_dir
ac_install_sh="$ac_aux_dir/install-sh -c"
@@ -1385,15 +1376,14 @@ for ac_dir in build-aux $srcdir/build-aux; do
fi
done
if test -z "$ac_aux_dir"; then
- { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in build-aux $srcdir/build-aux" >&5
-echo "$as_me: error: cannot find install-sh or install.sh in build-aux $srcdir/build-aux" >&2;}
+ { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&5
+echo "$as_me: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&2;}
{ (exit 1); exit 1; }; }
fi
ac_config_guess="$SHELL $ac_aux_dir/config.guess"
ac_config_sub="$SHELL $ac_aux_dir/config.sub"
ac_configure="$SHELL $ac_aux_dir/configure" # This should be Cygnus configure.
-am__api_version="1.9"
# Find a good install program. We prefer a C program (faster),
# so one script is as good as another. But avoid the broken or
# incompatible versions:
@@ -1675,7 +1665,7 @@ fi
# Define the identity of the package.
PACKAGE='tophat'
- VERSION='2.0.12'
+ VERSION='2.0.13'
cat >>confdefs.h <<_ACEOF
@@ -1806,62 +1796,11 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
-#AM_PATH_CPPUNIT(1.10.2)
-
- # Make sure CXXFLAGS is defined so that AC_PROG_CXX doesn't set it.
+# Make sure CXXFLAGS is defined so that AC_PROG_CXX doesn't set it.
CXXFLAGS="$CXXFLAGS"
CFLAGS="$CFLAGS"
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-# Checks for programs.
-for ac_prog in gawk mawk nawk awk
-do
- # Extract the first word of "$ac_prog", so it can be a program name with args.
-set dummy $ac_prog; ac_word=$2
-echo "$as_me:$LINENO: checking for $ac_word" >&5
-echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_AWK+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- if test -n "$AWK"; then
- ac_cv_prog_AWK="$AWK" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_AWK="$ac_prog"
- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
-done
-
-fi
-fi
-AWK=$ac_cv_prog_AWK
-if test -n "$AWK"; then
- echo "$as_me:$LINENO: result: $AWK" >&5
-echo "${ECHO_T}$AWK" >&6
-else
- echo "$as_me:$LINENO: result: no" >&5
-echo "${ECHO_T}no" >&6
-fi
-
- test -n "$AWK" && break
-done
-
ac_ext=cc
ac_cpp='$CXXCPP $CPPFLAGS'
ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -2592,59 +2531,29 @@ else
fi
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
-set dummy ${ac_tool_prefix}gcc; ac_word=$2
-echo "$as_me:$LINENO: checking for $ac_word" >&5
-echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_CC+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_CC="${ac_tool_prefix}gcc"
- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
-done
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-fi
-fi
-CC=$ac_cv_prog_CC
-if test -n "$CC"; then
- echo "$as_me:$LINENO: result: $CC" >&5
-echo "${ECHO_T}$CC" >&6
-else
- echo "$as_me:$LINENO: result: no" >&5
-echo "${ECHO_T}no" >&6
-fi
-fi
-if test -z "$ac_cv_prog_CC"; then
- ac_ct_CC=$CC
- # Extract the first word of "gcc", so it can be a program name with args.
-set dummy gcc; ac_word=$2
+# AC_LANG([C])
+
+
+
+# Checks for programs.
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+if test "${ac_cv_prog_AWK+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- if test -n "$ac_ct_CC"; then
- ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
@@ -2653,7 +2562,7 @@ do
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_ac_ct_CC="gcc"
+ ac_cv_prog_AWK="$ac_prog"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
@@ -2662,31 +2571,35 @@ done
fi
fi
-ac_ct_CC=$ac_cv_prog_ac_ct_CC
-if test -n "$ac_ct_CC"; then
- echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
-echo "${ECHO_T}$ac_ct_CC" >&6
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ echo "$as_me:$LINENO: result: $AWK" >&5
+echo "${ECHO_T}$AWK" >&6
else
echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6
fi
- CC=$ac_ct_CC
-else
- CC="$ac_cv_prog_CC"
-fi
+ test -n "$AWK" && break
+done
-if test -z "$CC"; then
- if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
-set dummy ${ac_tool_prefix}cc; ac_word=$2
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_CC+set}" = set; then
+if test "${ac_cv_prog_CXX+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
@@ -2695,7 +2608,7 @@ do
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_CC="${ac_tool_prefix}cc"
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
@@ -2704,27 +2617,31 @@ done
fi
fi
-CC=$ac_cv_prog_CC
-if test -n "$CC"; then
- echo "$as_me:$LINENO: result: $CC" >&5
-echo "${ECHO_T}$CC" >&6
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ echo "$as_me:$LINENO: result: $CXX" >&5
+echo "${ECHO_T}$CXX" >&6
else
echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6
fi
+ test -n "$CXX" && break
+ done
fi
-if test -z "$ac_cv_prog_CC"; then
- ac_ct_CC=$CC
- # Extract the first word of "cc", so it can be a program name with args.
-set dummy cc; ac_word=$2
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- if test -n "$ac_ct_CC"; then
- ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
@@ -2733,7 +2650,7 @@ do
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_ac_ct_CC="cc"
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
@@ -2742,174 +2659,26 @@ done
fi
fi
-ac_ct_CC=$ac_cv_prog_ac_ct_CC
-if test -n "$ac_ct_CC"; then
- echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
-echo "${ECHO_T}$ac_ct_CC" >&6
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5
+echo "${ECHO_T}$ac_ct_CXX" >&6
else
echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6
fi
- CC=$ac_ct_CC
-else
- CC="$ac_cv_prog_CC"
-fi
-
-fi
-if test -z "$CC"; then
- # Extract the first word of "cc", so it can be a program name with args.
-set dummy cc; ac_word=$2
-echo "$as_me:$LINENO: checking for $ac_word" >&5
-echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_CC+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-else
- ac_prog_rejected=no
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
- ac_prog_rejected=yes
- continue
- fi
- ac_cv_prog_CC="cc"
- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
+ test -n "$ac_ct_CXX" && break
done
+test -n "$ac_ct_CXX" || ac_ct_CXX="g++"
-if test $ac_prog_rejected = yes; then
- # We found a bogon in the path, so make sure we never use it.
- set dummy $ac_cv_prog_CC
- shift
- if test $# != 0; then
- # We chose a different compiler from the bogus one.
- # However, it has the same basename, so the bogon will be chosen
- # first if we set CC to just the basename; use the full file name.
- shift
- ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
- fi
-fi
-fi
-fi
-CC=$ac_cv_prog_CC
-if test -n "$CC"; then
- echo "$as_me:$LINENO: result: $CC" >&5
-echo "${ECHO_T}$CC" >&6
-else
- echo "$as_me:$LINENO: result: no" >&5
-echo "${ECHO_T}no" >&6
+ CXX=$ac_ct_CXX
fi
-fi
-if test -z "$CC"; then
- if test -n "$ac_tool_prefix"; then
- for ac_prog in cl
- do
- # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
-set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-echo "$as_me:$LINENO: checking for $ac_word" >&5
-echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_CC+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- if test -n "$CC"; then
- ac_cv_prog_CC="$CC" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
-done
-
-fi
-fi
-CC=$ac_cv_prog_CC
-if test -n "$CC"; then
- echo "$as_me:$LINENO: result: $CC" >&5
-echo "${ECHO_T}$CC" >&6
-else
- echo "$as_me:$LINENO: result: no" >&5
-echo "${ECHO_T}no" >&6
-fi
-
- test -n "$CC" && break
- done
-fi
-if test -z "$CC"; then
- ac_ct_CC=$CC
- for ac_prog in cl
-do
- # Extract the first word of "$ac_prog", so it can be a program name with args.
-set dummy $ac_prog; ac_word=$2
-echo "$as_me:$LINENO: checking for $ac_word" >&5
-echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- if test -n "$ac_ct_CC"; then
- ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_ac_ct_CC="$ac_prog"
- echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
-done
-
-fi
-fi
-ac_ct_CC=$ac_cv_prog_ac_ct_CC
-if test -n "$ac_ct_CC"; then
- echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
-echo "${ECHO_T}$ac_ct_CC" >&6
-else
- echo "$as_me:$LINENO: result: no" >&5
-echo "${ECHO_T}no" >&6
-fi
-
- test -n "$ac_ct_CC" && break
-done
-
- CC=$ac_ct_CC
-fi
-
-fi
-
-
-test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
-See \`config.log' for more details." >&5
-echo "$as_me: error: no acceptable C compiler found in \$PATH
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }
# Provide some information about the compiler.
echo "$as_me:$LINENO:" \
- "checking for C compiler version" >&5
+ "checking for C++ compiler version" >&5
ac_compiler=`set X $ac_compile; echo $2`
{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
(eval $ac_compiler --version </dev/null >&5) 2>&5
@@ -2927,9 +2696,9 @@ ac_compiler=`set X $ac_compile; echo $2`
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }
-echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
-echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6
-if test "${ac_cv_c_compiler_gnu+set}" = set; then
+echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5
+echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
cat >conftest.$ac_ext <<_ACEOF
@@ -2959,7 +2728,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -2980,18 +2749,18 @@ sed 's/^/| /' conftest.$ac_ext >&5
ac_compiler_gnu=no
fi
rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
-ac_cv_c_compiler_gnu=$ac_compiler_gnu
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
fi
-echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
-echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6
-GCC=`test $ac_compiler_gnu = yes && echo yes`
-ac_test_CFLAGS=${CFLAGS+set}
-ac_save_CFLAGS=$CFLAGS
-CFLAGS="-g"
-echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
-echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6
-if test "${ac_cv_prog_cc_g+set}" = set; then
+echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5
+echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6
+GXX=`test $ac_compiler_gnu = yes && echo yes`
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+CXXFLAGS="-g"
+echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5
+echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6
+if test "${ac_cv_prog_cxx_g+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
cat >conftest.$ac_ext <<_ACEOF
@@ -3018,7 +2787,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -3031,102 +2800,57 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ac_cv_prog_cc_g=yes
+ ac_cv_prog_cxx_g=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-ac_cv_prog_cc_g=no
+ac_cv_prog_cxx_g=no
fi
rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
-echo "${ECHO_T}$ac_cv_prog_cc_g" >&6
-if test "$ac_test_CFLAGS" = set; then
- CFLAGS=$ac_save_CFLAGS
-elif test $ac_cv_prog_cc_g = yes; then
- if test "$GCC" = yes; then
- CFLAGS="-g -O2"
+echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5
+echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
else
- CFLAGS="-g"
+ CXXFLAGS="-g"
fi
else
- if test "$GCC" = yes; then
- CFLAGS="-O2"
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
else
- CFLAGS=
+ CXXFLAGS=
fi
fi
-echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5
-echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6
-if test "${ac_cv_prog_cc_stdc+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- ac_cv_prog_cc_stdc=no
-ac_save_CC=$CC
-cat >conftest.$ac_ext <<_ACEOF
+for ac_declaration in \
+ '' \
+ 'extern "C" void std::exit (int) throw (); using std::exit;' \
+ 'extern "C" void std::exit (int); using std::exit;' \
+ 'extern "C" void exit (int) throw ();' \
+ 'extern "C" void exit (int);' \
+ 'void exit (int);'
+do
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdarg.h>
-#include <stdio.h>
-#include <sys/types.h>
-#include <sys/stat.h>
-/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
-struct buf { int x; };
-FILE * (*rcsopen) (struct buf *, struct stat *, int);
-static char *e (p, i)
- char **p;
- int i;
-{
- return p[i];
-}
-static char *f (char * (*g) (char **, int), char **p, ...)
-{
- char *s;
- va_list v;
- va_start (v,p);
- s = g (p, va_arg (v,int));
- va_end (v);
- return s;
-}
-
-/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
- function prototypes and stuff, but not '\xHH' hex character constants.
- These don't provoke an error unfortunately, instead are silently treated
- as 'x'. The following induces an error, until -std1 is added to get
- proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
- array size at least. It's necessary to write '\x00'==0 to get something
- that's true only with -std1. */
-int osf4_cc_array ['\x00' == 0 ? 1 : -1];
-
-int test (int i, double x);
-struct s1 {int (*f) (int a);};
-struct s2 {int (*f) (double a);};
-int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
-int argc;
-char **argv;
+$ac_declaration
+#include <stdlib.h>
int
main ()
{
-return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+exit (42);
;
return 0;
}
_ACEOF
-# Don't try gcc -ansi; that turns off useful extensions and
-# breaks some systems' header files.
-# AIX -qlanglvl=ansi
-# Ultrix and OSF/1 -std1
-# HP-UX 10.20 and later -Ae
-# HP-UX older versions -Aa -D_HPUX_SOURCE
-# SVR4 -Xc -D__EXTENSIONS__
-for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
-do
- CC="$ac_save_CC $ac_arg"
- rm -f conftest.$ac_objext
+rm -f conftest.$ac_objext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>conftest.er1
ac_status=$?
@@ -3135,7 +2859,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -3148,117 +2872,16 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ac_cv_prog_cc_stdc=$ac_arg
-break
+ :
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
+continue
fi
-rm -f conftest.err conftest.$ac_objext
-done
-rm -f conftest.$ac_ext conftest.$ac_objext
-CC=$ac_save_CC
-
-fi
-
-case "x$ac_cv_prog_cc_stdc" in
- x|xno)
- echo "$as_me:$LINENO: result: none needed" >&5
-echo "${ECHO_T}none needed" >&6 ;;
- *)
- echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5
-echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6
- CC="$CC $ac_cv_prog_cc_stdc" ;;
-esac
-
-# Some people use a C++ compiler to compile C. Since we use `exit',
-# in C++ we need to declare it. In case someone uses the same compiler
-# for both compiling C and C++ we need to have the C++ compiler decide
-# the declaration of exit, since it's the most demanding environment.
-cat >conftest.$ac_ext <<_ACEOF
-#ifndef __cplusplus
- choke me
-#endif
-_ACEOF
-rm -f conftest.$ac_objext
-if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
- (eval $ac_compile) 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
- || test ! -s conftest.err'
- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
- (eval $ac_try) 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; } &&
- { ac_try='test -s conftest.$ac_objext'
- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
- (eval $ac_try) 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- for ac_declaration in \
- '' \
- 'extern "C" void std::exit (int) throw (); using std::exit;' \
- 'extern "C" void std::exit (int); using std::exit;' \
- 'extern "C" void exit (int) throw ();' \
- 'extern "C" void exit (int);' \
- 'void exit (int);'
-do
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_declaration
-#include <stdlib.h>
-int
-main ()
-{
-exit (42);
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
- (eval $ac_compile) 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
- || test ! -s conftest.err'
- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
- (eval $ac_try) 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; } &&
- { ac_try='test -s conftest.$ac_objext'
- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
- (eval $ac_try) 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- :
-else
- echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-continue
-fi
-rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
@@ -3281,7 +2904,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -3309,23 +2932,17 @@ if test -n "$ac_declaration"; then
echo '#endif' >>confdefs.h
fi
-else
- echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-fi
-rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-depcc="$CC" am_compiler_list=
+depcc="$CXX" am_compiler_list=
echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6
-if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
@@ -3347,7 +2964,7 @@ else
# directory.
mkdir sub
- am_cv_CC_dependencies_compiler_type=none
+ am_cv_CXX_dependencies_compiler_type=none
if test "$am_compiler_list" = ""; then
am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
fi
@@ -3400,7 +3017,7 @@ else
# icc: Command line remark: option '-MP' not supported
if (grep 'ignoring option' conftest.err ||
grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
- am_cv_CC_dependencies_compiler_type=$depmode
+ am_cv_CXX_dependencies_compiler_type=$depmode
break
fi
fi
@@ -3409,66 +3026,80 @@ else
cd ..
rm -rf conftest.dir
else
- am_cv_CC_dependencies_compiler_type=none
+ am_cv_CXX_dependencies_compiler_type=none
fi
fi
-echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
-echo "${ECHO_T}$am_cv_CC_dependencies_compiler_type" >&6
-CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5
+echo "${ECHO_T}$am_cv_CXX_dependencies_compiler_type" >&6
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
if
test "x$enable_dependency_tracking" != xno \
- && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
- am__fastdepCC_TRUE=
- am__fastdepCC_FALSE='#'
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
else
- am__fastdepCC_TRUE='#'
- am__fastdepCC_FALSE=
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
fi
-echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
-echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6
-set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y,:./+-,___p_,'`
-if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\" = set"; then
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_CC+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- cat >conftest.make <<\_ACEOF
-all:
- @echo 'ac_maketemp="$(MAKE)"'
-_ACEOF
-# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
-eval `${MAKE-make} -f conftest.make 2>/dev/null | grep temp=`
-if test -n "$ac_maketemp"; then
- eval ac_cv_prog_make_${ac_make}_set=yes
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
else
- eval ac_cv_prog_make_${ac_make}_set=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
fi
-rm -f conftest.make
fi
-if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then
- echo "$as_me:$LINENO: result: yes" >&5
-echo "${ECHO_T}yes" >&6
- SET_MAKE=
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6
else
echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6
- SET_MAKE="MAKE=${MAKE-make}"
fi
-if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
-set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_RANLIB+set}" = set; then
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- if test -n "$RANLIB"; then
- ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
@@ -3477,7 +3108,7 @@ do
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+ ac_cv_prog_ac_ct_CC="gcc"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
@@ -3486,27 +3117,31 @@ done
fi
fi
-RANLIB=$ac_cv_prog_RANLIB
-if test -n "$RANLIB"; then
- echo "$as_me:$LINENO: result: $RANLIB" >&5
-echo "${ECHO_T}$RANLIB" >&6
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+echo "${ECHO_T}$ac_ct_CC" >&6
else
echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6
fi
+ CC=$ac_ct_CC
+else
+ CC="$ac_cv_prog_CC"
fi
-if test -z "$ac_cv_prog_RANLIB"; then
- ac_ct_RANLIB=$RANLIB
- # Extract the first word of "ranlib", so it can be a program name with args.
-set dummy ranlib; ac_word=$2
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then
+if test "${ac_cv_prog_CC+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- if test -n "$ac_ct_RANLIB"; then
- ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
@@ -3515,399 +3150,316 @@ do
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_prog_ac_ct_RANLIB="ranlib"
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
done
- test -z "$ac_cv_prog_ac_ct_RANLIB" && ac_cv_prog_ac_ct_RANLIB=":"
fi
fi
-ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
-if test -n "$ac_ct_RANLIB"; then
- echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5
-echo "${ECHO_T}$ac_ct_RANLIB" >&6
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6
else
echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6
fi
- RANLIB=$ac_ct_RANLIB
-else
- RANLIB="$ac_cv_prog_RANLIB"
fi
-
-# Find a good install program. We prefer a C program (faster),
-# so one script is as good as another. But avoid the broken or
-# incompatible versions:
-# SysV /etc/install, /usr/sbin/install
-# SunOS /usr/etc/install
-# IRIX /sbin/install
-# AIX /bin/install
-# AmigaOS /C/install, which installs bootblocks on floppy discs
-# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
-# AFS /usr/afsws/bin/install, which mishandles nonexistent args
-# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
-# OS/2's system install, which has a completely different semantic
-# ./install, which can be erroneously created by make from ./install.sh.
-echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
-echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6
-if test -z "$INSTALL"; then
-if test "${ac_cv_path_install+set}" = set; then
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- # Account for people who put trailing slashes in PATH elements.
-case $as_dir/ in
- ./ | .// | /cC/* | \
- /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
- ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
- /usr/ucb/* ) ;;
- *)
- # OSF1 and SCO ODT 3.0 have their own names for install.
- # Don't use installbsd from OSF since it installs stuff as root
- # by default.
- for ac_prog in ginstall scoinst install; do
- for ac_exec_ext in '' $ac_executable_extensions; do
- if $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then
- if test $ac_prog = install &&
- grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
- # AIX install. It has an incompatible calling convention.
- :
- elif test $ac_prog = install &&
- grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
- # program-specific install script used by HP pwplus--don't use.
- :
- else
- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
- break 3
- fi
- fi
- done
- done
- ;;
-esac
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_CC="cc"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
done
-
fi
- if test "${ac_cv_path_install+set}" = set; then
- INSTALL=$ac_cv_path_install
- else
- # As a last resort, use the slow shell script. We don't cache a
- # path for INSTALL within a source directory, because that will
- # break other packages using the cache if that directory is
- # removed, or if the path is relative.
- INSTALL=$ac_install_sh
- fi
fi
-echo "$as_me:$LINENO: result: $INSTALL" >&5
-echo "${ECHO_T}$INSTALL" >&6
-
-# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
-# It thinks the first close brace ends the variable substitution.
-test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
-
-test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
-
-test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
-
-
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+echo "${ECHO_T}$ac_ct_CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+ CC=$ac_ct_CC
+else
+ CC="$ac_cv_prog_CC"
+fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_CC+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
- if test -n "$PYTHON"; then
- # If the user set $PYTHON, use it and don't search something else.
- echo "$as_me:$LINENO: checking whether $PYTHON version >= 2.4" >&5
-echo $ECHO_N "checking whether $PYTHON version >= 2.4... $ECHO_C" >&6
- prog="import sys, string
-# split strings by '.' and convert to numeric. Append some zeros
-# because we need at least 4 digits for the hex conversion.
-minver = map(int, string.split('2.4', '.')) + [0, 0, 0]
-minverhex = 0
-for i in xrange(0, 4): minverhex = (minverhex << 8) + minver[i]
-sys.exit(sys.hexversion < minverhex)"
- if { echo "$as_me:$LINENO: $PYTHON -c "$prog"" >&5
- ($PYTHON -c "$prog") >&5 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; then
- echo "$as_me:$LINENO: result: yes" >&5
-echo "${ECHO_T}yes" >&6
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6
else
- { { echo "$as_me:$LINENO: error: too old" >&5
-echo "$as_me: error: too old" >&2;}
- { (exit 1); exit 1; }; }
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
fi
- am_display_PYTHON=$PYTHON
- else
- # Otherwise, try each interpreter until we find one that satisfies
- # VERSION.
- echo "$as_me:$LINENO: checking for a Python interpreter with version >= 2.4" >&5
-echo $ECHO_N "checking for a Python interpreter with version >= 2.4... $ECHO_C" >&6
-if test "${am_cv_pathless_PYTHON+set}" = set; then
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_CC+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
- for am_cv_pathless_PYTHON in python python2 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 python1.6 python1.5 none; do
- test "$am_cv_pathless_PYTHON" = none && break
- prog="import sys, string
-# split strings by '.' and convert to numeric. Append some zeros
-# because we need at least 4 digits for the hex conversion.
-minver = map(int, string.split('2.4', '.')) + [0, 0, 0]
-minverhex = 0
-for i in xrange(0, 4): minverhex = (minverhex << 8) + minver[i]
-sys.exit(sys.hexversion < minverhex)"
- if { echo "$as_me:$LINENO: $am_cv_pathless_PYTHON -c "$prog"" >&5
- ($am_cv_pathless_PYTHON -c "$prog") >&5 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; then
- break
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
fi
- done
+ test -n "$CC" && break
+ done
fi
-echo "$as_me:$LINENO: result: $am_cv_pathless_PYTHON" >&5
-echo "${ECHO_T}$am_cv_pathless_PYTHON" >&6
- # Set $PYTHON to the absolute path of $am_cv_pathless_PYTHON.
- if test "$am_cv_pathless_PYTHON" = none; then
- PYTHON=:
- else
- # Extract the first word of "$am_cv_pathless_PYTHON", so it can be a program name with args.
-set dummy $am_cv_pathless_PYTHON; ac_word=$2
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
echo "$as_me:$LINENO: checking for $ac_word" >&5
echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
-if test "${ac_cv_path_PYTHON+set}" = set; then
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- case $PYTHON in
- [\\/]* | ?:[\\/]*)
- ac_cv_path_PYTHON="$PYTHON" # Let the user override the test with a path.
- ;;
- *)
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_path_PYTHON="$as_dir/$ac_word$ac_exec_ext"
+ ac_cv_prog_ac_ct_CC="$ac_prog"
echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
done
- ;;
-esac
fi
-PYTHON=$ac_cv_path_PYTHON
-
-if test -n "$PYTHON"; then
- echo "$as_me:$LINENO: result: $PYTHON" >&5
-echo "${ECHO_T}$PYTHON" >&6
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+echo "${ECHO_T}$ac_ct_CC" >&6
else
echo "$as_me:$LINENO: result: no" >&5
echo "${ECHO_T}no" >&6
fi
- fi
- am_display_PYTHON=$am_cv_pathless_PYTHON
- fi
+ test -n "$ac_ct_CC" && break
+done
+ CC=$ac_ct_CC
+fi
- if test "$PYTHON" = :; then
- { { echo "$as_me:$LINENO: error: no suitable Python interpreter found" >&5
-echo "$as_me: error: no suitable Python interpreter found" >&2;}
- { (exit 1); exit 1; }; }
- else
+fi
- echo "$as_me:$LINENO: checking for $am_display_PYTHON version" >&5
-echo $ECHO_N "checking for $am_display_PYTHON version... $ECHO_C" >&6
-if test "${am_cv_python_version+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- am_cv_python_version=`$PYTHON -c "import sys; print sys.version[:3]"`
-fi
-echo "$as_me:$LINENO: result: $am_cv_python_version" >&5
-echo "${ECHO_T}$am_cv_python_version" >&6
- PYTHON_VERSION=$am_cv_python_version
-
-
-
- PYTHON_PREFIX='${prefix}'
-
- PYTHON_EXEC_PREFIX='${exec_prefix}'
-
+test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&5
+echo "$as_me: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }
+# Provide some information about the compiler.
+echo "$as_me:$LINENO:" \
+ "checking for C compiler version" >&5
+ac_compiler=`set X $ac_compile; echo $2`
+{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
+ (eval $ac_compiler --version </dev/null >&5) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v </dev/null >&5\"") >&5
+ (eval $ac_compiler -v </dev/null >&5) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V </dev/null >&5\"") >&5
+ (eval $ac_compiler -V </dev/null >&5) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
- echo "$as_me:$LINENO: checking for $am_display_PYTHON platform" >&5
-echo $ECHO_N "checking for $am_display_PYTHON platform... $ECHO_C" >&6
-if test "${am_cv_python_platform+set}" = set; then
+echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
+echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6
+if test "${ac_cv_c_compiler_gnu+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- am_cv_python_platform=`$PYTHON -c "import sys; print sys.platform"`
-fi
-echo "$as_me:$LINENO: result: $am_cv_python_platform" >&5
-echo "${ECHO_T}$am_cv_python_platform" >&6
- PYTHON_PLATFORM=$am_cv_python_platform
-
-
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
- echo "$as_me:$LINENO: checking for $am_display_PYTHON script directory" >&5
-echo $ECHO_N "checking for $am_display_PYTHON script directory... $ECHO_C" >&6
-if test "${am_cv_python_pythondir+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_compiler_gnu=yes
else
- am_cv_python_pythondir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(0,0,prefix='$PYTHON_PREFIX')" 2>/dev/null ||
- echo "$PYTHON_PREFIX/lib/python$PYTHON_VERSION/site-packages"`
-fi
-echo "$as_me:$LINENO: result: $am_cv_python_pythondir" >&5
-echo "${ECHO_T}$am_cv_python_pythondir" >&6
- pythondir=$am_cv_python_pythondir
-
-
-
- pkgpythondir=\${pythondir}/$PACKAGE
-
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
- echo "$as_me:$LINENO: checking for $am_display_PYTHON extension module directory" >&5
-echo $ECHO_N "checking for $am_display_PYTHON extension module directory... $ECHO_C" >&6
-if test "${am_cv_python_pyexecdir+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- am_cv_python_pyexecdir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(1,0,prefix='$PYTHON_EXEC_PREFIX')" 2>/dev/null ||
- echo "${PYTHON_EXEC_PREFIX}/lib/python${PYTHON_VERSION}/site-packages"`
+ac_compiler_gnu=no
fi
-echo "$as_me:$LINENO: result: $am_cv_python_pyexecdir" >&5
-echo "${ECHO_T}$am_cv_python_pyexecdir" >&6
- pyexecdir=$am_cv_python_pyexecdir
-
-
-
- pkgpyexecdir=\${pyexecdir}/$PACKAGE
-
-
-
- fi
-
-
-
-
-
-# Check whether --with-boost or --without-boost was given.
-if test "${with_boost+set}" = set; then
- withval="$with_boost"
-
- if test "$withval" = "no"; then
- want_boost="no"
- elif test "$withval" = "yes"; then
- want_boost="yes"
- ac_boost_path=""
- else
- want_boost="yes"
- ac_boost_path="$withval"
- fi
-
-else
- want_boost="yes"
-fi;
-
-
-
-# Check whether --with-boost-libdir or --without-boost-libdir was given.
-if test "${with_boost_libdir+set}" = set; then
- withval="$with_boost_libdir"
-
- if test -d $withval
- then
- ac_boost_lib_path="$withval"
- else
- { { echo "$as_me:$LINENO: error: --with-boost-libdir expected directory name" >&5
-echo "$as_me: error: --with-boost-libdir expected directory name" >&2;}
- { (exit 1); exit 1; }; }
- fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+fi
+echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
+echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6
+GCC=`test $ac_compiler_gnu = yes && echo yes`
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+CFLAGS="-g"
+echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
+echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6
+if test "${ac_cv_prog_cc_g+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
else
- ac_boost_lib_path=""
-
-fi;
-
-if test "x$want_boost" = "xyes"; then
- boost_lib_version_req=1.38.0
- boost_lib_version_req_shorten=`expr $boost_lib_version_req : '\([0-9]*\.[0-9]*\)'`
- boost_lib_version_req_major=`expr $boost_lib_version_req : '\([0-9]*\)'`
- boost_lib_version_req_minor=`expr $boost_lib_version_req : '[0-9]*\.\([0-9]*\)'`
- boost_lib_version_req_sub_minor=`expr $boost_lib_version_req : '[0-9]*\.[0-9]*\.\([0-9]*\)'`
- if test "x$boost_lib_version_req_sub_minor" = "x" ; then
- boost_lib_version_req_sub_minor="0"
- fi
- WANT_BOOST_VERSION=`expr $boost_lib_version_req_major \* 100000 \+ $boost_lib_version_req_minor \* 100 \+ $boost_lib_version_req_sub_minor`
- echo "$as_me:$LINENO: checking for boostlib >= $boost_lib_version_req" >&5
-echo $ECHO_N "checking for boostlib >= $boost_lib_version_req... $ECHO_C" >&6
- succeeded=no
-
- if test "$ac_boost_path" != ""; then
- BOOST_LDFLAGS="-L$ac_boost_path/lib"
- BOOST_CPPFLAGS="-I$ac_boost_path/include"
- else
- for ac_boost_path_tmp in /usr /usr/local /opt /opt/local ; do
- if test -d "$ac_boost_path_tmp/include/boost" && test -r "$ac_boost_path_tmp/include/boost"; then
- BOOST_LDFLAGS="-L$ac_boost_path_tmp/lib"
- BOOST_CPPFLAGS="-I$ac_boost_path_tmp/include"
- break;
- fi
- done
- fi
-
- if test "$ac_boost_lib_path" != ""; then
- BOOST_LDFLAGS="-L$ac_boost_lib_path"
- fi
-
- CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
- export CPPFLAGS
-
- LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
- export LDFLAGS
-
- ac_ext=cc
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
- cat >conftest.$ac_ext <<_ACEOF
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
- #include <boost/version.hpp>
-
int
main ()
{
- #if BOOST_VERSION >= $WANT_BOOST_VERSION
- // Everything is okay
- #else
- # error Boost version is too old
- #endif
-
;
return 0;
}
@@ -3921,7 +3473,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_cxx_werror_flag"
+ { ac_try='test -z "$ac_c_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -3934,111 +3486,198 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
-
- echo "$as_me:$LINENO: result: yes" >&5
-echo "${ECHO_T}yes" >&6
- succeeded=yes
- found_system=yes
-
+ ac_cv_prog_cc_g=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-
-
+ac_cv_prog_cc_g=no
fi
rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-
-
- if test "x$succeeded" != "xyes"; then
- _version=0
- if test "$ac_boost_path" != ""; then
- if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
- for i in `ls -d $ac_boost_path/include/boost-* 2>/dev/null`; do
- _version_tmp=`echo $i | sed "s#$ac_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
- V_CHECK=`expr $_version_tmp \> $_version`
- if test "$V_CHECK" = "1" ; then
- _version=$_version_tmp
- fi
- VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
- BOOST_CPPFLAGS="-I$ac_boost_path/include/boost-$VERSION_UNDERSCORE"
- done
- fi
- else
- for ac_boost_path in /usr /usr/local /opt /opt/local ; do
- if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
- for i in `ls -d $ac_boost_path/include/boost-* 2>/dev/null`; do
- _version_tmp=`echo $i | sed "s#$ac_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
- V_CHECK=`expr $_version_tmp \> $_version`
- if test "$V_CHECK" = "1" ; then
- _version=$_version_tmp
- best_path=$ac_boost_path
- fi
- done
- fi
- done
+fi
+echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
+echo "${ECHO_T}$ac_cv_prog_cc_g" >&6
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5
+echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6
+if test "${ac_cv_prog_cc_stdc+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ ac_cv_prog_cc_stdc=no
+ac_save_CC=$CC
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
- VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
- boost_major_version=`echo "$VERSION_UNDERSCORE" | sed 's/_//;s/_.*//'`
- BOOST_CPPFLAGS="-I$best_path/include/boost-$VERSION_UNDERSCORE"
- if test "$ac_boost_lib_path" = ""
- then
- BOOST_LDFLAGS="-L$best_path/lib"
- fi
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std1 is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std1. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
- if test "x$BOOST_ROOT" != "x"; then
- if test -d "$BOOST_ROOT" && test -r "$BOOST_ROOT" && test -d "$BOOST_ROOT/stage/lib" && test -r "$BOOST_ROOT/stage/lib"; then
- version_dir=`expr //$BOOST_ROOT : '.*/\(.*\)'`
- stage_version=`echo $version_dir | sed 's/boost_//' | sed 's/_/./g'`
- stage_version_shorten=`expr $stage_version : '\([0-9]*\.[0-9]*\)'`
- V_CHECK=`expr $stage_version_shorten \>\= $_version`
- if test "$V_CHECK" = "1" -a "$ac_boost_lib_path" = "" ; then
- { echo "$as_me:$LINENO: We will use a staged boost library from $BOOST_ROOT" >&5
-echo "$as_me: We will use a staged boost library from $BOOST_ROOT" >&6;}
- BOOST_CPPFLAGS="-I$BOOST_ROOT"
- BOOST_LDFLAGS="-L$BOOST_ROOT/stage/lib"
- fi
- fi
- fi
- fi
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+# Don't try gcc -ansi; that turns off useful extensions and
+# breaks some systems' header files.
+# AIX -qlanglvl=ansi
+# Ultrix and OSF/1 -std1
+# HP-UX 10.20 and later -Ae
+# HP-UX older versions -Aa -D_HPUX_SOURCE
+# SVR4 -Xc -D__EXTENSIONS__
+for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_prog_cc_stdc=$ac_arg
+break
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
- CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
- export CPPFLAGS
- LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
- export LDFLAGS
+fi
+rm -f conftest.err conftest.$ac_objext
+done
+rm -f conftest.$ac_ext conftest.$ac_objext
+CC=$ac_save_CC
- ac_ext=cc
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+fi
- cat >conftest.$ac_ext <<_ACEOF
+case "x$ac_cv_prog_cc_stdc" in
+ x|xno)
+ echo "$as_me:$LINENO: result: none needed" >&5
+echo "${ECHO_T}none needed" >&6 ;;
+ *)
+ echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5
+echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6
+ CC="$CC $ac_cv_prog_cc_stdc" ;;
+esac
+
+# Some people use a C++ compiler to compile C. Since we use `exit',
+# in C++ we need to declare it. In case someone uses the same compiler
+# for both compiling C and C++ we need to have the C++ compiler decide
+# the declaration of exit, since it's the most demanding environment.
+cat >conftest.$ac_ext <<_ACEOF
+#ifndef __cplusplus
+ choke me
+#endif
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ for ac_declaration in \
+ '' \
+ 'extern "C" void std::exit (int) throw (); using std::exit;' \
+ 'extern "C" void std::exit (int); using std::exit;' \
+ 'extern "C" void exit (int) throw ();' \
+ 'extern "C" void exit (int);' \
+ 'void exit (int);'
+do
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
- #include <boost/version.hpp>
-
+$ac_declaration
+#include <stdlib.h>
int
main ()
{
-
- #if BOOST_VERSION >= $WANT_BOOST_VERSION
- // Everything is okay
- #else
- # error Boost version is too old
- #endif
-
+exit (42);
;
return 0;
}
@@ -4052,7 +3691,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_cxx_werror_flag"
+ { ac_try='test -z "$ac_c_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -4065,129 +3704,677 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
+ :
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+continue
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_declaration
+int
+main ()
+{
+exit (42);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ break
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+rm -f conftest*
+if test -n "$ac_declaration"; then
+ echo '#ifdef __cplusplus' >>confdefs.h
+ echo $ac_declaration >>confdefs.h
+ echo '#endif' >>confdefs.h
+fi
+
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+depcc="$CC" am_compiler_list=
+
+echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ case $depmode in
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ none) break ;;
+ esac
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this.
+ if depmode=$depmode \
+ source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
+echo "${ECHO_T}$am_cv_CC_dependencies_compiler_type" >&6
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+
+
+if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6
+set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y,:./+-,___p_,'`
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\" = set"; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.make <<\_ACEOF
+all:
+ @echo 'ac_maketemp="$(MAKE)"'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
+eval `${MAKE-make} -f conftest.make 2>/dev/null | grep temp=`
+if test -n "$ac_maketemp"; then
+ eval ac_cv_prog_make_${ac_make}_set=yes
+else
+ eval ac_cv_prog_make_${ac_make}_set=no
+fi
+rm -f conftest.make
+fi
+if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then
+ echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+ SET_MAKE=
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_RANLIB+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$RANLIB"; then
+ ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+RANLIB=$ac_cv_prog_RANLIB
+if test -n "$RANLIB"; then
+ echo "$as_me:$LINENO: result: $RANLIB" >&5
+echo "${ECHO_T}$RANLIB" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+fi
+if test -z "$ac_cv_prog_RANLIB"; then
+ ac_ct_RANLIB=$RANLIB
+ # Extract the first word of "ranlib", so it can be a program name with args.
+set dummy ranlib; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$ac_ct_RANLIB"; then
+ ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_RANLIB="ranlib"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+ test -z "$ac_cv_prog_ac_ct_RANLIB" && ac_cv_prog_ac_ct_RANLIB=":"
+fi
+fi
+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
+if test -n "$ac_ct_RANLIB"; then
+ echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5
+echo "${ECHO_T}$ac_ct_RANLIB" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+ RANLIB=$ac_ct_RANLIB
+else
+ RANLIB="$ac_cv_prog_RANLIB"
+fi
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
+echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in
+ ./ | .// | /cC/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+done
+
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. We don't cache a
+ # path for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the path is relative.
+ INSTALL=$ac_install_sh
+ fi
+fi
+echo "$as_me:$LINENO: result: $INSTALL" >&5
+echo "${ECHO_T}$INSTALL" >&6
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+
+
+
+
+ if test -n "$PYTHON"; then
+ # If the user set $PYTHON, use it and don't search something else.
+ echo "$as_me:$LINENO: checking whether $PYTHON version >= 2.4" >&5
+echo $ECHO_N "checking whether $PYTHON version >= 2.4... $ECHO_C" >&6
+ prog="import sys, string
+# split strings by '.' and convert to numeric. Append some zeros
+# because we need at least 4 digits for the hex conversion.
+minver = map(int, string.split('2.4', '.')) + [0, 0, 0]
+minverhex = 0
+for i in xrange(0, 4): minverhex = (minverhex << 8) + minver[i]
+sys.exit(sys.hexversion < minverhex)"
+ if { echo "$as_me:$LINENO: $PYTHON -c "$prog"" >&5
+ ($PYTHON -c "$prog") >&5 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+else
+ { { echo "$as_me:$LINENO: error: too old" >&5
+echo "$as_me: error: too old" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+ am_display_PYTHON=$PYTHON
+ else
+ # Otherwise, try each interpreter until we find one that satisfies
+ # VERSION.
+ echo "$as_me:$LINENO: checking for a Python interpreter with version >= 2.4" >&5
+echo $ECHO_N "checking for a Python interpreter with version >= 2.4... $ECHO_C" >&6
+if test "${am_cv_pathless_PYTHON+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+
+ for am_cv_pathless_PYTHON in python python2 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 python1.6 python1.5 none; do
+ test "$am_cv_pathless_PYTHON" = none && break
+ prog="import sys, string
+# split strings by '.' and convert to numeric. Append some zeros
+# because we need at least 4 digits for the hex conversion.
+minver = map(int, string.split('2.4', '.')) + [0, 0, 0]
+minverhex = 0
+for i in xrange(0, 4): minverhex = (minverhex << 8) + minver[i]
+sys.exit(sys.hexversion < minverhex)"
+ if { echo "$as_me:$LINENO: $am_cv_pathless_PYTHON -c "$prog"" >&5
+ ($am_cv_pathless_PYTHON -c "$prog") >&5 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ break
+fi
+
+ done
+fi
+echo "$as_me:$LINENO: result: $am_cv_pathless_PYTHON" >&5
+echo "${ECHO_T}$am_cv_pathless_PYTHON" >&6
+ # Set $PYTHON to the absolute path of $am_cv_pathless_PYTHON.
+ if test "$am_cv_pathless_PYTHON" = none; then
+ PYTHON=:
+ else
+ # Extract the first word of "$am_cv_pathless_PYTHON", so it can be a program name with args.
+set dummy $am_cv_pathless_PYTHON; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_path_PYTHON+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ case $PYTHON in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_PYTHON="$PYTHON" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_path_PYTHON="$as_dir/$ac_word$ac_exec_ext"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+ ;;
+esac
+fi
+PYTHON=$ac_cv_path_PYTHON
+
+if test -n "$PYTHON"; then
+ echo "$as_me:$LINENO: result: $PYTHON" >&5
+echo "${ECHO_T}$PYTHON" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+ fi
+ am_display_PYTHON=$am_cv_pathless_PYTHON
+ fi
+
+
+ if test "$PYTHON" = :; then
+ { { echo "$as_me:$LINENO: error: no suitable Python interpreter found" >&5
+echo "$as_me: error: no suitable Python interpreter found" >&2;}
+ { (exit 1); exit 1; }; }
+ else
+
+
+ echo "$as_me:$LINENO: checking for $am_display_PYTHON version" >&5
+echo $ECHO_N "checking for $am_display_PYTHON version... $ECHO_C" >&6
+if test "${am_cv_python_version+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ am_cv_python_version=`$PYTHON -c "import sys; print sys.version[:3]"`
+fi
+echo "$as_me:$LINENO: result: $am_cv_python_version" >&5
+echo "${ECHO_T}$am_cv_python_version" >&6
+ PYTHON_VERSION=$am_cv_python_version
+
+
+
+ PYTHON_PREFIX='${prefix}'
+
+ PYTHON_EXEC_PREFIX='${exec_prefix}'
+
+
+
+ echo "$as_me:$LINENO: checking for $am_display_PYTHON platform" >&5
+echo $ECHO_N "checking for $am_display_PYTHON platform... $ECHO_C" >&6
+if test "${am_cv_python_platform+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ am_cv_python_platform=`$PYTHON -c "import sys; print sys.platform"`
+fi
+echo "$as_me:$LINENO: result: $am_cv_python_platform" >&5
+echo "${ECHO_T}$am_cv_python_platform" >&6
+ PYTHON_PLATFORM=$am_cv_python_platform
+
- echo "$as_me:$LINENO: result: yes" >&5
-echo "${ECHO_T}yes" >&6
- succeeded=yes
- found_system=yes
+
+ echo "$as_me:$LINENO: checking for $am_display_PYTHON script directory" >&5
+echo $ECHO_N "checking for $am_display_PYTHON script directory... $ECHO_C" >&6
+if test "${am_cv_python_pythondir+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
else
- echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
+ am_cv_python_pythondir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(0,0,prefix='$PYTHON_PREFIX')" 2>/dev/null ||
+ echo "$PYTHON_PREFIX/lib/python$PYTHON_VERSION/site-packages"`
+fi
+echo "$as_me:$LINENO: result: $am_cv_python_pythondir" >&5
+echo "${ECHO_T}$am_cv_python_pythondir" >&6
+ pythondir=$am_cv_python_pythondir
+
+ pkgpythondir=\${pythondir}/$PACKAGE
+
+ echo "$as_me:$LINENO: checking for $am_display_PYTHON extension module directory" >&5
+echo $ECHO_N "checking for $am_display_PYTHON extension module directory... $ECHO_C" >&6
+if test "${am_cv_python_pyexecdir+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ am_cv_python_pyexecdir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(1,0,prefix='$PYTHON_EXEC_PREFIX')" 2>/dev/null ||
+ echo "${PYTHON_EXEC_PREFIX}/lib/python${PYTHON_VERSION}/site-packages"`
fi
-rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+echo "$as_me:$LINENO: result: $am_cv_python_pyexecdir" >&5
+echo "${ECHO_T}$am_cv_python_pyexecdir" >&6
+ pyexecdir=$am_cv_python_pyexecdir
- fi
- if test "$succeeded" != "yes" ; then
- if test "$_version" = "0" ; then
- { { echo "$as_me:$LINENO: error: We could not detect the boost libraries (version $boost_lib_version_req_shorten or higher). If you have a staged boost library (still not installed) please specify \$BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation." >&5
-echo "$as_me: error: We could not detect the boost libraries (version $boost_lib_version_req_shorten or higher). If you have a staged boost library (still not installed) please specify \$BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation." >&2;}
- { (exit 1); exit 1; }; }
- else
- { echo "$as_me:$LINENO: Your boost libraries seem to old (version $_version)." >&5
-echo "$as_me: Your boost libraries seem to old (version $_version)." >&6;}
- fi
- else
+ pkgpyexecdir=\${pyexecdir}/$PACKAGE
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BOOST
-_ACEOF
- fi
+ fi
+
+
+
+# ===========================================================================
+# http://autoconf-archive.cryp.to/ax_boost_base.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+# AX_BOOST_BASE([MINIMUM-VERSION])
+#
+# DESCRIPTION
+#
+# Test for the Boost C++ libraries of a particular version (or newer)
+#
+# If no path to the installed boost library is given the macro searchs
+# under /usr, /usr/local, /opt and /opt/local and evaluates the
+# $BOOST_ROOT environment variable. Further documentation is available at
+# <http://randspringer.de/boost/index.html>.
+#
+# This macro calls:
+#
+# AC_SUBST(BOOST_CPPFLAGS) / AC_SUBST(BOOST_LDFLAGS)
+#
+# And sets:
+#
+# HAVE_BOOST
+#
+# LICENSE
+#
+# Copyright (c) 2008 Thomas Porschberg <thomas at randspringer.de>
+#
+# Copying and distribution of this file, with or without modification, are
+# permitted in any medium without royalty provided the copyright notice
+# and this notice are preserved.
- CPPFLAGS="$CPPFLAGS_SAVED"
- LDFLAGS="$LDFLAGS_SAVED"
-fi
-# Check whether --with-bam or --without-bam was given.
-if test "${with_bam+set}" = set; then
- withval="$with_bam"
+# CXXFLAGS="$CXXFLAGS $threadLib"
+
+
+
+# Check whether --with-boost or --without-boost was given.
+if test "${with_boost+set}" = set; then
+ withval="$with_boost"
if test "$withval" = "no"; then
- want_bam="no"
+ want_boost="no"
elif test "$withval" = "yes"; then
- want_bam="yes"
- ac_bam_path=""
+ want_boost="yes"
+ ac_boost_path=""
else
- want_bam="yes"
- ac_bam_path="$withval"
+ want_boost="yes"
+ ac_boost_path="$withval"
fi
else
- want_bam="yes"
+ want_boost="yes"
fi;
-# Check whether --with-bam-libdir or --without-bam-libdir was given.
-if test "${with_bam_libdir+set}" = set; then
- withval="$with_bam_libdir"
+# Check whether --with-boost-libdir or --without-boost-libdir was given.
+if test "${with_boost_libdir+set}" = set; then
+ withval="$with_boost_libdir"
if test -d $withval
then
- ac_bam_lib_path="$withval"
+ ac_boost_lib_path="$withval"
else
- { { echo "$as_me:$LINENO: error: --with-bam-libdir expected directory name" >&5
-echo "$as_me: error: --with-bam-libdir expected directory name" >&2;}
+ { { echo "$as_me:$LINENO: error: --with-boost-libdir expected directory name" >&5
+echo "$as_me: error: --with-boost-libdir expected directory name" >&2;}
{ (exit 1); exit 1; }; }
fi
else
- ac_bam_lib_path=""
+ ac_boost_lib_path=""
fi;
-if test "x$want_bam" = "xyes"; then
-# bam_lib_version_req=ifelse([], ,1.20.0,)
-# bam_lib_version_req_shorten=`expr $bam_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
-# bam_lib_version_req_major=`expr $bam_lib_version_req : '\([[0-9]]*\)'`
-# bam_lib_version_req_minor=`expr $bam_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
-# bam_lib_version_req_sub_minor=`expr $bam_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
-# if test "x$bam_lib_version_req_sub_minor" = "x" ; then
-# bam_lib_version_req_sub_minor="0"
-# fi
-# WANT_BAM_VERSION=`expr $bam_lib_version_req_major \* 100000 \+ $bam_lib_version_req_minor \* 100 \+ $bam_lib_version_req_sub_minor`
- echo "$as_me:$LINENO: checking for bamlib" >&5
-echo $ECHO_N "checking for bamlib... $ECHO_C" >&6
+if test "x$want_boost" = "xyes"; then
+ boost_lib_version_req=1.38.0
+ boost_lib_version_req_shorten=`expr $boost_lib_version_req : '\([0-9]*\.[0-9]*\)'`
+ boost_lib_version_req_major=`expr $boost_lib_version_req : '\([0-9]*\)'`
+ boost_lib_version_req_minor=`expr $boost_lib_version_req : '[0-9]*\.\([0-9]*\)'`
+ boost_lib_version_req_sub_minor=`expr $boost_lib_version_req : '[0-9]*\.[0-9]*\.\([0-9]*\)'`
+ if test "x$boost_lib_version_req_sub_minor" = "x" ; then
+ boost_lib_version_req_sub_minor="0"
+ fi
+ WANT_BOOST_VERSION=`expr $boost_lib_version_req_major \* 100000 \+ $boost_lib_version_req_minor \* 100 \+ $boost_lib_version_req_sub_minor`
+ echo "$as_me:$LINENO: checking for boostlib >= $boost_lib_version_req" >&5
+echo $ECHO_N "checking for boostlib >= $boost_lib_version_req... $ECHO_C" >&6
succeeded=no
- if test "$ac_bam_path" != ""; then
- BAM_LDFLAGS="-L$ac_bam_path/lib"
- BAM_CPPFLAGS="-I$ac_bam_path/include"
+ if test "$ac_boost_path" != ""; then
+ BOOST_LDFLAGS="-L$ac_boost_path/lib"
+ BOOST_CPPFLAGS="-I$ac_boost_path/include"
else
- for ac_bam_path_tmp in /usr /usr/local /opt /opt/local ; do
- if test -d "$ac_bam_path_tmp/include/bam" && test -r "$ac_bam_path_tmp/include/bam"; then
- BAM_LDFLAGS="-L$ac_bam_path_tmp/lib"
- BAM_CPPFLAGS="-I$ac_bam_path_tmp/include"
+ for ac_boost_path_tmp in /usr /usr/local /opt /opt/local ; do
+ if test -d "$ac_boost_path_tmp/include/boost" && test -r "$ac_boost_path_tmp/include/boost"; then
+ BOOST_LDFLAGS="-L$ac_boost_path_tmp/lib"
+ BOOST_CPPFLAGS="-I$ac_boost_path_tmp/include"
break;
fi
done
fi
- if test "$ac_bam_lib_path" != ""; then
- BAM_LDFLAGS="-L$ac_bam_lib_path"
+ if test "$ac_boost_lib_path" != ""; then
+ BOOST_LDFLAGS="-L$ac_boost_lib_path"
fi
CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BAM_CPPFLAGS"
+ CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
export CPPFLAGS
LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BAM_LDFLAGS"
+ LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
export LDFLAGS
ac_ext=cc
@@ -4203,12 +4390,17 @@ cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
- #include <bam/bam.h>
+ #include <boost/version.hpp>
int
main ()
{
+ #if BOOST_VERSION >= $WANT_BOOST_VERSION
+ // Everything is okay
+ #else
+ # error Boost version is too old
+ #endif
;
return 0;
@@ -4250,67 +4442,70 @@ sed 's/^/| /' conftest.$ac_ext >&5
fi
rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
if test "x$succeeded" != "xyes"; then
_version=0
- if test "$ac_bam_path" != ""; then
- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
- for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
- _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
+ if test "$ac_boost_path" != ""; then
+ if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
+ for i in `ls -d $ac_boost_path/include/boost-* 2>/dev/null`; do
+ _version_tmp=`echo $i | sed "s#$ac_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
V_CHECK=`expr $_version_tmp \> $_version`
if test "$V_CHECK" = "1" ; then
_version=$_version_tmp
fi
VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
- BAM_CPPFLAGS="-I$ac_bam_path/include/bam-$VERSION_UNDERSCORE"
+ BOOST_CPPFLAGS="-I$ac_boost_path/include/boost-$VERSION_UNDERSCORE"
done
fi
else
- for ac_bam_path in /usr /usr/local /opt /opt/local ; do
- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
- for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
- _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
+ for ac_boost_path in /usr /usr/local /opt /opt/local ; do
+ if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
+ for i in `ls -d $ac_boost_path/include/boost-* 2>/dev/null`; do
+ _version_tmp=`echo $i | sed "s#$ac_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
V_CHECK=`expr $_version_tmp \> $_version`
if test "$V_CHECK" = "1" ; then
_version=$_version_tmp
- best_path=$ac_bam_path
+ best_path=$ac_boost_path
fi
done
fi
done
VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
- BAM_CPPFLAGS="-I$best_path/include/bam-$VERSION_UNDERSCORE"
- if test "$ac_bam_lib_path" = ""
+ boost_major_version=`echo "$VERSION_UNDERSCORE" | sed 's/_//;s/_.*//'`
+ BOOST_CPPFLAGS="-I$best_path/include/boost-$VERSION_UNDERSCORE"
+ if test "$ac_boost_lib_path" = ""
then
- BAM_LDFLAGS="-L$best_path/lib"
+ BOOST_LDFLAGS="-L$best_path/lib"
fi
- if test "x$BAM_ROOT" != "x"; then
- if test -d "$BAM_ROOT" && test -r "$BAM_ROOT" && test -d "$BAM_ROOT/stage/lib" && test -r "$BAM_ROOT/stage/lib"; then
- version_dir=`expr //$BAM_ROOT : '.*/\(.*\)'`
- stage_version=`echo $version_dir | sed 's/bam_//' | sed 's/_/./g'`
+ if test "x$BOOST_ROOT" != "x"; then
+ if test -d "$BOOST_ROOT" && test -r "$BOOST_ROOT" && test -d "$BOOST_ROOT/stage/lib" && test -r "$BOOST_ROOT/stage/lib"; then
+ version_dir=`expr //$BOOST_ROOT : '.*/\(.*\)'`
+ stage_version=`echo $version_dir | sed 's/boost_//' | sed 's/_/./g'`
stage_version_shorten=`expr $stage_version : '\([0-9]*\.[0-9]*\)'`
V_CHECK=`expr $stage_version_shorten \>\= $_version`
- if test "$V_CHECK" = "1" -a "$ac_bam_lib_path" = "" ; then
- { echo "$as_me:$LINENO: We will use a staged bam library from $BAM_ROOT" >&5
-echo "$as_me: We will use a staged bam library from $BAM_ROOT" >&6;}
- BAM_CPPFLAGS="-I$BAM_ROOT"
- BAM_LDFLAGS="-L$BAM_ROOT/stage/lib"
+ if test "$V_CHECK" = "1" -a "$ac_boost_lib_path" = "" ; then
+ { echo "$as_me:$LINENO: We will use a staged boost library from $BOOST_ROOT" >&5
+echo "$as_me: We will use a staged boost library from $BOOST_ROOT" >&6;}
+ BOOST_CPPFLAGS="-I$BOOST_ROOT"
+ BOOST_LDFLAGS="-L$BOOST_ROOT/stage/lib"
fi
fi
fi
fi
- CPPFLAGS="$CPPFLAGS $BAM_CPPFLAGS"
+ CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
export CPPFLAGS
- LDFLAGS="$LDFLAGS $BAM_LDFLAGS"
+ LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
export LDFLAGS
ac_ext=cc
@@ -4326,12 +4521,17 @@ cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
- #include <bam/version.hpp>
+ #include <boost/version.hpp>
int
main ()
{
+ #if BOOST_VERSION >= $WANT_BOOST_VERSION
+ // Everything is okay
+ #else
+ # error Boost version is too old
+ #endif
;
return 0;
@@ -4373,31 +4573,29 @@ sed 's/^/| /' conftest.$ac_ext >&5
fi
rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
fi
if test "$succeeded" != "yes" ; then
if test "$_version" = "0" ; then
- { { echo "$as_me:$LINENO: error: We could not detect the bam libraries (version $bam_lib_version_req_shorten or higher). If you have a staged bam library (still not installed) please specify \$BAM_ROOT in your environment and do not give a PATH to --with-bam option." >&5
-echo "$as_me: error: We could not detect the bam libraries (version $bam_lib_version_req_shorten or higher). If you have a staged bam library (still not installed) please specify \$BAM_ROOT in your environment and do not give a PATH to --with-bam option." >&2;}
+ { { echo "$as_me:$LINENO: error: We could not detect the boost libraries (version $boost_lib_version_req_shorten or higher). If you have a staged boost library (still not installed) please specify \$BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation." >&5
+echo "$as_me: error: We could not detect the boost libraries (version $boost_lib_version_req_shorten or higher). If you have a staged boost library (still not installed) please specify \$BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation." >&2;}
{ (exit 1); exit 1; }; }
else
- { echo "$as_me:$LINENO: Your bam libraries seem too old (version $_version)." >&5
-echo "$as_me: Your bam libraries seem too old (version $_version)." >&6;}
+ { echo "$as_me:$LINENO: Your boost libraries seem to old (version $_version)." >&5
+echo "$as_me: Your boost libraries seem to old (version $_version)." >&6;}
fi
else
- BAM_LIB="-lbam"
-
cat >>confdefs.h <<\_ACEOF
-#define HAVE_BAM
+#define HAVE_BOOST
_ACEOF
fi
@@ -4407,105 +4605,30 @@ _ACEOF
fi
-# Make sure we can run config.sub.
-$ac_config_sub sun4 >/dev/null 2>&1 ||
- { { echo "$as_me:$LINENO: error: cannot run $ac_config_sub" >&5
-echo "$as_me: error: cannot run $ac_config_sub" >&2;}
- { (exit 1); exit 1; }; }
-
-echo "$as_me:$LINENO: checking build system type" >&5
-echo $ECHO_N "checking build system type... $ECHO_C" >&6
-if test "${ac_cv_build+set}" = set; then
+echo "$as_me:$LINENO: checking whether the compiler implements namespaces" >&5
+echo $ECHO_N "checking whether the compiler implements namespaces... $ECHO_C" >&6
+if test "${ac_cv_cxx_namespaces+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- ac_cv_build_alias=$build_alias
-test -z "$ac_cv_build_alias" &&
- ac_cv_build_alias=`$ac_config_guess`
-test -z "$ac_cv_build_alias" &&
- { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
-echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
- { (exit 1); exit 1; }; }
-ac_cv_build=`$ac_config_sub $ac_cv_build_alias` ||
- { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_build_alias failed" >&5
-echo "$as_me: error: $ac_config_sub $ac_cv_build_alias failed" >&2;}
- { (exit 1); exit 1; }; }
-
-fi
-echo "$as_me:$LINENO: result: $ac_cv_build" >&5
-echo "${ECHO_T}$ac_cv_build" >&6
-build=$ac_cv_build
-build_cpu=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
-build_vendor=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
-build_os=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
-
-
-
-
-
-# Check whether --with-boost-thread or --without-boost-thread was given.
-if test "${with_boost_thread+set}" = set; then
- withval="$with_boost_thread"
-
- if test "$withval" = "no"; then
- want_boost="no"
- elif test "$withval" = "yes"; then
- want_boost="yes"
- ax_boost_user_thread_lib=""
- ax_booth_user_system_lib=""
- else
- want_boost="yes"
- echo "using $withval"
- ax_boost_user_thread_lib="$withval"
- fi
-
-else
- want_boost="yes"
-
-fi;
-
- if test "x$want_boost" = "xyes"; then
-
-
- CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
- export CPPFLAGS
- LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
- export LDFLAGS
- echo "$as_me:$LINENO: checking whether the Boost::Thread library is available" >&5
-echo $ECHO_N "checking whether the Boost::Thread library is available... $ECHO_C" >&6
-if test "${ax_cv_boost_thread+set}" = set; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- ac_ext=cc
+ ac_ext=cc
ac_cpp='$CXXCPP $CPPFLAGS'
ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
- CXXFLAGS_SAVE=$CXXFLAGS
-
- if test "x$build_os" = "xsolaris" ; then
- CXXFLAGS="-pthreads $CXXFLAGS"
- elif test "x$build_os" = "xming32" ; then
- CXXFLAGS="-mthreads $CXXFLAGS"
- else
- CXXFLAGS="-pthread $CXXFLAGS"
- fi
- cat >conftest.$ac_ext <<_ACEOF
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <boost/thread/thread.hpp>
+namespace Outer { namespace Inner { int i = 0; }}
int
main ()
{
-boost::thread_group thrds;
- return 0;
+using namespace Outer::Inner; return i;
;
return 0;
}
@@ -4532,131 +4655,129 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ax_cv_boost_thread=yes
+ ac_cv_cxx_namespaces=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-ax_cv_boost_thread=no
+ac_cv_cxx_namespaces=no
fi
rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
- CXXFLAGS=$CXXFLAGS_SAVE
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
fi
-echo "$as_me:$LINENO: result: $ax_cv_boost_thread" >&5
-echo "${ECHO_T}$ax_cv_boost_thread" >&6
- if test "x$ax_cv_boost_thread" = "xyes"; then
- if test "x$build_os" = "xsolaris" ; then
- BOOST_CPPFLAGS="-pthreads $BOOST_CPPFLAGS"
- elif test "x$build_os" = "xming32" ; then
- BOOST_CPPFLAGS="-mthreads $BOOST_CPPFLAGS"
- else
- BOOST_CPPFLAGS="-pthread $BOOST_CPPFLAGS"
- fi
+echo "$as_me:$LINENO: result: $ac_cv_cxx_namespaces" >&5
+echo "${ECHO_T}$ac_cv_cxx_namespaces" >&6
+if test "$ac_cv_cxx_namespaces" = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_NAMESPACES
+_ACEOF
+
+fi
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+CXXFLAGS_SAVE=$CXXFLAGS
+LIBS_SAVE=$LIBS
+
+CPPFLAGS_SAVED="$CPPFLAGS"
+CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+export CPPFLAGS
+LDFLAGS_SAVED="$LDFLAGS"
+LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+export LDFLAGS
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BOOST_THREAD
-_ACEOF
+CXXFLAGS="-pthread $CXXFLAGS"
- BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/[^\/]*//'`
-
- LDFLAGS_SAVE=$LDFLAGS
- case "x$build_os" in
- *bsd* )
- LDFLAGS="-pthread $LDFLAGS"
- break;
- ;;
- esac
- if test "x$ax_boost_user_thread_lib" = "x"; then
- for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- as_ac_Lib=`echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
-echo $ECHO_N "checking for exit in -l$ax_lib... $ECHO_C" >&6
-if eval "test \"\${$as_ac_Lib+set}\" = set"; then
+echo "$as_me:$LINENO: checking whether the Boost::Thread library is available" >&5
+echo $ECHO_N "checking whether the Boost::Thread library is available... $ECHO_C" >&6
+if test "${ax_cv_boost_thread+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
-/* Override any gcc2 internal prototype to avoid an error. */
-#ifdef __cplusplus
-extern "C"
-#endif
-/* We use char because int might match the return type of a gcc2
- builtin and then its argument prototype would still apply. */
-char exit ();
+#include <boost/thread/thread.hpp>
int
main ()
{
-exit ();
+boost::thread_group thrds; return 0;
;
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
- (eval $ac_link) 2>conftest.er1
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
ac_status=$?
grep -v '^ *+' conftest.er1 >conftest.err
rm -f conftest.er1
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; } &&
- { ac_try='test -s conftest$ac_exeext'
+ { ac_try='test -s conftest.$ac_objext'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- eval "$as_ac_Lib=yes"
+ ax_cv_boost_thread=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-eval "$as_ac_Lib=no"
-fi
-rm -f conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
+ax_cv_boost_thread=no
fi
-echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Lib'}'`" >&5
-echo "${ECHO_T}`eval echo '${'$as_ac_Lib'}'`" >&6
-if test `eval echo '${'$as_ac_Lib'}'` = yes; then
- BOOST_THREAD_LIB="-l$ax_lib"; link_thread="yes"; break
-else
- link_thread="no"
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+
fi
+echo "$as_me:$LINENO: result: $ax_cv_boost_thread" >&5
+echo "${ECHO_T}$ax_cv_boost_thread" >&6
+
+if test "$ax_cv_boost_thread" = yes; then
- done
- if test "x$link_thread" != "xyes"; then
- for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do
- ax_lib=${libextension}
- as_ac_Lib=`echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
-echo $ECHO_N "checking for exit in -l$ax_lib... $ECHO_C" >&6
+ BOOST_CPPFLAGS="-pthread $BOOST_CPPFLAGS"
+
+
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BOOST_THREAD
+_ACEOF
+
+
+# Check whether --with-boost-thread or --without-boost-thread was given.
+if test "${with_boost_thread+set}" = set; then
+ withval="$with_boost_thread"
+ if test "x$with_boost_thread" != "xno"; then
+ ax_boost_thread_lib=boost_thread$with_boost_thread
+ fi
+fi;
+ for ax_lib in $ax_boost_thread_lib boost_thread boost_thread-mt; do
+ as_ac_Lib=`echo "ac_cv_lib_$ax_lib''_main" | $as_tr_sh`
+echo "$as_me:$LINENO: checking for main in -l$ax_lib" >&5
+echo $ECHO_N "checking for main in -l$ax_lib... $ECHO_C" >&6
if eval "test \"\${$as_ac_Lib+set}\" = set"; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
@@ -4669,17 +4790,11 @@ cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-/* Override any gcc2 internal prototype to avoid an error. */
-#ifdef __cplusplus
-extern "C"
-#endif
-/* We use char because int might match the return type of a gcc2
- builtin and then its argument prototype would still apply. */
-char exit ();
+
int
main ()
{
-exit ();
+main ();
;
return 0;
}
@@ -4693,7 +4808,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -4720,64 +4835,29 @@ fi
echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Lib'}'`" >&5
echo "${ECHO_T}`eval echo '${'$as_ac_Lib'}'`" >&6
if test `eval echo '${'$as_ac_Lib'}'` = yes; then
- BOOST_THREAD_LIB="-l$ax_lib"; link_thread="yes"; break
-else
- link_thread="no"
+ BOOST_THREAD_LIBS=-l$ax_lib; break
fi
- done
- fi
-
- else
- BOOST_THREAD_LIB="$ax_boost_user_thread_lib";
-
- link_thread="yes";
-
-
- fi
- if test "x$link_thread" = "xno"; then
- { { echo "$as_me:$LINENO: error: Could not link against $ax_lib !" >&5
-echo "$as_me: error: Could not link against $ax_lib !" >&2;}
- { (exit 1); exit 1; }; }
- else
- case "x$build_os" in
- *bsd* )
- BOOST_LDFLAGS="-pthread $BOOST_LDFLAGS"
- break;
- ;;
- esac
-
- fi
+ done
- if test "x$ax_boost_user_system_lib" = "x"; then
- for libextension in `ls $BOOSTLIBDIR/libboost_system*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- as_ac_Lib=`echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
-echo $ECHO_N "checking for exit in -l$ax_lib... $ECHO_C" >&6
-if eval "test \"\${$as_ac_Lib+set}\" = set"; then
+ # in recent Boost versions, boost::thread depends on boost::system
+ echo "$as_me:$LINENO: checking whether Boost::Thread needs Boost::System library" >&5
+echo $ECHO_N "checking whether Boost::Thread needs Boost::System library... $ECHO_C" >&6
+if test "${ax_cv_boost_thread_system+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
+ LIBS="$LIBS $BOOST_THREAD_LIBS"
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
-/* Override any gcc2 internal prototype to avoid an error. */
-#ifdef __cplusplus
-extern "C"
-#endif
-/* We use char because int might match the return type of a gcc2
- builtin and then its argument prototype would still apply. */
-char exit ();
+#include <boost/thread/thread.hpp>
int
main ()
{
-exit ();
+boost::thread_group thrds; return 0;
;
return 0;
}
@@ -4791,7 +4871,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -4804,58 +4884,28 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- eval "$as_ac_Lib=yes"
+ ax_cv_boost_thread_system=no
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-eval "$as_ac_Lib=no"
-fi
-rm -f conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Lib'}'`" >&5
-echo "${ECHO_T}`eval echo '${'$as_ac_Lib'}'`" >&6
-if test `eval echo '${'$as_ac_Lib'}'` = yes; then
- BOOST_SYSTEM_LIB="-l$ax_lib"; link_system="yes"; break
-else
- link_system="no"
-fi
+LIBS="$LIBS $BOOST_THREAD_LIBS -lboost_system$with_boost_thread"
+ cat >conftest.$ac_ext <<_ACEOF
- done
- if test "x$link_system" != "xyes"; then
- for libextension in `ls $BOOSTLIBDIR/boost_system*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.a*$;\1;'` ; do
- ax_lib=${libextension}
- as_ac_Lib=`echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
-echo $ECHO_N "checking for exit in -l$ax_lib... $ECHO_C" >&6
-if eval "test \"\${$as_ac_Lib+set}\" = set"; then
- echo $ECHO_N "(cached) $ECHO_C" >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
+ /* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
-/* Override any gcc2 internal prototype to avoid an error. */
-#ifdef __cplusplus
-extern "C"
-#endif
-/* We use char because int might match the return type of a gcc2
- builtin and then its argument prototype would still apply. */
-char exit ();
+#include <boost/thread/thread.hpp>
int
main ()
{
-exit ();
+boost::thread_group thrds; return 0;
;
return 0;
}
+
_ACEOF
rm -f conftest.$ac_objext conftest$ac_exeext
if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
@@ -4866,7 +4916,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -4879,65 +4929,77 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- eval "$as_ac_Lib=yes"
+ BOOST_THREAD_LIBS="$BOOST_THREAD_LIBS -lboost_system$with_boost_thread"
+ ax_cv_boost_thread_system=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-eval "$as_ac_Lib=no"
+{ { echo "$as_me:$LINENO: error: Cannot use Boost::Thread" >&5
+echo "$as_me: error: Cannot use Boost::Thread" >&2;}
+ { (exit 1); exit 1; }; }
+
fi
rm -f conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
fi
-echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Lib'}'`" >&5
-echo "${ECHO_T}`eval echo '${'$as_ac_Lib'}'`" >&6
-if test `eval echo '${'$as_ac_Lib'}'` = yes; then
- BOOST_SYSTEM_LIB="-l$ax_lib"; link_system="yes"; break
-else
- link_system="no"
+rm -f conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+
fi
+echo "$as_me:$LINENO: result: $ax_cv_boost_thread_system" >&5
+echo "${ECHO_T}$ax_cv_boost_thread_system" >&6
- done
- fi
+ CXXFLAGS=$CXXFLAGS_SAVE
+ LIBS=$LIBS_SAVE
+ ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
- else
- BOOST_SYSTEM_LIB="$ax_boost_user_system_lib";
- link_system="yes";
+fi
+CPPFLAGS="$CPPFLAGS_SAVED"
+LDFLAGS="$LDFLAGS_SAVED"
+
+if test -z "$BOOST_THREAD_LIBS"; then
+ { { echo "$as_me:$LINENO: error: boost.thread not found. Aborting." >&5
+echo "$as_me: error: boost.thread not found. Aborting." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+
+
+
+# BAM related:
+ ac_bam_path=samtools-0.1.18
+ BAM_LIB="-lbam"
+ BAM_LDFLAGS="-L./$ac_bam_path"
+ BAM_CPPFLAGS="-I./$ac_bam_path"
- fi
- fi
- CPPFLAGS="$CPPFLAGS_SAVED"
- LDFLAGS="$LDFLAGS_SAVED"
- fi
-# AX_CHECK_ZLIB()
# Checks for header files.
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5
-echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6
-# On Suns, sometimes $CPP names a directory.
-if test -n "$CPP" && test -d "$CPP"; then
- CPP=
-fi
-if test -z "$CPP"; then
- if test "${ac_cv_prog_CPP+set}" = set; then
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5
+echo $ECHO_N "checking how to run the C++ preprocessor... $ECHO_C" >&6
+if test -z "$CXXCPP"; then
+ if test "${ac_cv_prog_CXXCPP+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
- # Double quotes because CPP needs to be expanded
- for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+ # Double quotes because CXXCPP needs to be expanded
+ for CXXCPP in "$CXX -E" "/lib/cpp"
do
ac_preproc_ok=false
-for ac_c_preproc_warn_flag in '' yes
+for ac_cxx_preproc_warn_flag in '' yes
do
# Use a header file that comes with gcc, so configuring glibc
# with a fresh cross-compiler works.
@@ -4967,8 +5029,8 @@ if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } >/dev/null; then
if test -s conftest.err; then
- ac_cpp_err=$ac_c_preproc_warn_flag
- ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ ac_cpp_err=$ac_cxx_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
else
ac_cpp_err=
fi
@@ -5005,8 +5067,8 @@ if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } >/dev/null; then
if test -s conftest.err; then
- ac_cpp_err=$ac_c_preproc_warn_flag
- ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ ac_cpp_err=$ac_cxx_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
else
ac_cpp_err=
fi
@@ -5034,17 +5096,17 @@ if $ac_preproc_ok; then
fi
done
- ac_cv_prog_CPP=$CPP
+ ac_cv_prog_CXXCPP=$CXXCPP
fi
- CPP=$ac_cv_prog_CPP
+ CXXCPP=$ac_cv_prog_CXXCPP
else
- ac_cv_prog_CPP=$CPP
+ ac_cv_prog_CXXCPP=$CXXCPP
fi
-echo "$as_me:$LINENO: result: $CPP" >&5
-echo "${ECHO_T}$CPP" >&6
+echo "$as_me:$LINENO: result: $CXXCPP" >&5
+echo "${ECHO_T}$CXXCPP" >&6
ac_preproc_ok=false
-for ac_c_preproc_warn_flag in '' yes
+for ac_cxx_preproc_warn_flag in '' yes
do
# Use a header file that comes with gcc, so configuring glibc
# with a fresh cross-compiler works.
@@ -5074,8 +5136,8 @@ if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } >/dev/null; then
if test -s conftest.err; then
- ac_cpp_err=$ac_c_preproc_warn_flag
- ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ ac_cpp_err=$ac_cxx_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
else
ac_cpp_err=
fi
@@ -5112,8 +5174,8 @@ if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } >/dev/null; then
if test -s conftest.err; then
- ac_cpp_err=$ac_c_preproc_warn_flag
- ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ ac_cpp_err=$ac_cxx_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
else
ac_cpp_err=
fi
@@ -5139,18 +5201,18 @@ rm -f conftest.err conftest.$ac_ext
if $ac_preproc_ok; then
:
else
- { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check
+ { { echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check
See \`config.log' for more details." >&5
-echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check
+echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check
See \`config.log' for more details." >&2;}
{ (exit 1); exit 1; }; }
fi
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
echo "$as_me:$LINENO: checking for egrep" >&5
@@ -5201,7 +5263,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -5372,7 +5434,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -5442,7 +5504,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -5486,8 +5548,8 @@ if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } >/dev/null; then
if test -s conftest.err; then
- ac_cpp_err=$ac_c_preproc_warn_flag
- ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ ac_cpp_err=$ac_cxx_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
else
ac_cpp_err=
fi
@@ -5507,7 +5569,7 @@ echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
echo "${ECHO_T}$ac_header_preproc" >&6
# So? What about this header?
-case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in
yes:no: )
{ echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
@@ -5593,7 +5655,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -5789,7 +5851,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -5845,7 +5907,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -5915,7 +5977,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -5989,7 +6051,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6055,7 +6117,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6121,7 +6183,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6229,7 +6291,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6311,7 +6373,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6341,7 +6403,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6412,7 +6474,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6465,7 +6527,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6537,7 +6599,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6590,7 +6652,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6666,7 +6728,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6737,7 +6799,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -6781,8 +6843,8 @@ if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } >/dev/null; then
if test -s conftest.err; then
- ac_cpp_err=$ac_c_preproc_warn_flag
- ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ ac_cpp_err=$ac_cxx_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
else
ac_cpp_err=
fi
@@ -6802,7 +6864,7 @@ echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
echo "${ECHO_T}$ac_header_preproc" >&6
# So? What about this header?
-case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in
yes:no: )
{ echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
@@ -7007,7 +7069,7 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
- { ac_try='test -z "$ac_c_werror_flag"
+ { ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
@@ -7042,6 +7104,38 @@ done
# check the platform
+# Make sure we can run config.sub.
+$ac_config_sub sun4 >/dev/null 2>&1 ||
+ { { echo "$as_me:$LINENO: error: cannot run $ac_config_sub" >&5
+echo "$as_me: error: cannot run $ac_config_sub" >&2;}
+ { (exit 1); exit 1; }; }
+
+echo "$as_me:$LINENO: checking build system type" >&5
+echo $ECHO_N "checking build system type... $ECHO_C" >&6
+if test "${ac_cv_build+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ ac_cv_build_alias=$build_alias
+test -z "$ac_cv_build_alias" &&
+ ac_cv_build_alias=`$ac_config_guess`
+test -z "$ac_cv_build_alias" &&
+ { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
+echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
+ { (exit 1); exit 1; }; }
+ac_cv_build=`$ac_config_sub $ac_cv_build_alias` ||
+ { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_build_alias failed" >&5
+echo "$as_me: error: $ac_config_sub $ac_cv_build_alias failed" >&2;}
+ { (exit 1); exit 1; }; }
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_build" >&5
+echo "${ECHO_T}$ac_cv_build" >&6
+build=$ac_cv_build
+build_cpu=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
+build_vendor=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
+build_os=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
+
+
echo "$as_me:$LINENO: checking host system type" >&5
echo $ECHO_N "checking host system type... $ECHO_C" >&6
if test "${ac_cv_host+set}" = set; then
@@ -7112,7 +7206,7 @@ fi
CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
CXXFLAGS="$CFLAGS"
CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3"
-LDFLAGS="$user_LDFLAGS"
+LDFLAGS="$BOOST_LDFLAGS $BAM_LDFLAGS $user_LDFLAGS"
# test to see if srcdir already configured
if test "`cd $srcdir && pwd`" != "`pwd`" &&
@@ -7134,7 +7228,7 @@ fi
# Define the identity of the package.
PACKAGE='tophat'
- VERSION='2.0.12'
+ VERSION='2.0.13'
cat >>confdefs.h <<_ACEOF
@@ -7674,6 +7768,13 @@ echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
Usually this means the macro was only invoked conditionally." >&2;}
{ (exit 1); exit 1; }; }
fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ { { echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
{ { echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined.
Usually this means the macro was only invoked conditionally." >&5
@@ -7966,7 +8067,7 @@ _ASBOX
} >&5
cat >&5 <<_CSEOF
-This file was extended by tophat $as_me 2.0.12, which was
+This file was extended by tophat $as_me 2.0.13, which was
generated by GNU Autoconf 2.59. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -8029,7 +8130,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF
ac_cs_version="\\
-tophat config.status 2.0.12
+tophat config.status 2.0.13
configured by $0, generated by GNU Autoconf 2.59,
with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\"
@@ -8285,18 +8386,17 @@ s, at pyexecdir@,$pyexecdir,;t t
s, at pkgpyexecdir@,$pkgpyexecdir,;t t
s, at BOOST_CPPFLAGS@,$BOOST_CPPFLAGS,;t t
s, at BOOST_LDFLAGS@,$BOOST_LDFLAGS,;t t
+s, at BOOST_THREAD_LIBS@,$BOOST_THREAD_LIBS,;t t
s, at BAM_CPPFLAGS@,$BAM_CPPFLAGS,;t t
s, at BAM_LDFLAGS@,$BAM_LDFLAGS,;t t
s, at BAM_LIB@,$BAM_LIB,;t t
+s, at CXXCPP@,$CXXCPP,;t t
+s, at EGREP@,$EGREP,;t t
+s, at LIBOBJS@,$LIBOBJS,;t t
s, at build@,$build,;t t
s, at build_cpu@,$build_cpu,;t t
s, at build_vendor@,$build_vendor,;t t
s, at build_os@,$build_os,;t t
-s, at BOOST_THREAD_LIB@,$BOOST_THREAD_LIB,;t t
-s, at BOOST_SYSTEM_LIB@,$BOOST_SYSTEM_LIB,;t t
-s, at CPP@,$CPP,;t t
-s, at EGREP@,$EGREP,;t t
-s, at LIBOBJS@,$LIBOBJS,;t t
s, at host@,$host,;t t
s, at host_cpu@,$host_cpu,;t t
s, at host_vendor@,$host_vendor,;t t
@@ -9023,7 +9123,8 @@ echo \
"
-- ${PACKAGE_STRING} Configuration Results --
C++ compiler: ${CXX} ${CXXFLAGS}
- Linker flags: ${LDFLAGS}"
+ Linker flags: ${LDFLAGS}
+ BOOST libraries: ${BOOST_THREAD_LIBS}"
if test x"${GCC}" = x"yes" ; then
gcc_version=`${CC} --version | head -n 1`
diff --git a/configure.ac b/configure.ac
index 21fb895..9b0d898 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,26 +1,23 @@
-m4_include([ax_boost_base.m4])
-m4_include([ax_boost_thread.m4])
-m4_include([ax_bam.m4])
-#m4_include([ax_check_zlib.m4])
-
define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl
-AC_INIT([tophat],[2.0.12],[tophat.cufflinks at gmail.com])
+AC_INIT([tophat],[2.0.13],[tophat.cufflinks at gmail.com])
AC_DEFINE(SVN_REVISION, "svnversion", [SVN Revision])
AC_CONFIG_SRCDIR([config.h.in])
AC_CONFIG_HEADERS([config.h])
-AC_CONFIG_AUX_DIR([build-aux])
+# AC_CONFIG_AUX_DIR([build-aux])
AM_INIT_AUTOMAKE
-#AM_PATH_CPPUNIT(1.10.2)
-
AC_ARG_VAR(PYTHON, [python program])
- # Make sure CXXFLAGS is defined so that AC_PROG_CXX doesn't set it.
+# Make sure CXXFLAGS is defined so that AC_PROG_CXX doesn't set it.
CXXFLAGS="$CXXFLAGS"
CFLAGS="$CFLAGS"
+AC_PROG_CXX
+AC_LANG([C++])
+
+# AC_LANG([C])
-AC_LANG(C)
+m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
# Checks for programs.
AC_PROG_AWK
@@ -30,10 +27,27 @@ AC_PROG_MAKE_SET
AC_PROG_RANLIB
AC_PROG_INSTALL
AM_PATH_PYTHON([2.4])
+
+m4_include([ax_boost_base.m4])
+m4_include([ax_boost_thread.m4])
+# CXXFLAGS="$CXXFLAGS $threadLib"
AX_BOOST_BASE([1.38.0])
-AX_BAM
AX_BOOST_THREAD
-# AX_CHECK_ZLIB()
+if test -z "$BOOST_THREAD_LIBS"; then
+ AC_MSG_ERROR([boost.thread not found. Aborting.])
+fi
+
+
+
+
+# BAM related:
+ ac_bam_path=samtools-0.1.18
+ BAM_LIB="-lbam"
+ BAM_LDFLAGS="-L./$ac_bam_path"
+ BAM_CPPFLAGS="-I./$ac_bam_path"
+ AC_SUBST(BAM_CPPFLAGS)
+ AC_SUBST(BAM_LDFLAGS)
+ AC_SUBST(BAM_LIB)
# Checks for header files.
@@ -94,7 +108,7 @@ AS_IF([test "x$enable_debug" = xyes],
CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
CXXFLAGS="$CFLAGS"
CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3"
-LDFLAGS="$user_LDFLAGS"
+LDFLAGS="$BOOST_LDFLAGS $BAM_LDFLAGS $user_LDFLAGS"
AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
@@ -109,7 +123,8 @@ echo \
"
-- ${PACKAGE_STRING} Configuration Results --
C++ compiler: ${CXX} ${CXXFLAGS}
- Linker flags: ${LDFLAGS}"
+ Linker flags: ${LDFLAGS}
+ BOOST libraries: ${BOOST_THREAD_LIBS}"
if test x"${GCC}" = x"yes" ; then
gcc_version=`${CC} --version | head -n 1`
diff --git a/build-aux/depcomp b/depcomp
similarity index 100%
rename from build-aux/depcomp
rename to depcomp
diff --git a/build-aux/install-sh b/install-sh
similarity index 100%
rename from build-aux/install-sh
rename to install-sh
diff --git a/build-aux/missing b/missing
similarity index 100%
rename from build-aux/missing
rename to missing
diff --git a/src/GBase.cpp b/src/GBase.cpp
index ed117f5..4af86ff 100644
--- a/src/GBase.cpp
+++ b/src/GBase.cpp
@@ -64,10 +64,11 @@ void GError(const char* format,...){
char msg[4096];
va_list arguments;
va_start(arguments,format);
- vsprintf(msg,format,arguments);
+ _vsnprintf(msg, 4095, format, arguments);
+ vfprintf(stderr, format, arguments); // if a console is available
+ msg[4095]=0;
va_end(arguments);
OutputDebugString(msg);
- fprintf(stderr,"%s",msg); // if a console is available
MessageBox(NULL,msg,NULL,MB_OK|MB_ICONEXCLAMATION|MB_APPLMODAL);
#else
va_list arguments;
@@ -75,7 +76,7 @@ void GError(const char* format,...){
vfprintf(stderr,format,arguments);
va_end(arguments);
#ifdef DEBUG
- // modify here if you want a core dump
+ // modify here if you [don't] want a core dump
abort();
#endif
#endif
@@ -84,15 +85,21 @@ void GError(const char* format,...){
// Warning routine (just print message without exiting)
void GMessage(const char* format,...){
- char msg[4096];
- va_list arguments;
- va_start(arguments,format);
- vsprintf(msg,format,arguments);
- va_end(arguments);
#ifdef __WIN32__
+ char msg[4096];
+ va_list arguments;
+ va_start(arguments,format);
+ vfprintf(stderr, format , arguments); // if a console is available
+ _vsnprintf(msg, 4095, format, arguments);
+ msg[4095]=0;
+ va_end(arguments);
OutputDebugString(msg);
+ #else
+ va_list arguments;
+ va_start(arguments,format);
+ vfprintf(stderr,format,arguments);
+ va_end(arguments);
#endif
- fprintf(stderr,"%s",msg);fflush(stderr);
}
/*************** Memory management routines *****************/
@@ -286,7 +293,7 @@ char* Gsubstr(const char* str, char* from, char* to) {
}
if (to<from) return newEmptyStr();
int newlen=to-from+1;
- char* subs;
+ char* subs=NULL;
GMALLOC(subs, newlen);
memcpy(subs, str, newlen-1);
subs[newlen]='\0';
@@ -412,7 +419,7 @@ char* strchrs(const char* s, const char* chrs) {
char* upCase(const char* str) {
if (str==NULL) return NULL;
int len=strlen(str);
- char* upstr;
+ char* upstr=NULL;
GMALLOC(upstr, len+1);
upstr[len]='\0';
for (int i=0;i<len;i++) upstr[i]=toupper(str[i]);
@@ -422,7 +429,7 @@ char* upCase(const char* str) {
char* loCase(const char* str) {
if (str==NULL) return NULL;
int len=strlen(str);
- char* lostr;
+ char* lostr=NULL;
GMALLOC(lostr, len+1);
lostr[len]='\0';
for (int i=0;i<len;i++) lostr[i]=tolower(str[i]);
@@ -475,7 +482,7 @@ char* rstrfind(const char* str, const char* substr) {
char* strifind(const char* str, const char* substr) {
- // the case insensitive version of strstr -- finding a string within a strin
+ // case insensitive version of strstr -- finding a string within another
int l,i;
if (str==NULL || *str==0) return NULL;
if (substr==NULL || *substr==0) return NULL;
@@ -753,25 +760,15 @@ void writeFasta(FILE *fw, const char* seqid, const char* descr,
fflush(fw);
}
-char* commaprint(uint64 n) {
- int comma = '\0';
+char* commaprintnum(uint64 n) {
+ int comma = ',';
char retbuf[48];
char *p = &retbuf[sizeof(retbuf)-1];
int i = 0;
- if(comma == '\0') {
- /* struct lconv *lcp = localeconv();
- if(lcp != NULL) {
- if(lcp->thousands_sep != NULL &&
- *lcp->thousands_sep != '\0')
- comma = *lcp->thousands_sep;
- else */
- comma = ',';
- // }
- }
*p = '\0';
do {
if(i%3 == 0 && i != 0)
- *--p = comma;
+ *--p = comma;
*--p = '0' + n % 10;
n /= 10;
i++;
diff --git a/src/GBase.h b/src/GBase.h
index fc3c5ba..aaf06fd 100644
--- a/src/GBase.h
+++ b/src/GBase.h
@@ -419,7 +419,7 @@ char* fgetline(char* & buf, int& buflen, FILE* stream, off_t* f_pos=NULL, int* l
//print int/values nicely formatted in 3-digit groups
-char* commaprint(uint64 n);
+char* commaprintnum(uint64 n);
/*********************** File management functions *********************/
diff --git a/src/Makefile.am b/src/Makefile.am
index b845c2c..fadec38 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -7,6 +7,90 @@
EXTRA_DIST = \
tophat.py \
tophat2.in \
+samtools-0.1.18/AUTHORS \
+samtools-0.1.18/COPYING \
+samtools-0.1.18/ChangeLog \
+samtools-0.1.18/INSTALL \
+samtools-0.1.18/Makefile \
+samtools-0.1.18/Makefile.mingw \
+samtools-0.1.18/NEWS \
+samtools-0.1.18/bam.c \
+samtools-0.1.18/bam.h \
+samtools-0.1.18/bam2bcf.c \
+samtools-0.1.18/bam2bcf.h \
+samtools-0.1.18/bam2bcf_indel.c \
+samtools-0.1.18/bam2depth.c \
+samtools-0.1.18/bam_aux.c \
+samtools-0.1.18/bam_cat.c \
+samtools-0.1.18/bam_color.c \
+samtools-0.1.18/bam_endian.h \
+samtools-0.1.18/bam_import.c \
+samtools-0.1.18/bam_index.c \
+samtools-0.1.18/bam_lpileup.c \
+samtools-0.1.18/bam_mate.c \
+samtools-0.1.18/bam_md.c \
+samtools-0.1.18/bam_pileup.c \
+samtools-0.1.18/bam_plcmd.c \
+samtools-0.1.18/bam_reheader.c \
+samtools-0.1.18/bam_rmdup.c \
+samtools-0.1.18/bam_rmdupse.c \
+samtools-0.1.18/bam_sort.c \
+samtools-0.1.18/bam_stat.c \
+samtools-0.1.18/bam_tview.c \
+samtools-0.1.18/bamtk.c \
+samtools-0.1.18/bedidx.c \
+samtools-0.1.18/bgzf.c \
+samtools-0.1.18/bgzf.h \
+samtools-0.1.18/bgzip.c \
+samtools-0.1.18/cut_target.c \
+samtools-0.1.18/errmod.c \
+samtools-0.1.18/errmod.h \
+samtools-0.1.18/faidx.c \
+samtools-0.1.18/faidx.h \
+samtools-0.1.18/kaln.c \
+samtools-0.1.18/kaln.h \
+samtools-0.1.18/khash.h \
+samtools-0.1.18/klist.h \
+samtools-0.1.18/knetfile.c \
+samtools-0.1.18/knetfile.h \
+samtools-0.1.18/kprobaln.c \
+samtools-0.1.18/kprobaln.h \
+samtools-0.1.18/kseq.h \
+samtools-0.1.18/ksort.h \
+samtools-0.1.18/kstring.c \
+samtools-0.1.18/kstring.h \
+samtools-0.1.18/phase.c \
+samtools-0.1.18/razf.c \
+samtools-0.1.18/razf.h \
+samtools-0.1.18/razip.c \
+samtools-0.1.18/sam.c \
+samtools-0.1.18/sam.h \
+samtools-0.1.18/sam_header.c \
+samtools-0.1.18/sam_header.h \
+samtools-0.1.18/sam_view.c \
+samtools-0.1.18/sample.c \
+samtools-0.1.18/sample.h \
+samtools-0.1.18/samtools.1 \
+samtools-0.1.18/bcftools/Makefile \
+samtools-0.1.18/bcftools/README \
+samtools-0.1.18/bcftools/bcf.c \
+samtools-0.1.18/bcftools/bcf.h \
+samtools-0.1.18/bcftools/bcf.tex \
+samtools-0.1.18/bcftools/bcf2qcall.c \
+samtools-0.1.18/bcftools/bcfutils.c \
+samtools-0.1.18/bcftools/call1.c \
+samtools-0.1.18/bcftools/em.c \
+samtools-0.1.18/bcftools/fet.c \
+samtools-0.1.18/bcftools/index.c \
+samtools-0.1.18/bcftools/kfunc.c \
+samtools-0.1.18/bcftools/kmin.c \
+samtools-0.1.18/bcftools/kmin.h \
+samtools-0.1.18/bcftools/main.c \
+samtools-0.1.18/bcftools/mut.c \
+samtools-0.1.18/bcftools/prob1.c \
+samtools-0.1.18/bcftools/prob1.h \
+samtools-0.1.18/bcftools/vcf.c \
+samtools-0.1.18/bcftools/vcfutils.pl \
SeqAn-1.3/COPYING \
SeqAn-1.3/README \
SeqAn-1.3/seqan/chaining/chain_generic.h \
@@ -516,8 +600,17 @@ SeqAn-1.3/seqan/find_motif/find_motif_pms1.h \
SeqAn-1.3/seqan/find_motif/frequency_distribution.h \
SeqAn-1.3/seqan.h
+SAMDIR = ./samtools-0.1.18
+SAMLIB = libbam.a
+SAMPROG = samtools_0.1.18
+BAM_LIB = -lbam
+BAM_CPPFLAGS = -I$(SAMDIR)
+BAM_LDFLAGS = -L$(SAMDIR)
+
#-- progs to be installed in $prefix/bin
+
bin_PROGRAMS = \
+ $(SAMPROG) \
prep_reads \
gtf_to_fasta \
fix_map_ordering \
@@ -531,6 +624,7 @@ bin_PROGRAMS = \
tophat_reports \
sam_juncs
+# $(SAMPROG)
bin_SCRIPTS = \
tophat2 \
tophat
@@ -542,23 +636,25 @@ dist_bin_SCRIPTS = \
sra_to_solid \
tophat-fusion-post
+
+#samtools_0_1_18_SOURCES =
+#samtools_0_1_18_LDADD =
+
CLEANFILES = \
tophat2 \
tophat
+clean-local:
+ cd $(SAMDIR) && make clean
+
tophat2: tophat2.in
sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
tophat: tophat.py
sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat
-#SUFFIXES = .py
-#.py:
-# (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@
-
-
#-- tophat library for linking convienence
-noinst_LIBRARIES = libtophat.a libgc.a
+noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
noinst_HEADERS = \
reads.h \
@@ -611,7 +707,7 @@ libtophat_a_SOURCES = \
bam_merge_impl.cpp \
utils.cpp \
coverage.cpp
-
+
libgc_a_SOURCES = \
GBase.cpp \
codons.cpp \
@@ -627,11 +723,11 @@ prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
segment_juncs_SOURCES = segment_juncs.cpp
-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
long_spanning_reads_SOURCES = long_spanning_reads.cpp
-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
gtf_juncs_SOURCES = gtf_juncs.cpp
@@ -643,7 +739,7 @@ juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
tophat_reports_SOURCES = tophat_reports.cpp
-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
fix_map_ordering_SOURCES = fix_map_ordering.cpp
@@ -669,3 +765,13 @@ map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+
+
+libbam_a_SOURCES =
+samtools_0_1_18_SOURCES =
+
+$(SAMPROG): $(SAMLIB)
+
+
+$(SAMLIB):
+ cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
diff --git a/src/Makefile.in b/src/Makefile.in
index 5b55459..6c8009f 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -41,18 +41,18 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
-bin_PROGRAMS = prep_reads$(EXEEXT) gtf_to_fasta$(EXEEXT) \
- fix_map_ordering$(EXEEXT) bam2fastx$(EXEEXT) \
- segment_juncs$(EXEEXT) gtf_juncs$(EXEEXT) juncs_db$(EXEEXT) \
- long_spanning_reads$(EXEEXT) bam_merge$(EXEEXT) \
- map2gtf$(EXEEXT) tophat_reports$(EXEEXT) sam_juncs$(EXEEXT)
+bin_PROGRAMS = $(am__EXEEXT_1) prep_reads$(EXEEXT) \
+ gtf_to_fasta$(EXEEXT) fix_map_ordering$(EXEEXT) \
+ bam2fastx$(EXEEXT) segment_juncs$(EXEEXT) gtf_juncs$(EXEEXT) \
+ juncs_db$(EXEEXT) long_spanning_reads$(EXEEXT) \
+ bam_merge$(EXEEXT) map2gtf$(EXEEXT) tophat_reports$(EXEEXT) \
+ sam_juncs$(EXEEXT)
subdir = src
DIST_COMMON = $(dist_bin_SCRIPTS) $(noinst_HEADERS) \
$(srcdir)/Makefile.am $(srcdir)/Makefile.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/ax_boost_base.m4 \
- $(top_srcdir)/ax_boost_thread.m4 $(top_srcdir)/ax_bam.m4 \
- $(top_srcdir)/configure.ac
+ $(top_srcdir)/ax_boost_thread.m4 $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
mkinstalldirs = $(install_sh) -d
@@ -61,6 +61,10 @@ CONFIG_CLEAN_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+libbam_a_AR = $(AR) $(ARFLAGS)
+libbam_a_LIBADD =
+am_libbam_a_OBJECTS =
+libbam_a_OBJECTS = $(am_libbam_a_OBJECTS)
libgc_a_AR = $(AR) $(ARFLAGS)
libgc_a_LIBADD =
am_libgc_a_OBJECTS = GBase.$(OBJEXT) codons.$(OBJEXT) gdna.$(OBJEXT) \
@@ -75,6 +79,7 @@ am_libtophat_a_OBJECTS = reads.$(OBJEXT) alphabet.$(OBJEXT) \
inserts.$(OBJEXT) qual.$(OBJEXT) bam_merge_impl.$(OBJEXT) \
utils.$(OBJEXT) coverage.$(OBJEXT)
libtophat_a_OBJECTS = $(am_libtophat_a_OBJECTS)
+am__EXEEXT_1 = samtools_0.1.18$(EXEEXT)
am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" \
"$(DESTDIR)$(bindir)"
binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
@@ -107,8 +112,7 @@ juncs_db_DEPENDENCIES = $(top_builddir)/src/libtophat.a \
am_long_spanning_reads_OBJECTS = long_spanning_reads.$(OBJEXT)
long_spanning_reads_OBJECTS = $(am_long_spanning_reads_OBJECTS)
long_spanning_reads_DEPENDENCIES = $(top_builddir)/src/libtophat.a \
- $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
- $(am__DEPENDENCIES_1)
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
am_map2gtf_OBJECTS = map2gtf.$(OBJEXT)
map2gtf_OBJECTS = $(am_map2gtf_OBJECTS)
map2gtf_DEPENDENCIES = $(top_builddir)/src/libtophat.a libgc.a \
@@ -121,21 +125,22 @@ am_sam_juncs_OBJECTS = sam_juncs.$(OBJEXT)
sam_juncs_OBJECTS = $(am_sam_juncs_OBJECTS)
sam_juncs_DEPENDENCIES = $(top_builddir)/src/libtophat.a \
$(am__DEPENDENCIES_1)
+am_samtools_0_1_18_OBJECTS =
+samtools_0_1_18_OBJECTS = $(am_samtools_0_1_18_OBJECTS)
+samtools_0_1_18_LDADD = $(LDADD)
am_segment_juncs_OBJECTS = segment_juncs.$(OBJEXT)
segment_juncs_OBJECTS = $(am_segment_juncs_OBJECTS)
segment_juncs_DEPENDENCIES = $(top_builddir)/src/libtophat.a \
- $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
- $(am__DEPENDENCIES_1)
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
am_tophat_reports_OBJECTS = tophat_reports.$(OBJEXT)
tophat_reports_OBJECTS = $(am_tophat_reports_OBJECTS)
tophat_reports_DEPENDENCIES = $(top_builddir)/src/libtophat.a \
- $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
- $(am__DEPENDENCIES_1)
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
binSCRIPT_INSTALL = $(INSTALL_SCRIPT)
dist_binSCRIPT_INSTALL = $(INSTALL_SCRIPT)
SCRIPTS = $(bin_SCRIPTS) $(dist_bin_SCRIPTS)
DEFAULT_INCLUDES = -I. -I$(srcdir) -I$(top_builddir)
-depcomp = $(SHELL) $(top_srcdir)/build-aux/depcomp
+depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
@@ -146,20 +151,22 @@ CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
-SOURCES = $(libgc_a_SOURCES) $(libtophat_a_SOURCES) \
- $(bam2fastx_SOURCES) $(bam_merge_SOURCES) \
- $(fix_map_ordering_SOURCES) $(gtf_juncs_SOURCES) \
- $(gtf_to_fasta_SOURCES) $(juncs_db_SOURCES) \
- $(long_spanning_reads_SOURCES) $(map2gtf_SOURCES) \
- $(prep_reads_SOURCES) $(sam_juncs_SOURCES) \
- $(segment_juncs_SOURCES) $(tophat_reports_SOURCES)
-DIST_SOURCES = $(libgc_a_SOURCES) $(libtophat_a_SOURCES) \
- $(bam2fastx_SOURCES) $(bam_merge_SOURCES) \
- $(fix_map_ordering_SOURCES) $(gtf_juncs_SOURCES) \
- $(gtf_to_fasta_SOURCES) $(juncs_db_SOURCES) \
- $(long_spanning_reads_SOURCES) $(map2gtf_SOURCES) \
- $(prep_reads_SOURCES) $(sam_juncs_SOURCES) \
- $(segment_juncs_SOURCES) $(tophat_reports_SOURCES)
+SOURCES = $(libbam_a_SOURCES) $(libgc_a_SOURCES) \
+ $(libtophat_a_SOURCES) $(bam2fastx_SOURCES) \
+ $(bam_merge_SOURCES) $(fix_map_ordering_SOURCES) \
+ $(gtf_juncs_SOURCES) $(gtf_to_fasta_SOURCES) \
+ $(juncs_db_SOURCES) $(long_spanning_reads_SOURCES) \
+ $(map2gtf_SOURCES) $(prep_reads_SOURCES) $(sam_juncs_SOURCES) \
+ $(samtools_0_1_18_SOURCES) $(segment_juncs_SOURCES) \
+ $(tophat_reports_SOURCES)
+DIST_SOURCES = $(libbam_a_SOURCES) $(libgc_a_SOURCES) \
+ $(libtophat_a_SOURCES) $(bam2fastx_SOURCES) \
+ $(bam_merge_SOURCES) $(fix_map_ordering_SOURCES) \
+ $(gtf_juncs_SOURCES) $(gtf_to_fasta_SOURCES) \
+ $(juncs_db_SOURCES) $(long_spanning_reads_SOURCES) \
+ $(map2gtf_SOURCES) $(prep_reads_SOURCES) $(sam_juncs_SOURCES) \
+ $(samtools_0_1_18_SOURCES) $(segment_juncs_SOURCES) \
+ $(tophat_reports_SOURCES)
HEADERS = $(noinst_HEADERS)
ETAGS = etags
CTAGS = ctags
@@ -172,19 +179,18 @@ AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
AWK = @AWK@
-BAM_CPPFLAGS = @BAM_CPPFLAGS@
-BAM_LDFLAGS = @BAM_LDFLAGS@
-BAM_LIB = @BAM_LIB@
+BAM_CPPFLAGS = -I$(SAMDIR)
+BAM_LDFLAGS = -L$(SAMDIR)
+BAM_LIB = -lbam
BOOST_CPPFLAGS = @BOOST_CPPFLAGS@
BOOST_LDFLAGS = @BOOST_LDFLAGS@
-BOOST_SYSTEM_LIB = @BOOST_SYSTEM_LIB@
-BOOST_THREAD_LIB = @BOOST_THREAD_LIB@
+BOOST_THREAD_LIBS = @BOOST_THREAD_LIBS@
CC = @CC@
CCDEPMODE = @CCDEPMODE@
CFLAGS = @CFLAGS@
-CPP = @CPP@
CPPFLAGS = @CPPFLAGS@
CXX = @CXX@
+CXXCPP = @CXXCPP@
CXXDEPMODE = @CXXDEPMODE@
CXXFLAGS = @CXXFLAGS@
CYGPATH_W = @CYGPATH_W@
@@ -275,6 +281,90 @@ target_alias = @target_alias@
EXTRA_DIST = \
tophat.py \
tophat2.in \
+samtools-0.1.18/AUTHORS \
+samtools-0.1.18/COPYING \
+samtools-0.1.18/ChangeLog \
+samtools-0.1.18/INSTALL \
+samtools-0.1.18/Makefile \
+samtools-0.1.18/Makefile.mingw \
+samtools-0.1.18/NEWS \
+samtools-0.1.18/bam.c \
+samtools-0.1.18/bam.h \
+samtools-0.1.18/bam2bcf.c \
+samtools-0.1.18/bam2bcf.h \
+samtools-0.1.18/bam2bcf_indel.c \
+samtools-0.1.18/bam2depth.c \
+samtools-0.1.18/bam_aux.c \
+samtools-0.1.18/bam_cat.c \
+samtools-0.1.18/bam_color.c \
+samtools-0.1.18/bam_endian.h \
+samtools-0.1.18/bam_import.c \
+samtools-0.1.18/bam_index.c \
+samtools-0.1.18/bam_lpileup.c \
+samtools-0.1.18/bam_mate.c \
+samtools-0.1.18/bam_md.c \
+samtools-0.1.18/bam_pileup.c \
+samtools-0.1.18/bam_plcmd.c \
+samtools-0.1.18/bam_reheader.c \
+samtools-0.1.18/bam_rmdup.c \
+samtools-0.1.18/bam_rmdupse.c \
+samtools-0.1.18/bam_sort.c \
+samtools-0.1.18/bam_stat.c \
+samtools-0.1.18/bam_tview.c \
+samtools-0.1.18/bamtk.c \
+samtools-0.1.18/bedidx.c \
+samtools-0.1.18/bgzf.c \
+samtools-0.1.18/bgzf.h \
+samtools-0.1.18/bgzip.c \
+samtools-0.1.18/cut_target.c \
+samtools-0.1.18/errmod.c \
+samtools-0.1.18/errmod.h \
+samtools-0.1.18/faidx.c \
+samtools-0.1.18/faidx.h \
+samtools-0.1.18/kaln.c \
+samtools-0.1.18/kaln.h \
+samtools-0.1.18/khash.h \
+samtools-0.1.18/klist.h \
+samtools-0.1.18/knetfile.c \
+samtools-0.1.18/knetfile.h \
+samtools-0.1.18/kprobaln.c \
+samtools-0.1.18/kprobaln.h \
+samtools-0.1.18/kseq.h \
+samtools-0.1.18/ksort.h \
+samtools-0.1.18/kstring.c \
+samtools-0.1.18/kstring.h \
+samtools-0.1.18/phase.c \
+samtools-0.1.18/razf.c \
+samtools-0.1.18/razf.h \
+samtools-0.1.18/razip.c \
+samtools-0.1.18/sam.c \
+samtools-0.1.18/sam.h \
+samtools-0.1.18/sam_header.c \
+samtools-0.1.18/sam_header.h \
+samtools-0.1.18/sam_view.c \
+samtools-0.1.18/sample.c \
+samtools-0.1.18/sample.h \
+samtools-0.1.18/samtools.1 \
+samtools-0.1.18/bcftools/Makefile \
+samtools-0.1.18/bcftools/README \
+samtools-0.1.18/bcftools/bcf.c \
+samtools-0.1.18/bcftools/bcf.h \
+samtools-0.1.18/bcftools/bcf.tex \
+samtools-0.1.18/bcftools/bcf2qcall.c \
+samtools-0.1.18/bcftools/bcfutils.c \
+samtools-0.1.18/bcftools/call1.c \
+samtools-0.1.18/bcftools/em.c \
+samtools-0.1.18/bcftools/fet.c \
+samtools-0.1.18/bcftools/index.c \
+samtools-0.1.18/bcftools/kfunc.c \
+samtools-0.1.18/bcftools/kmin.c \
+samtools-0.1.18/bcftools/kmin.h \
+samtools-0.1.18/bcftools/main.c \
+samtools-0.1.18/bcftools/mut.c \
+samtools-0.1.18/bcftools/prob1.c \
+samtools-0.1.18/bcftools/prob1.h \
+samtools-0.1.18/bcftools/vcf.c \
+samtools-0.1.18/bcftools/vcfutils.pl \
SeqAn-1.3/COPYING \
SeqAn-1.3/README \
SeqAn-1.3/seqan/chaining/chain_generic.h \
@@ -784,6 +874,11 @@ SeqAn-1.3/seqan/find_motif/find_motif_pms1.h \
SeqAn-1.3/seqan/find_motif/frequency_distribution.h \
SeqAn-1.3/seqan.h
+SAMDIR = ./samtools-0.1.18
+SAMLIB = libbam.a
+SAMPROG = samtools_0.1.18
+
+# $(SAMPROG)
bin_SCRIPTS = \
tophat2 \
tophat
@@ -796,17 +891,16 @@ dist_bin_SCRIPTS = \
sra_to_solid \
tophat-fusion-post
+
+#samtools_0_1_18_SOURCES =
+#samtools_0_1_18_LDADD =
CLEANFILES = \
tophat2 \
tophat
-#SUFFIXES = .py
-#.py:
-# (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@
-
#-- tophat library for linking convienence
-noinst_LIBRARIES = libtophat.a libgc.a
+noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
noinst_HEADERS = \
reads.h \
codons.h \
@@ -873,10 +967,10 @@ prep_reads_SOURCES = prep_reads.cpp
prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
segment_juncs_SOURCES = segment_juncs.cpp
-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
long_spanning_reads_SOURCES = long_spanning_reads.cpp
-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
gtf_juncs_SOURCES = gtf_juncs.cpp
gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
@@ -885,7 +979,7 @@ juncs_db_SOURCES = juncs_db.cpp
juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
tophat_reports_SOURCES = tophat_reports.cpp
-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
fix_map_ordering_SOURCES = fix_map_ordering.cpp
fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
@@ -905,6 +999,8 @@ map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+libbam_a_SOURCES =
+samtools_0_1_18_SOURCES =
all: all-am
.SUFFIXES:
@@ -941,6 +1037,10 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+libbam.a: $(libbam_a_OBJECTS) $(libbam_a_DEPENDENCIES)
+ -rm -f libbam.a
+ $(libbam_a_AR) libbam.a $(libbam_a_OBJECTS) $(libbam_a_LIBADD)
+ $(RANLIB) libbam.a
libgc.a: $(libgc_a_OBJECTS) $(libgc_a_DEPENDENCIES)
-rm -f libgc.a
$(libgc_a_AR) libgc.a $(libgc_a_OBJECTS) $(libgc_a_LIBADD)
@@ -1002,6 +1102,9 @@ prep_reads$(EXEEXT): $(prep_reads_OBJECTS) $(prep_reads_DEPENDENCIES)
sam_juncs$(EXEEXT): $(sam_juncs_OBJECTS) $(sam_juncs_DEPENDENCIES)
@rm -f sam_juncs$(EXEEXT)
$(CXXLINK) $(sam_juncs_LDFLAGS) $(sam_juncs_OBJECTS) $(sam_juncs_LDADD) $(LIBS)
+samtools_0.1.18$(EXEEXT): $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_DEPENDENCIES)
+ @rm -f samtools_0.1.18$(EXEEXT)
+ $(LINK) $(samtools_0_1_18_LDFLAGS) $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_LDADD) $(LIBS)
segment_juncs$(EXEEXT): $(segment_juncs_OBJECTS) $(segment_juncs_DEPENDENCIES)
@rm -f segment_juncs$(EXEEXT)
$(CXXLINK) $(segment_juncs_LDFLAGS) $(segment_juncs_OBJECTS) $(segment_juncs_LDADD) $(LIBS)
@@ -1167,7 +1270,7 @@ distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
distdir: $(DISTFILES)
- $(mkdir_p) $(distdir)/SeqAn-1.3 $(distdir)/SeqAn-1.3/seqan $(distdir)/SeqAn-1.3/seqan/align $(distdir)/SeqAn-1.3/seqan/basic $(distdir)/SeqAn-1.3/seqan/blast $(distdir)/SeqAn-1.3/seqan/chaining $(distdir)/SeqAn-1.3/seqan/consensus $(distdir)/SeqAn-1.3/seqan/file $(distdir)/SeqAn-1.3/seqan/find $(distdir)/SeqAn-1.3/seqan/find2 $(distdir)/SeqAn-1.3/seqan/find_motif $(distdir)/SeqAn-1.3/seqan/graph_algorithms $(distdir)/SeqAn-1.3/seqan/graph_align $(distdir)/SeqAn-1.3/seqan/graph_msa $(dis [...]
+ $(mkdir_p) $(distdir)/SeqAn-1.3 $(distdir)/SeqAn-1.3/seqan $(distdir)/SeqAn-1.3/seqan/align $(distdir)/SeqAn-1.3/seqan/basic $(distdir)/SeqAn-1.3/seqan/blast $(distdir)/SeqAn-1.3/seqan/chaining $(distdir)/SeqAn-1.3/seqan/consensus $(distdir)/SeqAn-1.3/seqan/file $(distdir)/SeqAn-1.3/seqan/find $(distdir)/SeqAn-1.3/seqan/find2 $(distdir)/SeqAn-1.3/seqan/find_motif $(distdir)/SeqAn-1.3/seqan/graph_algorithms $(distdir)/SeqAn-1.3/seqan/graph_align $(distdir)/SeqAn-1.3/seqan/graph_msa $(dis [...]
@srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
list='$(DISTFILES)'; for file in $$list; do \
@@ -1228,8 +1331,8 @@ maintainer-clean-generic:
@echo "it deletes files that may require special tools to rebuild."
clean: clean-am
-clean-am: clean-binPROGRAMS clean-generic clean-noinstLIBRARIES \
- mostlyclean-am
+clean-am: clean-binPROGRAMS clean-generic clean-local \
+ clean-noinstLIBRARIES mostlyclean-am
distclean: distclean-am
-rm -rf ./$(DEPDIR)
@@ -1279,10 +1382,10 @@ uninstall-am: uninstall-binPROGRAMS uninstall-binSCRIPTS \
uninstall-dist_binSCRIPTS uninstall-info-am
.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic clean-noinstLIBRARIES ctags distclean \
- distclean-compile distclean-generic distclean-tags distdir dvi \
- dvi-am html html-am info info-am install install-am \
- install-binPROGRAMS install-binSCRIPTS install-data \
+ clean-generic clean-local clean-noinstLIBRARIES ctags \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-binSCRIPTS install-data \
install-data-am install-dist_binSCRIPTS install-exec \
install-exec-am install-info install-info-am install-man \
install-strip installcheck installcheck-am installdirs \
@@ -1293,11 +1396,19 @@ uninstall-am: uninstall-binPROGRAMS uninstall-binSCRIPTS \
uninstall-info-am
+clean-local:
+ cd $(SAMDIR) && make clean
+
tophat2: tophat2.in
sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
tophat: tophat.py
sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat
+
+$(SAMPROG): $(SAMLIB)
+
+$(SAMLIB):
+ cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
diff --git a/src/align_status.h b/src/align_status.h
index a237821..c50ed0d 100755
--- a/src/align_status.h
+++ b/src/align_status.h
@@ -14,7 +14,7 @@
#include <cassert>
#include <cstring>
#include <seqan/sequence.h>
-#include <bam/sam.h>
+#include <sam.h>
#include "common.h"
#include "bwt_map.h"
diff --git a/src/bam2fastx.cpp b/src/bam2fastx.cpp
index 51f755e..e500fa8 100644
--- a/src/bam2fastx.cpp
+++ b/src/bam2fastx.cpp
@@ -5,8 +5,8 @@
#include <assert.h>
#include <string>
-#include "bam/bam.h"
-#include "bam/sam.h"
+#include "bam.h"
+#include "sam.h"
using namespace std;
diff --git a/src/bed_to_juncs b/src/bed_to_juncs
index 97ebb14..0e82115 100755
--- a/src/bed_to_juncs
+++ b/src/bed_to_juncs
@@ -52,10 +52,11 @@ def main(argv=None):
orientation = cols[5]
block_starts = [int(x) for x in cols[11].split(",")]
block_sizes = [int(x) for x in cols[10].split(",")]
-
left_pos = int(cols[1]) + block_starts[0] + block_sizes[0] - 1
- right_pos = int(cols[1]) + block_starts[1]
- print "%s\t%d\t%d\t%s" % (chromosome, left_pos, right_pos, orientation)
+ right_pos = int(cols[1]) + block_starts[1]
+ #print "%s\t%d\t%d\t%s" % (chromosome, left_pos, right_pos, orientation)
+ counts = cols[4]
+ print "%s\t%d\t%d\t%s\t%s" % (chromosome, left_pos, right_pos, orientation, counts)
except Usage, err:
diff --git a/src/bwt_map.h b/src/bwt_map.h
index c712bcb..4c43782 100644
--- a/src/bwt_map.h
+++ b/src/bwt_map.h
@@ -16,7 +16,7 @@
#include <algorithm>
#include <seqan/sequence.h>
-#include <bam/sam.h>
+#include <sam.h>
using namespace std;
#include "common.h"
@@ -922,13 +922,7 @@ class SplicedBowtieHitFactory : public LineHitFactory {
SplicedBowtieHitFactory(ReadTable& insert_table,
RefSequenceTable& reference_table,
int anchor_length) :
- LineHitFactory(insert_table, reference_table),
- _anchor_length(anchor_length){}
-
- private:
- int _anchor_length;
- int _seg_offset;
- int _size_buf;
+ LineHitFactory(insert_table, reference_table) {}
};
class SplicedSAMHitFactory : public LineHitFactory {
diff --git a/src/common.cpp b/src/common.cpp
index bc6664e..e6173aa 100644
--- a/src/common.cpp
+++ b/src/common.cpp
@@ -151,7 +151,7 @@ string ium_reads = "";
string sam_header = "";
string sam_readgroup_id = "";
string zpacker = "";
-string samtools_path = "samtools";
+string samtools_path = "samtools_0.1.18";
bool solexa_quals = false;
bool phred64_quals = false;
diff --git a/src/common.h b/src/common.h
index 49f904e..5e601e1 100644
--- a/src/common.h
+++ b/src/common.h
@@ -15,8 +15,8 @@
#include <cstdio>
#include <string>
#include <vector>
-#include "bam/bam.h"
-#include "bam/sam.h"
+#include "bam.h"
+#include "sam.h"
#define MAX_READ_LEN 1024
diff --git a/src/map2gtf.h b/src/map2gtf.h
index 9e163ff..96b51fe 100644
--- a/src/map2gtf.h
+++ b/src/map2gtf.h
@@ -20,8 +20,8 @@
#include <sstream>
#include <vector>
-#include <bam/bam.h>
-#include <bam/sam.h>
+#include <bam.h>
+#include <sam.h>
#include <seqan/sequence.h>
diff --git a/src/samtools-0.1.18/AUTHORS b/src/samtools-0.1.18/AUTHORS
new file mode 100644
index 0000000..95afabb
--- /dev/null
+++ b/src/samtools-0.1.18/AUTHORS
@@ -0,0 +1,20 @@
+Heng Li from the Sanger Institute wrote most of the initial source codes
+of SAMtools and various converters.
+
+Bob Handsaker from the Broad Institute is a major contributor to the
+SAM/BAM specification. He designed and implemented the BGZF format, the
+underlying indexable compression format for the BAM format. BGZF does
+not support arithmetic between file offsets.
+
+Jue Ruan for the Beijing Genome Institute designed and implemented the
+RAZF format, an alternative indexable compression format. RAZF supports
+arithmetic between file offsets, at the cost of increased index file
+size and the full compatibility with gzip. RAZF is optional and only
+used in `faidx' for indexing RAZF compressed fasta files.
+
+Colin Hercus updated novo2sam.pl to support gapped alignment by
+novoalign.
+
+Petr Danecek contributed the header parsing library sam_header.c and
+sam2vcf.pl script and added knet support to the RAZF library.
+
diff --git a/src/samtools-0.1.18/COPYING b/src/samtools-0.1.18/COPYING
new file mode 100644
index 0000000..82fa2f4
--- /dev/null
+++ b/src/samtools-0.1.18/COPYING
@@ -0,0 +1,21 @@
+The MIT License
+
+Copyright (c) 2008-2009 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
\ No newline at end of file
diff --git a/src/samtools-0.1.18/ChangeLog b/src/samtools-0.1.18/ChangeLog
new file mode 100644
index 0000000..a471838
--- /dev/null
+++ b/src/samtools-0.1.18/ChangeLog
@@ -0,0 +1,5948 @@
+------------------------------------------------------------------------
+r925 | lh3lh3 | 2011-02-28 15:45:17 -0500 (Mon, 28 Feb 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/phase.c
+
+minor changes to a heuristic rule
+
+------------------------------------------------------------------------
+r924 | lh3lh3 | 2011-02-28 15:24:04 -0500 (Mon, 28 Feb 2011) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bcftools/vcfutils.pl
+ M /trunk/samtools/phase.c
+
+ * 0.1.12-r924:126
+ * fixed a bug in phase (due to recent changes)
+ * fixed a bug in vcf2fq
+
+------------------------------------------------------------------------
+r923 | lh3lh3 | 2011-02-28 12:57:39 -0500 (Mon, 28 Feb 2011) | 5 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/phase.c
+
+ * put version number in bam.h
+ * write version to BCF
+ * in phase, change the default -q to 37
+ * output a little more information during phasing
+
+------------------------------------------------------------------------
+r922 | lh3lh3 | 2011-02-25 16:40:09 -0500 (Fri, 25 Feb 2011) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.tex
+ M /trunk/samtools/bcftools/bcf2qcall.c
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/ld.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/vcf.c
+ M /trunk/samtools/cut_target.c
+
+ * change the order of PL/GL according to the latest VCF spec
+ * change the type of SP to int32_t
+
+------------------------------------------------------------------------
+r921 | lh3lh3 | 2011-02-25 14:40:56 -0500 (Fri, 25 Feb 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.tex
+
+update the BCF spec
+
+------------------------------------------------------------------------
+r920 | lh3lh3 | 2011-02-25 00:59:27 -0500 (Fri, 25 Feb 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/cut_target.c
+ M /trunk/samtools/errmod.h
+ M /trunk/samtools/faidx.c
+ M /trunk/samtools/khash.h
+ M /trunk/samtools/kstring.c
+ M /trunk/samtools/kstring.h
+ A /trunk/samtools/phase.c
+ M /trunk/samtools/samtools.1
+
+added the phase command
+
+------------------------------------------------------------------------
+r918 | lh3lh3 | 2011-02-24 10:05:54 -0500 (Thu, 24 Feb 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+
+added "const" to bcf_p1_cal()
+
+------------------------------------------------------------------------
+r917 | lh3lh3 | 2011-02-24 09:36:30 -0500 (Thu, 24 Feb 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+
+more meaningful BAM truncation message
+
+------------------------------------------------------------------------
+r916 | lh3lh3 | 2011-02-24 09:35:06 -0500 (Thu, 24 Feb 2011) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/vcf.c
+
+ * automatically fix errors in GL
+ * output unrecognized FORMAT as "."
+
+------------------------------------------------------------------------
+r913 | lh3lh3 | 2011-02-10 22:59:47 -0500 (Thu, 10 Feb 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/vcf.c
+
+finished VCF->BCF conversion
+
+------------------------------------------------------------------------
+r910 | petulda | 2011-02-03 03:13:48 -0500 (Thu, 03 Feb 2011) | 1 line
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+Prevent division by zero
+------------------------------------------------------------------------
+r909 | lh3lh3 | 2011-02-02 11:29:20 -0500 (Wed, 02 Feb 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+
+fixed a typo in the VCF header
+
+------------------------------------------------------------------------
+r908 | lh3lh3 | 2011-02-02 11:28:24 -0500 (Wed, 02 Feb 2011) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam_index.c
+
+ * fixed an out-of-boundary bug
+ * improved sorting order checking in index
+
+------------------------------------------------------------------------
+r907 | lh3lh3 | 2011-01-29 22:59:20 -0500 (Sat, 29 Jan 2011) | 4 lines
+Changed paths:
+ M /trunk/samtools/INSTALL
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/knetfile.c
+
+ * avoid a segfault when network connect fails
+ * update INSTALL
+ * fixed a bug in tview on big-endian by Nathan Weeks
+
+------------------------------------------------------------------------
+r903 | lh3lh3 | 2011-01-27 14:50:02 -0500 (Thu, 27 Jan 2011) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_md.c
+
+ * fixed a rare memory issue in bam_md.c
+ * fixed a bug in indel calling related to unmapped and refskip reads
+
+------------------------------------------------------------------------
+r902 | lh3lh3 | 2011-01-23 21:46:18 -0500 (Sun, 23 Jan 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/fet.c
+
+fixed two minor bugs in Fisher's exact test
+
+------------------------------------------------------------------------
+r899 | petulda | 2011-01-19 09:28:02 -0500 (Wed, 19 Jan 2011) | 1 line
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+Skip sites with unknown ref
+------------------------------------------------------------------------
+r898 | lh3lh3 | 2011-01-15 12:56:05 -0500 (Sat, 15 Jan 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_md.c
+
+move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
+
+------------------------------------------------------------------------
+r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/call1.c
+
+ * samtools-0.1.12-10 (r896)
+ * allow to exclude read groups in mpileup
+
+------------------------------------------------------------------------
+r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.tex
+
+sorry. It is SP not ST
+
+------------------------------------------------------------------------
+r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.tex
+
+added ST
+
+------------------------------------------------------------------------
+r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+
+Fixed a typo in read_samples
+------------------------------------------------------------------------
+r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/examples/Makefile
+
+System libraries go *after* user libraries in link commands, because
+the user libraries may themselves have dependencies that are satisfied
+by the system libraries. It's not rocket science!
+
+This makes a difference with some linkers; or with -static or --as-needed.
+
+The examples/Makefile fix is from Charles Plessy.
+See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
+
+------------------------------------------------------------------------
+r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/call1.c
+
+ * samtools-0.1.12-9 (r891)
+ * allow to call SNPs from a subset of samples
+
+------------------------------------------------------------------------
+r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.12-12 (r889)
+ * set mapQ as 20 if it equals 255
+
+------------------------------------------------------------------------
+r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+When -B is applied to mpileup, still use paired reads only unless -A is flagged.
+
+------------------------------------------------------------------------
+r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.12-6 (r887)
+ * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
+
+------------------------------------------------------------------------
+r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+(Arguably) improved the indel caller a tiny bit for lowCov data.
+
+------------------------------------------------------------------------
+r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+
+Fixed the VCF header to pass validation
+------------------------------------------------------------------------
+r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * samtools-0.1.12-4 (r884)
+ * fixed a long-existing flaw in the INDEL calling model
+
+------------------------------------------------------------------------
+r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+compute max SP and max GQ from sample genotypes
+
+------------------------------------------------------------------------
+r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+ D /trunk/samtools/bcftools/bcf-fix.pl
+
+drop bcf-fix.pl as it is redundant by the latest changes
+
+------------------------------------------------------------------------
+r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/vcf.c
+
+ * fixed a minor issue in printing VCFs
+ * write bcftools specific INFO and FORMAT in the header
+
+------------------------------------------------------------------------
+r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/call1.c
+
+Make sure that the GT genotype field is the first
+
+------------------------------------------------------------------------
+r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.12-2 (r877)
+
+ * allow to fine control the selection of indel candidates. The current
+ setting is okay for lowCov and highCov with ~100 samples, but it
+ skips too many indels for highCov with >250 samples.
+
+
+------------------------------------------------------------------------
+r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+a spelling error..
+
+------------------------------------------------------------------------
+r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.12-1 (r873)
+ * added a switch to allow anomalous read pairs in calling
+
+------------------------------------------------------------------------
+r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+fixed a bug in vcf2fq
+
+------------------------------------------------------------------------
+r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+added a warning for the Windows version
+
+------------------------------------------------------------------------
+r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+
+In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
+According to the manual page, this change is valid. However, MinGW seems
+to interpret "%lf" as "%Lf".
+
+------------------------------------------------------------------------
+r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+ M /trunk/samtools/bam_aux.c
+
+bring back the windows support
+
+------------------------------------------------------------------------
+r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_reheader.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+Fixed a compiling error when knetfile is not used.
+
+------------------------------------------------------------------------
+r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+vcf->fastq
+
+------------------------------------------------------------------------
+r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+
+ * remove "-f". Instead always compute consensus quality
+ * increase the upper limit of quality
+
+------------------------------------------------------------------------
+r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+
+more informative error message
+
+------------------------------------------------------------------------
+r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.12a
+
+------------------------------------------------------------------------
+r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+
+a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
+
+------------------------------------------------------------------------
+r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+Release samtools-0.1.12
+
+------------------------------------------------------------------------
+r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/bcf.c
+
+ * samtools-0.1.11-1 (r858)
+ * fixed a bug in mpileup which causes segfaults
+ * bcftools: do not segfault when BCF contains errors
+
+------------------------------------------------------------------------
+r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+fixed a memory leak in bam_fetch()
+
+------------------------------------------------------------------------
+r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * fixed a memory violation
+ * added splitchr to vcfutils.pl
+
+------------------------------------------------------------------------
+r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/ld.c
+
+fixed a typo/bug in r^2 computation
+
+------------------------------------------------------------------------
+r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+forget to change the version information
+
+------------------------------------------------------------------------
+r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bcftools/bcftools.1
+ M /trunk/samtools/samtools.1
+
+Release samtools-0.1.11
+
+------------------------------------------------------------------------
+r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+
+ * samtools-0.1.10-9 (r844)
+ * added the "folded" or reference-free mode for variant calling
+
+------------------------------------------------------------------------
+r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bam_sort.c
+
+In merging, if -R is specified, do not abort if the sequence dictionary is different.
+
+------------------------------------------------------------------------
+r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+
+When merging BAM headers, compare the list of target reference sequences
+strictly (and fail/abort if there is a mismatch), but allow one list to be a
+prefix of the other. (i.e., check that the lists are identical up until the
+shorter runs out, and add the excess targets from the longer to the output.)
+
+------------------------------------------------------------------------
+r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10 (r841)
+ * fixed a bug in pileup when the first CIGAR operation is D
+ * fixed a bug in view with range query
+
+------------------------------------------------------------------------
+r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-4 (r840)
+
+ * drop the MNP caller. It is slow while does not diliver too much
+ benefit. Possibly I will work on it in future given more time.
+
+ * there is a segfault in pileup
+
+ * someone has reported segfault from view/index/sort
+
+
+------------------------------------------------------------------------
+r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-6 (r839)
+
+ * call MNPs without realignment because it seems to me that it is not
+ worthwhile to significantly slow down SNP calling.
+
+ * the result looks quite different from the previous version. I have
+ work to do...
+
+
+------------------------------------------------------------------------
+r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+Apply a patch by Rob Davis, which improves fault detection.
+
+------------------------------------------------------------------------
+r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-r836
+ * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
+
+------------------------------------------------------------------------
+r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * modify the filtering rule: also filter SNPs around filtered indels
+ * added MNP filter
+
+------------------------------------------------------------------------
+r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-4 (r834)
+ * fixed a silly bug in printing MNP
+ * restrict to at most 1 alternative allele
+
+------------------------------------------------------------------------
+r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bamtk.c
+
+fixed a bug in printing MNPs
+
+------------------------------------------------------------------------
+r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+minor change to how seqQ is applied
+
+------------------------------------------------------------------------
+r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10 (r831)
+ * initial MNP caller
+
+------------------------------------------------------------------------
+r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.10 (r829)
+
+------------------------------------------------------------------------
+r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+update version information: samtools-0.1.9-20 (r828)
+
+------------------------------------------------------------------------
+r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+
+bcftools: allow to skip indels
+
+------------------------------------------------------------------------
+r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+
+remove ZQ if both BQ and ZQ are present
+
+------------------------------------------------------------------------
+r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.9-18 (r825)
+ * change the behaviour of calmd such that by default it does not change the base quality
+
+------------------------------------------------------------------------
+r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.9-17 (r824)
+ * added command line options to change the default parameters in indel calling
+ * update the manual
+
+------------------------------------------------------------------------
+r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-r823
+ * the BQ tag is now 64 shifted, not 33 shifted
+
+------------------------------------------------------------------------
+r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.9-16 (r822)
+ * keep the raw depth because in indel calling, DP4 may be way off the true depth
+
+------------------------------------------------------------------------
+r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-15 (r821)
+ * calmd: write BQ
+ * skip realignment if BQ is present
+
+------------------------------------------------------------------------
+r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-14 (r820)
+ * penalize reads with excessive differences in indel calling
+
+------------------------------------------------------------------------
+r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-13 (r819)
+ * fixed a bug in pileup given refskip
+
+------------------------------------------------------------------------
+r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-r818
+ * for indel calling, do two rounds of probabilistic realignments
+
+------------------------------------------------------------------------
+r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * samtools-0.1.19-11 (r817)
+ * only initiate indel calling when 0.2% of reads contain a gap
+
+------------------------------------------------------------------------
+r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-10 (r816)
+
+ * I know why the forward method fails. it is because of zero base
+ qualities. when that is fixed, the forward method seems to give
+ better results than Viterbi, as it should be. I am tired...
+
+
+------------------------------------------------------------------------
+r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam2bcf_indel.c
+
+effectively revert to the viterbi version. The forward realignment gives too many false positives.
+
+------------------------------------------------------------------------
+r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-9 (r810)
+ * use forward, instead of viterbi, for realignment
+ * realignment is now quality aware
+
+------------------------------------------------------------------------
+r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/kprobaln.c
+ M /trunk/samtools/kprobaln.h
+
+ * prepare to replace kaln with kprobaln in realignment
+
+------------------------------------------------------------------------
+r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+
+fixed a typo
+
+------------------------------------------------------------------------
+r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+
+use zlib for direct reading when BCF_LITE is in use
+
+------------------------------------------------------------------------
+r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+
+ * do not use reads containing too many mismatches for indel calling
+ * fixed a trivial bug in case of multi-allelic indels
+
+------------------------------------------------------------------------
+r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-8 (r809)
+ * fixed a bug in the indel caller
+
+------------------------------------------------------------------------
+r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+minor change to makefile
+
+------------------------------------------------------------------------
+r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * samtools-0.1.9-8 (r807)
+ * collect indel candidates only from specified platforms (@RG-PL)
+ * merge varFilter and filter4vcf in vcfutils.pl
+
+------------------------------------------------------------------------
+r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+
+bcftools: compute equal-tail (Bayesian) credible interval
+
+------------------------------------------------------------------------
+r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+added a double-hit filter to avoid overestimated indel likelihood
+
+------------------------------------------------------------------------
+r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-7 (r804)
+ * fixed a bug in the gap caller
+
+------------------------------------------------------------------------
+r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/prob1.c
+
+ * samtools-0.1.9-6 (r803)
+ * mpileup: apply homopolymer correction when calculating GL, instead of before
+ * bcftools: apply a different prior to indels
+
+------------------------------------------------------------------------
+r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-5 (r802)
+ * relax tandem penalty. this will be made a command-line option in future.
+
+------------------------------------------------------------------------
+r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-4 (r801)
+ * fixed a minor issue in printing indel VCF
+
+------------------------------------------------------------------------
+r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+fixed another silly bug in mpileup's indel caller
+
+------------------------------------------------------------------------
+r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+
+fixed a silly bug in the indel caller
+
+------------------------------------------------------------------------
+r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/sam_view.c
+ M /trunk/samtools/samtools.1
+
+Incorporate patches by Marcel Martin for read counting.
+
+------------------------------------------------------------------------
+r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-2 (r797)
+ * mpileup: indel calling seems to be working
+
+------------------------------------------------------------------------
+r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/kaln.c
+
+indel calling is apparently working, but more information needs to be collected
+
+------------------------------------------------------------------------
+r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf_indel.c
+
+fixed a few bugs in the indel caller. Probably there are more.
+
+------------------------------------------------------------------------
+r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ A /trunk/samtools/bam2bcf_indel.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/kaln.h
+
+prepare for the indel caller. It is not ready yet.
+
+------------------------------------------------------------------------
+r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+
+Revert to r790. The recent changes are not good...
+
+------------------------------------------------------------------------
+r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+
+ * this revision is UNSTABLE
+
+ * indel caller seems working, but it is very insensitive and has
+ several things I do not quite understand.
+
+
+------------------------------------------------------------------------
+r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+
+for backup. no effective changes
+
+------------------------------------------------------------------------
+r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+ M /trunk/samtools/kprobaln.c
+
+fixed a minor problem in the example coming with kprobaln.c
+
+------------------------------------------------------------------------
+r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/kaln.h
+ A /trunk/samtools/kprobaln.c
+ A /trunk/samtools/kprobaln.h
+
+Separate kaln and kprobaln as I am preparing further changes. At
+present, the results should be identical to the previous.
+
+
+------------------------------------------------------------------------
+r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+Added -b option: read file names from a file
+------------------------------------------------------------------------
+r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-2 (r787)
+
+ * Allow to set a maximum per-sample depth to reduce memory. However,
+ BAQ computation is still applied to every read. The speed is not
+ improved.
+
+
+------------------------------------------------------------------------
+r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/vcf.c
+
+ * samtools-0.1.9-1 (r786)
+ * samtools: optionally perform exact test for each sample
+
+------------------------------------------------------------------------
+r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bcftools/bcf.c
+
+Optionally output "DP", the individual read depth
+
+------------------------------------------------------------------------
+r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+acknowledge Petr and John who have greatly contributed to the project.
+
+------------------------------------------------------------------------
+r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+Release samtools-0.1.9 (r783)
+
+------------------------------------------------------------------------
+r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+fixed a silly bug in pileup
+
+------------------------------------------------------------------------
+r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.8-22 (r781)
+ * made BAQ the default behavior of mpileup
+ * updated manual
+ * in merge, force to exit given inconsistent header when "-R" is not in use.
+
+------------------------------------------------------------------------
+r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-21 (r780)
+ * minor speedup to pileup
+
+------------------------------------------------------------------------
+r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/examples/toy.sam
+
+improve pileup a little bit
+
+------------------------------------------------------------------------
+r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-20 (r778)
+ * speed up pileup, although I do not know how much is the improvement
+
+------------------------------------------------------------------------
+r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/examples/Makefile
+
+ * samtools-0.1.8-19 (r777)
+ * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
+
+------------------------------------------------------------------------
+r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+
+remove local realignment (probabilistic realignment is still there)
+
+------------------------------------------------------------------------
+r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/sam_view.c
+
+Add the relevant filename or region to error messages, and cause a failure
+exit status where appropriate. Based on a patch provided by Marcel Martin.
+
+------------------------------------------------------------------------
+r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/examples/toy.sam
+ M /trunk/samtools/kaln.c
+
+ * Minor code changes. No real effect.
+ * change quality to 30 in toy.sam
+
+------------------------------------------------------------------------
+r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/examples/toy.fa
+ M /trunk/samtools/examples/toy.sam
+
+added another toy example
+
+------------------------------------------------------------------------
+r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/ld.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+improve the LD statistics
+
+------------------------------------------------------------------------
+r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * a minor fix to the -L option
+ * add ldstats to vcfutils.pl
+
+------------------------------------------------------------------------
+r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+
+a minor change
+
+------------------------------------------------------------------------
+r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ A /trunk/samtools/bcftools/ld.c
+
+forget to add the key file
+
+------------------------------------------------------------------------
+r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * vcfutils.pl: fixed a typo in help message
+ * added APIs: bcf_append_info() and bcf_cpy()
+ * calculate adjacent LD
+
+------------------------------------------------------------------------
+r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+added filter for samtools/bcftools genetated VCFs
+
+------------------------------------------------------------------------
+r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+ M /trunk/samtools/kaln.c
+
+ * removed a comment line in kaln.c
+ * vcfutils.pl fillac works when GT is not the first field
+
+------------------------------------------------------------------------
+r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
+Changed paths:
+ A /trunk/samtools/bcftools/bcf-fix.pl
+
+Convert VCF output of "bcftools view -bgcv" to a valid VCF file
+------------------------------------------------------------------------
+r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/bcftools/bcftools.1
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.8-18 (r763)
+ * added bcftools manual page
+ * minor fix to mpileup and view command lines
+
+------------------------------------------------------------------------
+r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * vcfutils.pl qstats: calculate marginal ts/tv
+ * allow to call genotypes at variant sites
+
+------------------------------------------------------------------------
+r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/misc/HmmGlocal.java
+
+I am changing the gap open probability back to 0.001. It seems that
+being conservative here is a good thing...
+
+------------------------------------------------------------------------
+r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kaln.c
+ A /trunk/samtools/misc/HmmGlocal.java
+
+ * samtools-0.1.8-17 (r760)
+ * the default gap open penalty is too small (a typo)
+ * added comments on hmm_realn
+ * Java implementation
+
+------------------------------------------------------------------------
+r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+mark samtools-0.1.8-16 (r759)
+
+------------------------------------------------------------------------
+r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+round to the nearest integer
+
+------------------------------------------------------------------------
+r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+I was trying to accelerate ka_prob_glocal() as this will be the
+bottleneck. After an hour, the only gain is to change division to
+multiplication. OK. I will stop.
+
+------------------------------------------------------------------------
+r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+this is interesting. multiplication is much faster than division, at least on my Mac
+
+------------------------------------------------------------------------
+r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+minor changes
+
+------------------------------------------------------------------------
+r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/kaln.c
+
+prob_realn() seems working!
+
+------------------------------------------------------------------------
+r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+minor
+
+------------------------------------------------------------------------
+r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/kaln.h
+
+Convert phredQ to probabilities
+
+------------------------------------------------------------------------
+r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/kaln.h
+
+Implement the glocal HMM; discard the extention HMM
+
+------------------------------------------------------------------------
+r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+improve numerical stability
+
+------------------------------------------------------------------------
+r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+more comments
+
+------------------------------------------------------------------------
+r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+fixed a bug in banded DP
+
+------------------------------------------------------------------------
+r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+ * fixed that weird issue.
+ * the banded version is NOT working
+
+------------------------------------------------------------------------
+r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+More comments. This version seems working, but something is a little weird...
+
+------------------------------------------------------------------------
+r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
+Changed paths:
+ M /trunk/samtools/kaln.c
+
+A little code cleanup. Now the forward and backback algorithms give
+nearly identical P(x), which means both are close to the correct
+forms. However, I have only tested on toy examples. Minor errors in
+the implementation may not be obvious.
+
+
+------------------------------------------------------------------------
+r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/kaln.h
+
+...
+
+------------------------------------------------------------------------
+r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+
+Abort if merge -h's INH.SAM cannot be opened, just as we abort
+if any of the IN#.BAM input files cannot be opened.
+
+Also propagate any error indication returned by bam_merge_core()
+to samtools merge's exit status.
+
+------------------------------------------------------------------------
+r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+Use bam_validate1() to detect garbage records in the event of a corrupt
+BAI index file that causes a bam_seek() to an invalid position. At most
+one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
+call, so the cost is insignificant in the normal case.
+
+------------------------------------------------------------------------
+r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+
+Add bam_validate1().
+
+------------------------------------------------------------------------
+r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-15 (r379)
+ * allow to change capQ parameter in calmd
+
+------------------------------------------------------------------------
+r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/sam_view.c
+
+When bam_read1() returns an error (return value <= -2), propagate that error
+to bam_iter_read()'s own return value. Similarly, also propagate it up to
+bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
+callers ignored its return value anyway. With this change, 0 continues to
+indicate success, while <= -2 (which can be written as < 0, as -1 is never
+returned) indicates corrupted input.
+
+bam_iter_read() ought also to propagate errors returned by bam_seek().
+
+main_samview() can now print an error message and fail when bam_fetch()
+detects that a .bai index file is corrupted or otherwise does not correspond
+to the .bam file it is being used with.
+
+------------------------------------------------------------------------
+r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+0 is a successful return value from bam_read1(). (In practice, it never
+returns 0 anyway; but all the other callers treat 0 as successful.)
+
+------------------------------------------------------------------------
+r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_sort.c
+
+ * merge files region-by-region. work on small examples but more tests are needed.
+
+------------------------------------------------------------------------
+r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+improve qstats by checking the alleles as well
+
+------------------------------------------------------------------------
+r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+convert UCSC SNP SQL dump to VCF
+
+------------------------------------------------------------------------
+r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+hapmap2vcf convertor
+
+------------------------------------------------------------------------
+r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/vcf.c
+
+ * added comments
+ * VCF->BCF is not possible without knowing the sequence dictionary before hand...
+
+------------------------------------------------------------------------
+r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/vcf.c
+
+ * put n_smpl to "bcf1_t" to simplify API a little
+
+------------------------------------------------------------------------
+r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/index.c
+
+fixed a bug in indexing
+
+------------------------------------------------------------------------
+r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_pileup.c
+
+ * fixed a bug in capQ
+ * valgrind identifies a use of uninitialised value, but I have not fixed it.
+
+------------------------------------------------------------------------
+r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bgzip.c
+ M /trunk/samtools/razip.c
+
+ * fixed a bug in razip: -c will delete the input file
+ * copy tabix/bgzip to here
+
+------------------------------------------------------------------------
+r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-14 (r727)
+ * allow to change the capQ parameter at the command line
+
+------------------------------------------------------------------------
+r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+ M /trunk/samtools/misc/samtools.pl
+
+ * added varFilter to vcfutils.pl
+ * reimplement realn(). now it performs a local alignment
+ * added cap_mapQ() to cap mapping quality when there are many substitutions
+
+------------------------------------------------------------------------
+r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ A /trunk/samtools/bcftools/bcf2qcall.c
+ M /trunk/samtools/bcftools/call1.c
+
+ * convert BCF to QCALL input
+
+------------------------------------------------------------------------
+r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+
+dynamic band width in realignment
+
+------------------------------------------------------------------------
+r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+
+fixed a bug in realignment
+
+------------------------------------------------------------------------
+r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/prob1.c
+
+fixed a minor issue
+
+------------------------------------------------------------------------
+r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_md.c
+
+fixed a bug in realignment
+
+------------------------------------------------------------------------
+r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+minor changes. It is BUGGY now!
+
+------------------------------------------------------------------------
+r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/kaln.h
+
+ * aggressive gapped aligner is implemented in calmd.
+ * distinguish gap_open and gap_end_open in banded alignment
+ * make tview accepts alignment with heading and tailing D
+
+------------------------------------------------------------------------
+r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools
+
+Add svn:ignore properties for generated files that don't appear in "make all".
+
+------------------------------------------------------------------------
+r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools
+ M /trunk/samtools/bcftools
+ M /trunk/samtools/misc
+
+Add svn:ignore properties listing the generated files.
+(Except for *.o, which we'll assume is in global-ignores.)
+
+------------------------------------------------------------------------
+r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/sample.c
+ M /trunk/samtools/sample.h
+
+ * samtools-0.1.8-13 (r715)
+ * fixed a bug in identifying SM across files
+ * bcftools: estimate heterozygosity
+ * bcftools: allow to skip sites without reference bases
+
+------------------------------------------------------------------------
+r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+
+quite a lot changes to the contrast caller, but I still feel something is missing...
+
+------------------------------------------------------------------------
+r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+ * changed 3.434 to 4.343 (typo!)
+ * fixed a bug in the contrast caller
+ * calculate heterozygosity
+
+------------------------------------------------------------------------
+r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/call1.c
+
+SNP calling from the GL field
+
+------------------------------------------------------------------------
+r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcf.c
+
+fixed another problem
+
+------------------------------------------------------------------------
+r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/vcf.c
+
+ * fixed bugs in parsing VCF
+ * parser now works with GT/GQ/DP/PL/GL
+
+------------------------------------------------------------------------
+r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/bcftools/prob1.c
+
+Do not compile _BCF_QUAD by default
+
+------------------------------------------------------------------------
+r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/call1.c
+
+Write the correct ALT and PL in the SNP calling mode.
+
+------------------------------------------------------------------------
+r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfutils.pl
+
+more commands for my own uses
+
+------------------------------------------------------------------------
+r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+ A /trunk/samtools/bcftools/vcfutils.pl
+
+Utilities for processing VCF
+
+------------------------------------------------------------------------
+r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+
+preliminary contrast variant caller
+
+------------------------------------------------------------------------
+r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/call1.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+
+z' and z'' can be calculated
+
+------------------------------------------------------------------------
+r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
+ M /trunk/samtools/bcftools/prob1.c
+ D /trunk/samtools/bcftools/vcfout.c
+
+ * rename vcfout.c as call1.c
+ * prepare to add two-sample comparison
+
+------------------------------------------------------------------------
+r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfout.c
+
+fixed a bug in calculating the t statistics
+
+------------------------------------------------------------------------
+r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcftools/kfunc.c
+ M /trunk/samtools/bcftools/vcfout.c
+
+ * samtools-0.1.8-13 (r698)
+ * perform one-tailed t-test for baseQ, mapQ and endDist
+
+------------------------------------------------------------------------
+r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/kfunc.c
+
+added regularized incomplete beta function
+
+------------------------------------------------------------------------
+r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+
+change the default correlation coefficient
+
+------------------------------------------------------------------------
+r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/vcfout.c
+
+print QUAL as floating numbers
+
+------------------------------------------------------------------------
+r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/examples/Makefile
+ A /trunk/samtools/sample.c
+ A /trunk/samtools/sample.h
+
+ * samtools-0.1.8-12 (r692)
+ * group data by samples in "mpileup -g"
+
+------------------------------------------------------------------------
+r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ D /trunk/samtools/bam_mcns.c
+ D /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+
+remove VCF output in mpileup
+
+------------------------------------------------------------------------
+r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+
+ * use the revised MAQ error model for mpileup
+ * prepare to remove the independent model from mpileup
+
+------------------------------------------------------------------------
+r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ A /trunk/samtools/errmod.c
+ A /trunk/samtools/errmod.h
+ M /trunk/samtools/ksort.h
+
+added revised MAQ error model
+
+------------------------------------------------------------------------
+r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+ M /trunk/samtools/bcftools/vcfout.c
+
+allow to read the prior from the error output. EM iteration is working.
+
+------------------------------------------------------------------------
+r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/main.c
+ M /trunk/samtools/bcftools/vcf.c
+
+ * write a little more VCF header
+ * concatenate BCFs
+
+------------------------------------------------------------------------
+r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/bcf.tex
+
+use float for QUAL
+
+------------------------------------------------------------------------
+r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/prob1.c
+
+faster for large sample size (in principle)
+
+------------------------------------------------------------------------
+r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bcftools/prob1.c
+
+ * a numerically stable method to calculate z_{jk}
+ * currently slower than the old method but will be important for large sample size
+ * in principle, we can speed up for large n, but have not tried
+
+------------------------------------------------------------------------
+r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfout.c
+
+fixed an issue in parsing integer
+
+------------------------------------------------------------------------
+r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+
+do not print refname if file is converted from VCF
+
+------------------------------------------------------------------------
+r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcf.c
+
+ * parse PL
+ * fixed a bug in parsing VCF
+
+------------------------------------------------------------------------
+r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/main.c
+ M /trunk/samtools/bcftools/vcf.c
+ M /trunk/samtools/bcftools/vcfout.c
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/kstring.c
+
+ * fixed a bug in kstrtok at kstring.c
+ * preliminary VCF parser (not parse everything for now)
+ * improved view interface
+
+------------------------------------------------------------------------
+r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/vcfout.c
+ M /trunk/samtools/kstring.c
+ M /trunk/samtools/kstring.h
+
+ * improved kstring (added kstrtok)
+ * removed the limit on the format string length in bcftools
+ * use kstrtok to parse format which fixed a bug in the old code
+
+------------------------------------------------------------------------
+r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
+Changed paths:
+ A /trunk/samtools/bcftools/README
+ M /trunk/samtools/bcftools/vcfout.c
+
+help messages
+
+------------------------------------------------------------------------
+r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcfout.c
+
+perform single-tail test for ED4
+
+------------------------------------------------------------------------
+r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/bcftools/kfunc.c
+ M /trunk/samtools/bcftools/vcfout.c
+
+ * test depth, end distance and HWE
+
+------------------------------------------------------------------------
+r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/kfunc.c
+
+reimplement incomplete gamma functions. no copy-paste
+
+------------------------------------------------------------------------
+r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bcftools/fet.c
+ M /trunk/samtools/bcftools/prob1.c
+ M /trunk/samtools/bcftools/prob1.h
+ M /trunk/samtools/bcftools/vcfout.c
+
+ * bcftools: add HWE (no testing for now)
+ * record end dist in a 2x2 table, not avg, std any more
+
+------------------------------------------------------------------------
+r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
+Changed paths:
+ A /trunk/samtools/bcftools/kfunc.c
+
+ * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
+ * Not using Numerical Recipe due to licensing issues
+
+------------------------------------------------------------------------
+r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
+Changed paths:
+ A /trunk/samtools/bcftools/fet.c
+
+Fisher's exact test
+
+------------------------------------------------------------------------
+r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/examples/Makefile
+
+ * samtools-0.1.8-11 (r672)
+ * collect more stats for allele balance test in bcftools (not yet)
+
+------------------------------------------------------------------------
+r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/main.c
+
+ * the code base is stablized again.
+ * I will delay the vcf parser, which is quite complicated but with little value for now
+
+------------------------------------------------------------------------
+r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/examples/Makefile
+
+minor
+
+------------------------------------------------------------------------
+r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcftools/vcf.c
+
+unfinished vcf parser
+
+------------------------------------------------------------------------
+r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bcftools/Makefile
+ M /trunk/samtools/bcftools/bcf.c
+ M /trunk/samtools/bcftools/bcf.h
+ M /trunk/samtools/bcftools/bcfutils.c
+ M /trunk/samtools/bcftools/index.c
+ M /trunk/samtools/bcftools/main.c
+ A /trunk/samtools/bcftools/vcf.c
+ M /trunk/samtools/bcftools/vcfout.c
+
+ * added prelimiary VCF parser (not finished)
+ * change struct a bit
+
+------------------------------------------------------------------------
+r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bcftools/bcf.c
+
+ * allow to set min base q
+ * fixed a bug in mpileup -u
+
+------------------------------------------------------------------------
+r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+ A /trunk/samtools/bcftools/bcf.tex
+
+spec
+
+------------------------------------------------------------------------
+r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/examples/Makefile
+
+added more examples
+
+------------------------------------------------------------------------
+r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bcftools/Makefile
+
+fixed compilation error
+
+------------------------------------------------------------------------
+r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ D /trunk/samtools/bcf.c
+ D /trunk/samtools/bcf.h
+ A /trunk/samtools/bcftools
+ A /trunk/samtools/bcftools/Makefile
+ A /trunk/samtools/bcftools/bcf.c
+ A /trunk/samtools/bcftools/bcf.h
+ A /trunk/samtools/bcftools/bcfutils.c
+ A /trunk/samtools/bcftools/index.c
+ A /trunk/samtools/bcftools/main.c
+ A /trunk/samtools/bcftools/prob1.c
+ A /trunk/samtools/bcftools/prob1.h
+ A /trunk/samtools/bcftools/vcfout.c
+
+move bcftools to samtools
+
+------------------------------------------------------------------------
+r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+
+fixed another minor bug
+
+------------------------------------------------------------------------
+r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bcf.c
+
+ * samtools-0.1.8-10 (r658)
+ * fixed a bug in bam2bcf when the reference is N
+
+------------------------------------------------------------------------
+r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+
+ * fixed a bug
+ * treat ambiguous ref base as the fifth base
+
+------------------------------------------------------------------------
+r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/bcftools/bcf.c
+ M /trunk/samtools/bcf.c
+
+missing a column in VCF output...
+
+------------------------------------------------------------------------
+r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcf.c
+
+fixed a memory leak
+
+------------------------------------------------------------------------
+r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bcf.c
+
+fixed a bug in bcf reader
+
+------------------------------------------------------------------------
+r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam2bcf.c
+
+fixed a bug
+
+------------------------------------------------------------------------
+r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam2bcf.c
+ M /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-9 (r649)
+ * lossless representation of PL in BCF output
+
+------------------------------------------------------------------------
+r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ A /trunk/samtools/bam2bcf.c
+ A /trunk/samtools/bam2bcf.h
+ M /trunk/samtools/bam_plcmd.c
+ A /trunk/samtools/bcf.c
+ A /trunk/samtools/bcf.h
+
+Generate binary VCF
+
+------------------------------------------------------------------------
+r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-8 (r644)
+ * mpileup becomes a little stable again
+ * the method is slightly different, but is more theoretically correct
+ * snp calling is O(n^2) instead of O(n^3)
+
+------------------------------------------------------------------------
+r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+
+ * fixed a STUPID bug, which cost me a lot of time.
+ * I am going to clean up mcns a little bit
+
+------------------------------------------------------------------------
+r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+
+supposedly this is THE correct implementation, but more testing is needed
+
+------------------------------------------------------------------------
+r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+
+NOT ready yet. Going to make further changes...
+
+------------------------------------------------------------------------
+r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-7 (r639)
+ * fixed the reference allele assignment
+
+------------------------------------------------------------------------
+r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-6 (r638)
+ * skip isnan/isinf in case of float underflow
+ * added the flat prior
+ * fixed an issue where there are no reads supporting the reference
+
+------------------------------------------------------------------------
+r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+minor changes
+
+------------------------------------------------------------------------
+r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+minor tweaks
+
+------------------------------------------------------------------------
+r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+
+posterior expectation FINALLY working. I am so tired...
+
+------------------------------------------------------------------------
+r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+another minor fix to mpileup
+
+------------------------------------------------------------------------
+r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+added the format column
+
+------------------------------------------------------------------------
+r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+added an alternative prior
+
+------------------------------------------------------------------------
+r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+
+calculate posterior allele frequency
+
+------------------------------------------------------------------------
+r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-3 (r627)
+ * multi-sample snp calling appears to work. More tests needed.
+
+------------------------------------------------------------------------
+r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_tview.c
+
+ * preliminary multisample SNP caller.
+ * something looks not so right, but it largely works
+
+------------------------------------------------------------------------
+r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_mcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-2 (r617)
+ * allele frequency calculation apparently works...
+
+------------------------------------------------------------------------
+r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ A /trunk/samtools/bam_mcns.c
+ A /trunk/samtools/bam_mcns.h
+ M /trunk/samtools/bam_plcmd.c
+
+ * added mutli-sample framework. It is not working, yet.
+ * improved the mpileup interface
+
+------------------------------------------------------------------------
+r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/Makefile
+
+ * samtools-0.1.8-1 (r615)
+ * allow to get mpileup at required sites
+
+------------------------------------------------------------------------
+r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+Release samtools-0.1.8
+
+------------------------------------------------------------------------
+r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+fixed a compiling issue for Windows
+
+------------------------------------------------------------------------
+r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+
+fixed a bug in sorting when output to stdout (by Peter Chines)
+
+------------------------------------------------------------------------
+r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bam_plcmd.c
+
+change the command line option of pileup
+
+------------------------------------------------------------------------
+r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_pileup.c
+ A /trunk/samtools/examples/toy.fa
+ A /trunk/samtools/examples/toy.sam
+
+make pileup work with CIGAR with I/D at the beginning or in the end
+
+------------------------------------------------------------------------
+r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_tview.c
+
+ * make tview more friendly
+ * a temporary remedy for an issue in indel calling
+
+------------------------------------------------------------------------
+r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-r607
+ * improved the genotype accuracy for indels
+ * use the SOAPsnp model for SNP calling by default.
+
+------------------------------------------------------------------------
+r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/Makefile
+
+removed a debugging example
+
+------------------------------------------------------------------------
+r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-.1.7-18 (r605)
+ * fixed an issue when a deletion and mismatch occur at the same time
+ and the base quality is higher than 40 (if -I40).
+
+------------------------------------------------------------------------
+r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/misc/Makefile
+
+fixed a minor bug in idxstats
+
+------------------------------------------------------------------------
+r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+fixed a minor bug in indexing
+
+------------------------------------------------------------------------
+r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam.c
+
+change printf() to puts in exporting
+
+------------------------------------------------------------------------
+r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+minor fix. No actual effect.
+
+------------------------------------------------------------------------
+r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+added Makefile targets to compile shared/dynamic library
+
+------------------------------------------------------------------------
+r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-17 (r596)
+ * also keep the number of coor-less reads in the index file
+
+------------------------------------------------------------------------
+r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-16 (r595)
+ * write additional information to bam index
+
+------------------------------------------------------------------------
+r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+fixed a bug for unmapped sequences in indexing
+
+------------------------------------------------------------------------
+r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/samtools.1
+
+rename iterf as iter
+
+------------------------------------------------------------------------
+r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-15 (r592)
+ * fixed a few minor memory leaks in the new pileup code
+ * improved the functionality of mpileup
+
+------------------------------------------------------------------------
+r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-14 (r591)
+ * elementary multi-way pileup. More testing and more functionality to be done.
+
+------------------------------------------------------------------------
+r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-13 (r590)
+ * added mpileup APIs. No compiling errors, but not tested at all. It is late.
+
+------------------------------------------------------------------------
+r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-12 (r589)
+ * added iterator-like APIs for pileup
+
+------------------------------------------------------------------------
+r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-11 (r588)
+ * ported a few improvements from tabix back to samtools
+
+------------------------------------------------------------------------
+r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-10 (r587)
+ * added iterator interface for bam_fetch (ported back from tabix)
+
+------------------------------------------------------------------------
+r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ A /trunk/samtools/bam_reheader.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+
+ * samtools-0.1.7-9 (r586)
+ * added "reheader" to replace the BAM header
+
+------------------------------------------------------------------------
+r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kstring.h
+
+ * samtools-0.1.7-8 (r585)
+ * speed up "view"
+
+------------------------------------------------------------------------
+r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/kstring.h
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+ * samtools-0.1.7-7 (r584)
+ * ported tabix BGZF to samtools
+ * flush BGZF after writing the BAM header and between alignment boundaries
+
+------------------------------------------------------------------------
+r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
+Changed paths:
+ A /trunk/samtools/misc/varfilter.py
+
+Initial release on behalf of Aylwyn Scally
+------------------------------------------------------------------------
+r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+Added a note about the indels coordinates
+------------------------------------------------------------------------
+r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Added the possibility to print or not to print the reference allele
+------------------------------------------------------------------------
+r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+More descriptive message for space separated tags
+------------------------------------------------------------------------
+r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Speedup with -i, no need to query the reference all the time
+------------------------------------------------------------------------
+r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+Fixed the order of sequences in the header
+------------------------------------------------------------------------
+r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Added possibility to select indels only and fixed a bug in reporting homozygous indels.
+------------------------------------------------------------------------
+r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+
+Improve the invalid 'BAM\1' magic number error message, and also print it
+when no bytes can be read from the alleged BAM file, e.g., in the common
+user error case when a SAM file has accidentally been supplied.
+
+------------------------------------------------------------------------
+r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/AUTHORS
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/sam_header.c
+
+Improved efficiency of header parsing
+------------------------------------------------------------------------
+r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/export2sam.pl
+
+Updated export2sam.pl by Chris Saunders from Illumina.
+
+
+------------------------------------------------------------------------
+r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
+------------------------------------------------------------------------
+r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Print an error for pileups in simple format
+------------------------------------------------------------------------
+r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+added a hidden option in pileup to output the base position (for Erin)
+
+------------------------------------------------------------------------
+r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Added possibility to specify a custom column title for the data column
+------------------------------------------------------------------------
+r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+Added the -d option to limit maximum depth for indels.
+------------------------------------------------------------------------
+r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Added VCF header
+------------------------------------------------------------------------
+r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+ M /trunk/samtools/misc/wgsim.c
+
+ * samtools-0.1.7-6
+ * fixed a bug in faidx
+
+------------------------------------------------------------------------
+r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/faidx.c
+
+Put the right filename in the error message.
+
+------------------------------------------------------------------------
+r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-5 (r528)
+ * further add new consensus generation strategy
+
+------------------------------------------------------------------------
+r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+Fixed a bug in knet_seek
+------------------------------------------------------------------------
+r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Small fix in VCF format: dot for the empty INFO field
+------------------------------------------------------------------------
+r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+Allow tabs in the CO header field
+------------------------------------------------------------------------
+r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/Makefile.mingw
+
+Depend on libbam.a rather than the phony target, so that samtools is not
+unnecessarily rebuilt every time. Also clean bgzip.
+
+------------------------------------------------------------------------
+r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/Makefile.mingw
+
+Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
+is defined. Also introduce $(KNETFILE_O) which can be set to empty to
+facilitate non-knet builds.
+
+------------------------------------------------------------------------
+r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.7-4 (r522)
+ * fixed a bug in "view -r"
+ * added a new option "view -R" to read required read groups from a file
+
+------------------------------------------------------------------------
+r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-3 (r521)
+ * calmd: optionally mask matching bases as N
+
+------------------------------------------------------------------------
+r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.7-2 (r520)
+ * fixed a few issues with compilation in Windows (on behalf of John)
+ * choose a random base as the consensus (for population genetics studies)
+
+------------------------------------------------------------------------
+r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+Put libraries at the end, so they can resolve references from libbam.a
+as well, even with old-fashioned linkers.
+
+Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
+the freshly built library, not some other libbam.a lying around the system.
+
+------------------------------------------------------------------------
+r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/misc/Makefile
+
+Also clean *.exe (for Cygwin users using this makefile).
+
+------------------------------------------------------------------------
+r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+Index files should be opened in binary mode, not text mode.
+
+------------------------------------------------------------------------
+r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/examples/bam2bed.c
+
+another example program
+
+------------------------------------------------------------------------
+r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/wgsim_eval.pl
+ M /trunk/samtools/sam.c
+
+ * samtools-0.1.7-1 (r515)
+ * report an error when .fai contains duplicated names, instead of segfault
+
+------------------------------------------------------------------------
+r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+
+Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
+
+------------------------------------------------------------------------
+r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+
+Update Makefile.mingw for the same reason
+
+------------------------------------------------------------------------
+r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+Fixed a bug in compiling razip
+
+------------------------------------------------------------------------
+r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+Release samtools-0.1.7 (r510)
+
+------------------------------------------------------------------------
+r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-22 (r509)
+ * forget to fix a similar problem in glfgen
+
+------------------------------------------------------------------------
+r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.6-21 (r508)
+ * fixed a potential bug in the indel caller towards the end of a chromosome
+
+------------------------------------------------------------------------
+r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.6-19 (r494)
+ * allow to convert Illumina quality (64 based) to the BAM quality
+
+------------------------------------------------------------------------
+r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_header.c
+
+ * samtools-0.1.6-18 (r493)
+ * fixed the bugs due to improperly incorporating Petr's header parser
+ * a little code clean up in sam_header.c
+
+------------------------------------------------------------------------
+r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+Added sam_header_line_free call for sam_header_parse2
+------------------------------------------------------------------------
+r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/sam_view.c
+
+ * BUGGY VERSION
+ * fixed a minor bug
+
+------------------------------------------------------------------------
+r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/sam.c
+
+ * BUGGY VERSION
+ * improved the interface a bit
+ * bug unfixed
+
+------------------------------------------------------------------------
+r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+
+ * BUGGY VERSION. Please NOT use it.
+ * Fixed a minor bug, but the major bug is still there.
+
+------------------------------------------------------------------------
+r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+ M /trunk/samtools/sam_view.c
+
+ * This revision is SERIOUSLY BUGGY. Please NOT use it.
+ * Start to incorporate header parsing from Petr Danecek
+
+------------------------------------------------------------------------
+r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+
+Now possible to merge multiple HeaderDict dictionaries
+------------------------------------------------------------------------
+r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+
+------------------------------------------------------------------------
+r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
+Changed paths:
+ A /trunk/samtools/sam_header.c
+ A /trunk/samtools/sam_header.h
+
+
+------------------------------------------------------------------------
+r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/examples/Makefile
+
+ * samtools-0.1.6-17 (r484)
+ * fixed a memory leak in rmdupse
+ * fixed a bug in parsing @RG header lines
+ * test rmdup in examples/
+
+------------------------------------------------------------------------
+r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-16 (r483)
+ * unify the interface of rmdup and rmdupse
+ * a new bug found in rg2lib(). Have not been fixed yet.
+
+------------------------------------------------------------------------
+r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/klist.h
+
+ * samtools-0.1.6-15 (r482)
+ * rewrite rmdupse
+ * rmdupse is now library aware
+
+------------------------------------------------------------------------
+r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-14 (r480)
+ * rmdup is now RG aware
+
+------------------------------------------------------------------------
+r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+added a small unitity to parse SRA XML files
+
+------------------------------------------------------------------------
+r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-13 (r479)
+ * merge: optionally use file names as RG tags
+
+------------------------------------------------------------------------
+r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kaln.c
+
+ * samtools-0.1.6-12 (r478)
+ * fixed a bug in the indel caller
+
+------------------------------------------------------------------------
+r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-11 (r477)
+ * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
+
+------------------------------------------------------------------------
+r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
+Changed paths:
+ A /trunk/samtools/misc/sam2vcf.pl
+
+Added the sam2vcf.pl script.
+------------------------------------------------------------------------
+r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/kaln.c
+ A /trunk/samtools/kaln.h
+
+Unfinished modification. Please do not use this revision...
+
+------------------------------------------------------------------------
+r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+Removed the offending knet_seek message.
+------------------------------------------------------------------------
+r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/razf.c
+
+Bug fix - faidx on RAZF compressed files now working.
+------------------------------------------------------------------------
+r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+Clarify the meaning of a region like "chr2:1,000,000".
+
+------------------------------------------------------------------------
+r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/novo2sam.pl
+
+Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
+
+------------------------------------------------------------------------
+r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.6-9 (r470)
+ * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
+
+------------------------------------------------------------------------
+r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-9 (r469)
+ * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
+
+------------------------------------------------------------------------
+r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.6-7 (r468)
+ * make merge stable
+
+------------------------------------------------------------------------
+r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzip.c
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/razip.c
+
+Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
+------------------------------------------------------------------------
+r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-6 (r466)
+ * do not crash calmd when some sequences are absent from the reference.
+
+------------------------------------------------------------------------
+r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/knetfile.c
+
+Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
+no way to seek on a pipe and the messages always appear.
+
+------------------------------------------------------------------------
+r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/razf.c
+
+A bug fix, "samtools view" is now working again.
+------------------------------------------------------------------------
+r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/faidx.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/razf.h
+
+ * samtools-0.1.6-5 (r462)
+ * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
+
+------------------------------------------------------------------------
+r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+fixed a formatting issue
+
+------------------------------------------------------------------------
+r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-4 (r459)
+ * make sort output the result to stdout when -o is in use
+
+------------------------------------------------------------------------
+r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/faidx.c
+ M /trunk/samtools/faidx.h
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.6-2 (r458)
+ * added more interface to faidx (by Nils)
+ * updated documentation
+
+------------------------------------------------------------------------
+r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-2 (r457)
+ * get rid of three assert() in bam_sort.c
+
+------------------------------------------------------------------------
+r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/razf.c
+
+Return NULL from _razf_open() (and hence razf_open()/razf_open2())
+when opening the file fails.
+
+------------------------------------------------------------------------
+r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+ D /trunk/samtools/source.dot
+
+Release samtools-0.1.6
+
+------------------------------------------------------------------------
+r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.5-34 (r451)
+ * applied the patch by John
+ * improved the help message a little bit
+
+------------------------------------------------------------------------
+r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_color.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-33 (r450)
+ * fixed a bug in bam_color.c (on behalf of Nils Homer)
+
+------------------------------------------------------------------------
+r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.5-32 (r449)
+ * fillmd: fixed a bug in modifying MD/NM tags
+ * in import, give a warning if the read is aligned but there is no CIGAR.
+
+------------------------------------------------------------------------
+r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+ * samtools-0.1.5-31 (r448)
+ * fixed an issue when the last CIGAR is I or D
+
+------------------------------------------------------------------------
+r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-30 (r447)
+ * fixed a bug in bam_aux_get(): 'A' is not checked
+
+------------------------------------------------------------------------
+r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bamtk.c
+
+ *
+
+------------------------------------------------------------------------
+r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-28 (r444)
+ * bug in "merge -n"
+
+------------------------------------------------------------------------
+r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-27 (r443)
+ * SEQ and QUAL can be "*"
+ * parse CIGAR "=" and "X" as "M"
+
+------------------------------------------------------------------------
+r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/md5.c
+ M /trunk/samtools/misc/md5.h
+ M /trunk/samtools/misc/md5fa.c
+
+ * samtools-0.1.5-26 (r442)
+ * replace RSA Inc md5.* with ones under permissive lincense
+ * fixed a bug in detecting unsorted bam in pileup
+
+------------------------------------------------------------------------
+r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/bgzip.c
+
+Change copyright notices now that MIT has approved open source distribution.
+
+------------------------------------------------------------------------
+r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_stat.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-25 (r436)
+ * in flagstats, do not report singletons if both ends are unmapped
+
+------------------------------------------------------------------------
+r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/maq2sam.c
+
+fixed a SERIOUS bug in setting 0x20 flag
+
+------------------------------------------------------------------------
+r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+fixed two minor bugs (suggested by Tim M Storm)
+
+------------------------------------------------------------------------
+r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-24 (r435)
+ * fixed a typo
+
+------------------------------------------------------------------------
+r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-23 (r434)
+ * in tview, press 'r' to show read names rather than sequences
+
+------------------------------------------------------------------------
+r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+ * tried to fixed the buggy FTP random access in Windows. FAILED.
+ * anyway, MinGW seems to have problem with "%lld".
+
+------------------------------------------------------------------------
+r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/faidx.c
+ M /trunk/samtools/razf.c
+ A /trunk/samtools/win32/libcurses.a
+ A /trunk/samtools/win32/xcurses.h
+
+ * samtools-0.1.5-22 (r432)
+ * faidx: fixed compitability issue with _WIN32
+ * razf: fixed potential compitability issue with _WIN32
+ * PDCurses support in Windows
+
+------------------------------------------------------------------------
+r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/win32/libz.a
+
+replace the GnuWin32 version of libz.a with my own build with MinGW.
+
+------------------------------------------------------------------------
+r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+add comments
+
+------------------------------------------------------------------------
+r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.5-21 (r428)
+ * knetfile.c is now compatible with mingw-winsock
+
+------------------------------------------------------------------------
+r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+
+simplify MinGW Makefile
+
+------------------------------------------------------------------------
+r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
+Changed paths:
+ A /trunk/samtools/Makefile.mingw
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/win32
+ A /trunk/samtools/win32/libz.a
+ A /trunk/samtools/win32/zconf.h
+ A /trunk/samtools/win32/zlib.h
+
+ * samtools-0.1.5-20 (r427)
+ * MinGW support. At least SAM<->BAM conversion is working. Other
+ functionality are not tested at the moment.
+ * zlib headers and Windows version of libz.a are included in win32/
+
+------------------------------------------------------------------------
+r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-19 (r426)
+ * fixed a bug caused by recent modifications. Sorry.
+
+------------------------------------------------------------------------
+r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bgzf.c
+
+compatible with Windows binary files
+
+------------------------------------------------------------------------
+r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.5-18 (r423)
+ * output additional information in pileup indel lines, for the purepose
+ of debugging at the moment
+ * in tview, optionally allow to treat reference skip as deletion
+
+------------------------------------------------------------------------
+r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/misc/psl2sam.pl
+
+convert BLAT psl to SAM.
+
+------------------------------------------------------------------------
+r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-17 (r422)
+ * fixed a but in knetfile.c when seek type is not SEEK_SET
+ * write an empty BGZF block to every BGZF file
+ * check BGZF EOF marker in bam_header_read()
+ * update ChangeLog
+
+------------------------------------------------------------------------
+r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam.h
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-16 (r421)
+ * in view and pileup, load header from FASTA index if the input is SAM.
+
+------------------------------------------------------------------------
+r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/maq2sam.c
+
+do not set "read 1" if reads are not mapped in the PE mode of maq
+
+------------------------------------------------------------------------
+r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+ * samtools-0.1.5-15 (r419)
+ * in sam_open(), return NULL when the file cannot be opened.
+ * make wgsim_eval.pl more robust to imperfect SAM
+ * add "unique" command to samtools.pl
+
+------------------------------------------------------------------------
+r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+skip @header lines in SAM
+
+------------------------------------------------------------------------
+r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-14 (r417)
+ * more help in "samtools view" due to the recent changes.
+
+------------------------------------------------------------------------
+r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam.h
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-17 (r416)
+ * support import/export SAM with string tags
+
+------------------------------------------------------------------------
+r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam.h
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.5-12 (r415)
+ * FLAG now can be in HEX
+
+------------------------------------------------------------------------
+r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/kstring.h
+
+fixed a compiling error (thank Ken for fixing it)
+
+------------------------------------------------------------------------
+r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/kstring.c
+ M /trunk/samtools/kstring.h
+
+Implemented Boyer-Moore search in the kstring library.
+
+------------------------------------------------------------------------
+r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+do not include knetfile.h when _USE_KNETFILE is not defined
+
+------------------------------------------------------------------------
+r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+
+ * samtools-0.1.5-11 (r408)
+ * force to overwirte existing MD if it is different from the one calculated
+ from fillmd.
+ * bgzf.c: improved the compatibility with Windows headers
+
+------------------------------------------------------------------------
+r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.h
+
+ * samtools-0.1.5-10 (r407)
+ * implemented bam_aux_del() to remove a tag
+ * fillmd: generate the NM tag
+ * fillmd: cmd interface improvement
+
+------------------------------------------------------------------------
+r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+Sorry. The old Makefile is for PDCurses...
+
+------------------------------------------------------------------------
+r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-9 (r405)
+ * improved the compatibility with PDCurses a little bit
+
+------------------------------------------------------------------------
+r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-8 (r404)
+ * compatible with PDCurses
+
+------------------------------------------------------------------------
+r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kseq.h
+
+ * samtools-0.1.5-7 (r403)
+ * fixed a bug in kseq.h for binary files (text files are fine)
+
+------------------------------------------------------------------------
+r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+
+ * samtools-0.1.5-6 (r402)
+ * fixed compiling error when "-D_USE_NETFILE" is not applied
+ * improve portability to MinGW
+
+------------------------------------------------------------------------
+r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
+Changed paths:
+ A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
+ A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
+ D /trunk/samtools/bam_lite.c
+
+ * move bam_lite.c to bam-lite
+ * copy bam.h to bam-lite
+
+------------------------------------------------------------------------
+r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_lite.c
+ M /trunk/samtools/bam_lpileup.c
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-5 (r395)
+ * added bam_pileup_file() and removed bam_lpileup_file()
+
+------------------------------------------------------------------------
+r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.5-4 (r394)
+ * http_proxy support in knetfile library (check http_proxy ENV)
+
+------------------------------------------------------------------------
+r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.5-3 (r393)
+ * knetfile now supports HTTP (no proxy at the moment)
+ * fixed a potential issue in knetfile on opening ordinary file, although I have
+ not seen the sideeffect so far.
+
+------------------------------------------------------------------------
+r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+Remove the warning in tview
+
+------------------------------------------------------------------------
+r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-2 (r391)
+ * do not show a blank screen when no reads mapped
+
+------------------------------------------------------------------------
+r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ A /trunk/samtools/bam_lite.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.5-1 (r390)
+ * removed useless _IOLIB in bam.h. This should cause no change at all.
+ * added bam_lite.c for light-weight BAM reading
+
+------------------------------------------------------------------------
+r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+
+Release samtools-0.1.5c (fixed a bug in piping)
+
+------------------------------------------------------------------------
+r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+
+Release samtools-0.1.5b (BUG! so embarrassing!)
+
+------------------------------------------------------------------------
+r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
+
+------------------------------------------------------------------------
+r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+Release samtools-0.1.5
+
+------------------------------------------------------------------------
+r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+
+ * samtools-0.1.4-23 (r372)
+ * keep header text if "view -t" is used (by Gerton)
+
+------------------------------------------------------------------------
+r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+update documentation
+
+------------------------------------------------------------------------
+r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
+
+------------------------------------------------------------------------
+r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.4-22 (r369)
+ * in pileup, optionally print E2 and U2
+ * remove the debugging code in bam_aux_get() (Drat!)
+
+------------------------------------------------------------------------
+r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_lpileup.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_stat.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/faidx.c
+ M /trunk/samtools/faidx.h
+ M /trunk/samtools/glf.c
+
+ * samtools-0.1.4-21 (r368)
+ * propagate errors rather than exit or complain assertion failure. Assertion
+ should be only used for checking internal bugs, but not for external input
+ inconsistency. I was just a bit lazy.
+ * small memory leak may be present on failure, though
+
+------------------------------------------------------------------------
+r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+reduce the chance of blocking in FTP connection
+
+------------------------------------------------------------------------
+r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+minor changes to knetfile: invalid fd equals -1 rather than 0
+
+------------------------------------------------------------------------
+r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.4-20 (r365)
+ * download the BAM index file if it is not found in the current working directory.
+
+------------------------------------------------------------------------
+r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+
+ * samtools-0.1.4-19 (r364)
+ * knetfile: report error when the file is not present on FTP
+
+------------------------------------------------------------------------
+r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.4-18 (r363)
+ * knetfile: do not trigger network communication in FTP seek (lazy seek)
+ * bgzf: cache recent blocks (disabled by default)
+
+------------------------------------------------------------------------
+r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bgzf.c
+
+write changelog
+
+------------------------------------------------------------------------
+r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.4-17 (r361)
+ * if a file is given on FTP, search locally for the BAM index
+
+------------------------------------------------------------------------
+r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.4-16 (r360)
+ * report more information in index when the input is not sorted
+ * change the behaviour of knet_seek() such that it returns 0 on success
+ * support knetfile library in BGZF
+
+------------------------------------------------------------------------
+r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+fixed bugs in knetfile.*
+
+------------------------------------------------------------------------
+r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/knetfile.h
+
+this is the header file
+
+------------------------------------------------------------------------
+r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
+Changed paths:
+ A /trunk/samtools/knetfile.c
+
+ * open a file at FTP
+ * preliminary version
+
+------------------------------------------------------------------------
+r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.4-15 (r354)
+ * fixed a memory leak in bam_view1(), although samtools is not using this routine.
+
+------------------------------------------------------------------------
+r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/faidx.c
+
+ * samtools-0.1.4-13 (r351)
+ * make faidx more tolerant to empty lines right before or after > lines
+ * hope this does not introduce new bugs...
+
+------------------------------------------------------------------------
+r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.4-13 (r350)
+ * fixed a small memory leak in pileup, caused by recent modifications
+
+------------------------------------------------------------------------
+r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.4-12 (r347)
+ * added `-S' to pileup, similar to `view -S'
+
+------------------------------------------------------------------------
+r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.4-11 (r346)
+ * allow to select a read group at view command-line
+
+------------------------------------------------------------------------
+r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/examples/calDepth.c
+
+added more comments
+
+------------------------------------------------------------------------
+r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/examples/calDepth.c
+
+nothing really
+
+------------------------------------------------------------------------
+r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/examples/Makefile
+ A /trunk/samtools/examples/calDepth.c
+
+added an example of calculating read depth
+
+------------------------------------------------------------------------
+r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ A /trunk/samtools/bam_color.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam.h
+
+ * samtools-0.1.4-10 (r341)
+ * only include key APIs in libbam.a
+ * move color-specific routines to bam_color.c
+ * update documentations
+ * remove the support of -q in pileup
+
+------------------------------------------------------------------------
+r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
+Changed paths:
+ M /trunk/samtools/INSTALL
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.4-9 (r340)
+ * added a warning to razf.c if zlib<1.2.2.1
+ * fixed a compilation warning
+ * fixed a segfault caused by @RG parsing
+ * detect NCURSES in bam_tview.c
+
+------------------------------------------------------------------------
+r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/INSTALL
+
+update INSTALL
+
+------------------------------------------------------------------------
+r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kstring.h
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.4-8 (r338)
+ * parse the @RG header lines and allow to choose library at the "samtools view"
+ command line
+
+------------------------------------------------------------------------
+r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.4-7 (r337)
+ * bgzf.c: support mode string "wu": uncompressed output
+ * "samtools view" support "-u" command-line option
+
+------------------------------------------------------------------------
+r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/misc/Makefile
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/razf.h
+ M /trunk/samtools/razip.c
+
+ * no changes to samtools itself
+ * remove zlib source codes
+ * make RAZF reading compatible with old version of zlib
+ * on old version of zlib, writing is not available
+
+------------------------------------------------------------------------
+r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
+Changed paths:
+ D /trunk/samtools/zlib
+
+remove zlib for simplification...
+
+------------------------------------------------------------------------
+r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.4-6 (r334)
+ * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
+ been implemented in that.
+ * this version works with the latest Bio::DB::Sam (20090612)
+
+------------------------------------------------------------------------
+r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+
+update ChangeLog
+
+------------------------------------------------------------------------
+r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/AUTHORS
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/misc/Makefile
+
+fixed minor things in Makefile
+
+------------------------------------------------------------------------
+r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.4-5 (r3310
+ * no change to samtools itself. Version number is increased to reflect the
+ changes in the Makefile building system.
+
+------------------------------------------------------------------------
+r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/AUTHORS
+ D /trunk/samtools/README
+
+update information...
+
+------------------------------------------------------------------------
+r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/novo2sam.pl
+
+ * updated novoalign converter by Colin Hercus et al.
+ * this version works with indels
+
+------------------------------------------------------------------------
+r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/INSTALL
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/misc/Makefile
+ M /trunk/samtools/zlib/Makefile
+
+ * update Makefile
+ * update INSTALL instruction
+
+------------------------------------------------------------------------
+r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
+Changed paths:
+ A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
+ D /trunk/samtools/Makefile.am
+ D /trunk/samtools/Makefile.generic
+ D /trunk/samtools/Makefile.lite
+ D /trunk/samtools/autogen.sh
+ D /trunk/samtools/cleanup.sh
+ D /trunk/samtools/configure.ac
+ A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
+ D /trunk/samtools/misc/Makefile.am
+ D /trunk/samtools/misc/Makefile.generic
+ M /trunk/samtools/razf.c
+ A /trunk/samtools/zlib
+ A /trunk/samtools/zlib/Makefile
+ A /trunk/samtools/zlib/adler32.c
+ A /trunk/samtools/zlib/compress.c
+ A /trunk/samtools/zlib/crc32.c
+ A /trunk/samtools/zlib/crc32.h
+ A /trunk/samtools/zlib/deflate.c
+ A /trunk/samtools/zlib/deflate.h
+ A /trunk/samtools/zlib/gzio.c
+ A /trunk/samtools/zlib/infback.c
+ A /trunk/samtools/zlib/inffast.c
+ A /trunk/samtools/zlib/inffast.h
+ A /trunk/samtools/zlib/inffixed.h
+ A /trunk/samtools/zlib/inflate.c
+ A /trunk/samtools/zlib/inflate.h
+ A /trunk/samtools/zlib/inftrees.c
+ A /trunk/samtools/zlib/inftrees.h
+ A /trunk/samtools/zlib/trees.c
+ A /trunk/samtools/zlib/trees.h
+ A /trunk/samtools/zlib/uncompr.c
+ A /trunk/samtools/zlib/zconf.h
+ A /trunk/samtools/zlib/zlib.h
+ A /trunk/samtools/zlib/zutil.c
+ A /trunk/samtools/zlib/zutil.h
+ D /trunk/samtools/zutil.h
+
+ * added zlib-1.2.3 as razip requires that
+ * prepare to changed back to the Makefile building system
+ * unfinished! (will be soon)
+
+------------------------------------------------------------------------
+r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+Unfinished
+
+------------------------------------------------------------------------
+r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.4-4 (r325)
+ * further avoid wrong consensus calls in repetitive regions.
+
+------------------------------------------------------------------------
+r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam.h
+
+ * samtools-0.1.4-3 (r324)
+ * make maqcns generate the correct call in repetitive regions.
+ * allow filtering on mapQ at the pileup command line
+
+------------------------------------------------------------------------
+r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.3.2 (r322)
+ * indels and SNPs use different mapping quality threshold
+
+------------------------------------------------------------------------
+r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/export2sam.pl
+
+fixed a typo
+
+------------------------------------------------------------------------
+r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+just typo. no real change
+
+------------------------------------------------------------------------
+r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+a little bit code cleanup
+
+------------------------------------------------------------------------
+r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.3.1
+ * change default parameters
+ * optionally print filtered variants
+
+------------------------------------------------------------------------
+r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.3.0
+ * combine snpFilter and indelFilter
+
+------------------------------------------------------------------------
+r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.2.3
+ * change a default parameter
+
+------------------------------------------------------------------------
+r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+
+ * samtools-0.1.4-2 (r316)
+ * pileup: cap mapping quality at 60 (by default)
+ * pileup: always calculate RMS mapq
+ * pileup: allow to output variant sites only
+
+------------------------------------------------------------------------
+r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.2.2
+ * added pileup2fq
+
+------------------------------------------------------------------------
+r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * in snpFilter, suppress non-SNP sites
+
+------------------------------------------------------------------------
+r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.2.1
+ * fixed a typo
+
+------------------------------------------------------------------------
+r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.2.0
+ * snpFilter
+
+------------------------------------------------------------------------
+r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bgzf.c
+
+ * minor changes to bgzf: return NULL if fd == -1
+ * suggested by {kdj,jm18}@sanger.ac.uk
+
+------------------------------------------------------------------------
+r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/misc/interpolate_sam.pl
+
+Script for paired-end pileup, contributed by Stephen Montgomery.
+
+------------------------------------------------------------------------
+r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+
+ * samtools-0.1.4-1 (r304)
+ * fixed a minor bug in printing headers
+
+------------------------------------------------------------------------
+r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/maq2sam.c
+ M /trunk/samtools/samtools.1
+
+Release samtools-0.1.4
+
+------------------------------------------------------------------------
+r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-24 (r296)
+ * another similar bug in the indel caller
+
+------------------------------------------------------------------------
+r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-23 (r295)
+ * fixed a critical bug in the indel caller
+
+------------------------------------------------------------------------
+r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_stat.c
+
+added a missing header file
+
+------------------------------------------------------------------------
+r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-22 (r293)
+ * open tview in the dot-view mode by default
+
+------------------------------------------------------------------------
+r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+Added a note to the manual. Currently SAMtools used unaligned words in
+several places. Although this does not cause bus errors to me, it may
+affect portability. Please see the "Bus error" wiki page for more
+information. Also thank James Bonfields for pointing this out.
+
+
+------------------------------------------------------------------------
+r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-21 (286)
+ * declare bam_aux_get_core() in bam.h
+
+------------------------------------------------------------------------
+r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-20 (r276)
+ * remove bam1_t::hash again. We need to modify the Perl API anyway to
+ make it work with the latest SVN.
+ * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
+
+------------------------------------------------------------------------
+r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-19 (r275)
+ * a minor change to the bam1_t struct: added back "void *hash" for the
+ backward compatibility with Bio::DB::Sam
+
+------------------------------------------------------------------------
+r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-18 (r273)
+ * rmdupse: do not remove unmapped reads
+
+------------------------------------------------------------------------
+r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdupse.c
+
+change a parameter. It does nothing
+
+------------------------------------------------------------------------
+r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile.am
+ M /trunk/samtools/Makefile.generic
+ M /trunk/samtools/Makefile.lite
+ A /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/configure.ac
+
+ * samtools-0.1.3-17 (r271)
+ * added 'rmdupse' command
+
+------------------------------------------------------------------------
+r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-16 (r267)
+ * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
+
+------------------------------------------------------------------------
+r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-15 (r266)
+ * report an error if a non-* reference is present while @SQ is absent
+
+------------------------------------------------------------------------
+r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-14 (r262)
+ * make samopen() recognize @SQ header lines
+
+------------------------------------------------------------------------
+r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-13 (r260)
+ * report error for file I/O error
+
+------------------------------------------------------------------------
+r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.am
+
+update Makefile.am
+
+------------------------------------------------------------------------
+r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam.h
+
+ * samtools-0.1.3-12 (r259)
+ * use the new I/O interface in pileup
+
+------------------------------------------------------------------------
+r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile.generic
+ M /trunk/samtools/Makefile.lite
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/sam.c
+ A /trunk/samtools/sam.h
+ A /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-11 (r258)
+ * unify the interface to BAM and SAM I/O
+
+------------------------------------------------------------------------
+r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile.lite
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-10 (r257)
+ * allow hex with "pileup -m"
+
+------------------------------------------------------------------------
+r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_lpileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-9 (r256)
+ * fixed a bug in bam_lpileup.c
+ * I do not know if this also fixes the bug causing assertion failure in the tview
+
+------------------------------------------------------------------------
+r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-8 (r251)
+ * fixed a bug when there are reads without coordinates
+
+------------------------------------------------------------------------
+r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/AUTHORS
+ A /trunk/samtools/README
+ M /trunk/samtools/cleanup.sh
+
+added missing files
+
+------------------------------------------------------------------------
+r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.generic
+ M /trunk/samtools/Makefile.lite
+ M /trunk/samtools/configure.ac
+ M /trunk/samtools/misc/Makefile.generic
+
+improve large file support in compilation
+
+------------------------------------------------------------------------
+r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/INSTALL
+
+update INSTALL
+
+------------------------------------------------------------------------
+r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.am
+ M /trunk/samtools/autogen.sh
+ M /trunk/samtools/cleanup.sh
+ M /trunk/samtools/configure.ac
+ A /trunk/samtools/misc/Makefile.am
+
+fixed various issues about the GNU building scripts
+
+------------------------------------------------------------------------
+r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ D /trunk/samtools/Makefile
+ A /trunk/samtools/Makefile.am
+ A /trunk/samtools/Makefile.generic
+ A /trunk/samtools/autogen.sh
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/cleanup.sh
+ A /trunk/samtools/configure.ac
+ D /trunk/samtools/misc/Makefile
+ A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
+
+ * samtools-0.1.3-7 (r246)
+ * incorporated revisions from Nils Homer
+ * enhanced support of displaying color-space reads
+
+------------------------------------------------------------------------
+r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-6 (r244)
+ * fixed segfault for unmapped reads
+
+------------------------------------------------------------------------
+r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-5 (r243)
+ * fixed a long existing bug which may cause memory leak
+ * check MD
+ * consensus calling now works with "=", but indel calling not
+
+------------------------------------------------------------------------
+r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-4 (r242)
+ * fixed a memory leak
+
+------------------------------------------------------------------------
+r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/Makefile.lite
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ A /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-3 (r240)
+ * generate MD tag
+ * generate "=" bases
+ * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
+
+------------------------------------------------------------------------
+r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-2 (r239)
+ * fixed bugs in bam_aux.c (these functions nevered used by samtools)
+ * removed bam_aux_init()/bam_aux_destroy()
+ * added tagview for testing bam_aux
+
+------------------------------------------------------------------------
+r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-1
+ * fixed a bug in pileup: the first read in a chromosome may not be printed
+
+------------------------------------------------------------------------
+r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.lite
+
+a missing file in Makefile.lite
+
+------------------------------------------------------------------------
+r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.3
+
+------------------------------------------------------------------------
+r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-28
+ * make samtools more robust to weird input such as empty file
+
+------------------------------------------------------------------------
+r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/samtools.1
+
+prepare for release 0.1.3
+
+------------------------------------------------------------------------
+r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/misc/blast2sam.pl
+
+convert NCBI-BLASTN to SAM
+
+------------------------------------------------------------------------
+r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_lpileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-27
+ * fixed a small memory leak in tview
+
+------------------------------------------------------------------------
+r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-26
+ * fixed a bug in rmdup when there are unmapped reads
+
+------------------------------------------------------------------------
+r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+
+proposed NEWS for the new release (have not yet)
+
+------------------------------------------------------------------------
+r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.1.1
+ * improve indelFilter to avoid filtering true indels. The new filter relies
+ on the new pileup indel line implemented in samtools-0.1.2-25
+
+------------------------------------------------------------------------
+r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.2-25
+ * change the pileup indel line to shows the number of alignments actually
+ containing indels
+
+------------------------------------------------------------------------
+r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+
+update ChangeLog from "svn log"
+
+------------------------------------------------------------------------
+r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kseq.h
+
+ * samtools-0.1.2-24
+ * in merge, gives a warning rather than error if the target sequence length is different
+ * allow empty header
+
+------------------------------------------------------------------------
+r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-23
+ * recognize '*' at the QUAL field
+
+------------------------------------------------------------------------
+r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kseq.h
+
+ * samtools-0.1.2-22
+ * the field separater is TAB only, now
+
+------------------------------------------------------------------------
+r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/examples/ex1.sam.gz
+
+ * fixed the problem in the example alignment due to the bug in fixmate
+
+------------------------------------------------------------------------
+r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_mate.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/soap2sam.pl
+
+ * samtools-0.1.2-21
+ * fixed a nasty bug in `fixmate'
+
+------------------------------------------------------------------------
+r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/bowtie2sam.pl
+ M /trunk/samtools/misc/soap2sam.pl
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+make the script robust to the bugs in SOAP-2.1.7
+
+------------------------------------------------------------------------
+r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_stat.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-20
+ * check if file is truncated in flagstat
+
+------------------------------------------------------------------------
+r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-19
+ * print the header if requested
+
+------------------------------------------------------------------------
+r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-18
+ * fixed a minor bug reported by Nils Homer
+
+------------------------------------------------------------------------
+r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
+ D /trunk/samtools/Makefile.std
+ A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
+ D /trunk/samtools/misc/Makefile.std
+
+rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
+
+------------------------------------------------------------------------
+r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
+Changed paths:
+ D /trunk/samtools/Makefile
+ A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bam_tview.c
+ M /trunk/samtools/bamtk.c
+ D /trunk/samtools/misc/Makefile
+ A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.2-17
+ * incorporating Nils' changes
+ * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
+
+------------------------------------------------------------------------
+r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kseq.h
+ A /trunk/samtools/kstring.c
+ A /trunk/samtools/kstring.h
+
+ * samtools-0.1.2-16
+ * made pileup take a list of proposed indels. An insertion is N at the moment.
+ * added my kstring library for a bit complex parsing of the position list.
+
+------------------------------------------------------------------------
+r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/soap2sam.pl
+
+ * soap2sam.pl-0.1.2
+ * more robust to truncated soap output
+
+------------------------------------------------------------------------
+r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.lite
+
+added bam_stat.o to Makefile.lite
+
+------------------------------------------------------------------------
+r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-15
+ * generate RMS of mapQ instead of max mapQ
+
+------------------------------------------------------------------------
+r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/glf.c
+ M /trunk/samtools/glf.h
+ M /trunk/samtools/misc/Makefile
+
+ * samtools-0.1.2-14
+ * implemented GLFv3
+
+------------------------------------------------------------------------
+r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-13
+ * fixed a minor bug in displaying pileup
+
+------------------------------------------------------------------------
+r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-12
+ * optionally print SAM header
+
+------------------------------------------------------------------------
+r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/glf.c
+
+ * samtools-0.1.2-11
+ * use "GLF\3" as the magic for GLFv3 files
+
+------------------------------------------------------------------------
+r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/glf.c
+ M /trunk/samtools/glf.h
+
+ * samtools-0.1.2-10
+ * fixed a bug in import: core.bin is undefined for unmapped reads
+ * this bug can be alleviated (not completely solved) in bam_index.c
+ * update to GLFv3: pos is changed to offset for better compression
+
+------------------------------------------------------------------------
+r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/wgsim.c
+
+ * wgsim-0.2.3
+ * fixed a bug in simulating indels
+
+------------------------------------------------------------------------
+r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/misc/wgsim.c
+
+ * wgsim-0.2.2
+ * allow to print mismatch information as fastq comment. MAQ does
+ not like long read names.
+
+------------------------------------------------------------------------
+r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/misc/wgsim.c
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+ * wgsim-0.2.1
+ * fixed a bug about color read coordinates
+ * fixed a bug in read names
+ * wgsim_eval.pl-0.1.3
+ * make the script work with color reads
+
+------------------------------------------------------------------------
+r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/Makefile
+ M /trunk/samtools/misc/wgsim.c
+
+ * wgsim: added a note
+
+------------------------------------------------------------------------
+r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
+Changed paths:
+ M /trunk/samtools/misc/wgsim.c
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+ * wgsim-0.2.0
+ * considerable code clean up
+ * print number of substitutions/indels/errors on each read
+ * potentially support SOLiD simulation, though not tested at the moment
+ * wgsim_eval.pl-0.1.2
+ * change in accordant with wgsim
+
+------------------------------------------------------------------------
+r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-9
+ * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
+
+------------------------------------------------------------------------
+r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+Fix annoying segv when invalid region specified.
+
+------------------------------------------------------------------------
+r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
+Changed paths:
+ D /trunk/samtools/misc/indel_filter.pl
+ A /trunk/samtools/misc/samtools.pl
+
+ * move indel_filter.pl to samtools.pl
+
+------------------------------------------------------------------------
+r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_mate.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-7
+ * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
+
+------------------------------------------------------------------------
+r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_stat.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-7
+ * fixed a minor bug in flagstat
+
+------------------------------------------------------------------------
+r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/indel_filter.pl
+
+ * samtools-0.1.2-6
+ * improve indel caller by setting maximum window size
+
+------------------------------------------------------------------------
+r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * output max mapping quality in indel line
+
+------------------------------------------------------------------------
+r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/maq2sam.c
+
+fixed a bug in generating tag AM
+
+------------------------------------------------------------------------
+r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+fixed a potential memory problem in indexing
+
+------------------------------------------------------------------------
+r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+Pass LIBS to recursive targets to facilitate building at Broad.
+
+------------------------------------------------------------------------
+r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_stat.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-3
+ * fixed a bug in generating GLFv2 for indels
+ * improve flagstat report a little bit
+
+------------------------------------------------------------------------
+r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ A /trunk/samtools/bam_stat.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-1
+ * added flagstat command
+
+------------------------------------------------------------------------
+r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+Release SAMtools-0.1.2
+
+------------------------------------------------------------------------
+r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/misc/indel_filter.pl
+
+Script for filtering indel results
+
+------------------------------------------------------------------------
+r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/misc/zoom2sam.pl
+
+convert ZOOM to SAM
+
+------------------------------------------------------------------------
+r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/misc/novo2sam.pl
+
+add a script to convert novo alignment to SAM
+
+------------------------------------------------------------------------
+r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/ChangeLog.old
+ M /trunk/samtools/samtools.1
+
+update documentation and ChangeLog
+
+------------------------------------------------------------------------
+r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.1-19
+ * fixed a bug in "merge" command line
+
+------------------------------------------------------------------------
+r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/Makefile
+ A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
+ M /trunk/samtools/misc/export2sam.pl
+ A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
+ A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
+ A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
+
+ * merge from branches/dev/
+ * all future development will happen here
+
+------------------------------------------------------------------------
+r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/COPYING
+ M /trunk/samtools/ChangeLog
+ A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
+ M /trunk/samtools/Makefile
+ A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_lpileup.c
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/examples/00README.txt
+ A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
+ D /trunk/samtools/examples/ex1.fa.fai
+ M /trunk/samtools/examples/ex1.sam.gz
+ M /trunk/samtools/faidx.c
+ A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
+ M /trunk/samtools/glf.h
+ M /trunk/samtools/misc/Makefile
+ M /trunk/samtools/misc/maq2sam.c
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/source.dot
+
+ * Merge from branches/dev/
+ * all future development will happen here at trunk/
+
+------------------------------------------------------------------------
+r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_tview.c
+
+Fix problem with compiling without curses.
+
+------------------------------------------------------------------------
+r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+ A /trunk/samtools (from /branches/dev/samtools:62)
+
+Create trunk copy
+
+------------------------------------------------------------------------
+r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+ A /branches/dev/samtools/NEWS
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/samtools.1
+
+Release samtools-0.1.1
+
+------------------------------------------------------------------------
+r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
+Changed paths:
+ M /branches/dev/samtools/bam_aux.c
+ M /branches/dev/samtools/bam_index.c
+ M /branches/dev/samtools/bam_plcmd.c
+ M /branches/dev/samtools/bam_tview.c
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/razf.c
+ M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-66
+ * fixed a bug in razf.c: reset z_eof when razf_seek() is called
+ * fixed a memory leak in parsing a region
+ * changed pileup a little bit when -s is in use: output ^ and $
+ * when a bam is not indexed, output more meaningful error message
+ * fixed a bug in indexing for small alignment
+ * fixed a bug in the viewer when we come to the end of a reference file
+ * updated documentation
+ * prepare to release 0.1.1
+
+------------------------------------------------------------------------
+r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+ A /branches/dev/samtools/examples
+ A /branches/dev/samtools/examples/00README.txt
+ A /branches/dev/samtools/examples/ex1.fa
+ A /branches/dev/samtools/examples/ex1.fa.fai
+ A /branches/dev/samtools/examples/ex1.sam.gz
+
+example
+
+------------------------------------------------------------------------
+r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/ChangeLog
+
+update ChangeLog
+
+------------------------------------------------------------------------
+r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/misc/export2sam.pl
+
+ * added comments
+ * fixed several bugs
+
+------------------------------------------------------------------------
+r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
+Changed paths:
+ A /branches/dev/samtools/misc/export2sam.pl
+
+convert Export format to SAM; not thoroughly tested
+
+------------------------------------------------------------------------
+r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
+Changed paths:
+ M /branches/dev/samtools/bam_import.c
+ M /branches/dev/samtools/bam_plcmd.c
+ M /branches/dev/samtools/bam_tview.c
+ M /branches/dev/samtools/bamtk.c
+ A /branches/dev/samtools/source.dot
+
+ * samtools-0.1.0-65
+ * pileup: generate maq-like simple output
+ * pileup: allow to output pileup at required sites
+ * source.dot: source file relationship graph
+ * tview: fixed a minor bug
+
+------------------------------------------------------------------------
+r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
+Changed paths:
+ D /branches/dev/samtools/misc/all2sam.pl
+
+remove all2sam.pl
+
+------------------------------------------------------------------------
+r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
+Changed paths:
+ A /branches/dev/samtools/COPYING
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/faidx.h
+ M /branches/dev/samtools/khash.h
+ M /branches/dev/samtools/kseq.h
+ M /branches/dev/samtools/ksort.h
+ M /branches/dev/samtools/samtools.1
+
+Added copyright information and a bit more documentation. No code change.
+
+------------------------------------------------------------------------
+r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/bam.c
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/bam_index.c
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-64
+ * improved efficiency of the indel caller for spliced alignments
+
+------------------------------------------------------------------------
+r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/bam.c
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/bam_aux.c
+ M /branches/dev/samtools/bam_index.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-63
+ * a bit code cleanup: reduce the dependency between source files
+
+------------------------------------------------------------------------
+r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/bam_plcmd.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-62
+ * fixed a memory leak
+
+------------------------------------------------------------------------
+r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/ChangeLog
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/samtools.1
+
+update documentation, ChangeLog and a comment
+
+------------------------------------------------------------------------
+r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
+Changed paths:
+ M /branches/dev/samtools/Makefile
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/bam_maqcns.h
+ M /branches/dev/samtools/bam_pileup.c
+ A /branches/dev/samtools/bam_plcmd.c
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-61
+ * moved pileup command to a separate source file
+ * added indel caller
+ * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
+ * updated documentation
+
+------------------------------------------------------------------------
+r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-60
+ * fixed another bug in maqcns when there is a nearby deletion
+
+------------------------------------------------------------------------
+r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
+Changed paths:
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/bam_pileup.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-59
+ * pileup: outputing consensus is now optional
+ * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
+ I am not quite sure why the previous version may have problem.
+
+------------------------------------------------------------------------
+r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
+Changed paths:
+ M /branches/dev/samtools/bam_pileup.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-58
+ * add maq consensus to pileup. However, I will move this part to a new
+ command as strictly speaking, consensus callin is not part of pileup,
+ and imposing it would make it harder to generate for other language
+ bindings.
+
+------------------------------------------------------------------------
+r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/bgzf.c
+
+Fix bug in tell() after reads that consume to the exact end of a block.
+
+------------------------------------------------------------------------
+r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/samtools.1
+
+update manual
+
+------------------------------------------------------------------------
+r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
+Changed paths:
+ M /branches/dev/samtools/bam_import.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-57
+ * fixed a bug in parser when there is auxiliary fields
+ * made the parser a bit more robust
+
+------------------------------------------------------------------------
+r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
+Changed paths:
+ M /branches/dev/samtools/bam_index.c
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/bgzf.c
+
+ * samtools-0.1.0-56
+ * fixed a bug in bgzf (only reading is affected)
+ * fixed a typo in bam_index.c
+ * in bam_index.c, check potential bugs in the underlying I/O library
+
+------------------------------------------------------------------------
+r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/samtools.1
+
+update manual
+
+------------------------------------------------------------------------
+r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
+Changed paths:
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/bam_pileup.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-55
+ * tried to make pileup work with clipping (previously not), though NOT tested
+ * removed -v from pileup
+ * made pileup take the reference sequence
+
+------------------------------------------------------------------------
+r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
+Changed paths:
+ M /branches/dev/samtools/bam_import.c
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-54
+ * in parser, recognize "=", rather than ",", as a match
+ * in parser, correctl parse "=" at the MRNM field.
+
+------------------------------------------------------------------------
+r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/misc/maq2sam.c
+
+fixed a bug in handling maq flag 64 and 192
+
+------------------------------------------------------------------------
+r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/misc/md5fa.c
+
+also calculate unordered md5sum check
+
+------------------------------------------------------------------------
+r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/misc/md5fa.c
+
+fixed a minor bug when there are space in the sequence
+
+------------------------------------------------------------------------
+r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/misc/md5fa.c
+
+fixed a potential memory leak
+
+------------------------------------------------------------------------
+r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/bam_import.c
+ M /branches/dev/samtools/bam_index.c
+ M /branches/dev/samtools/bamtk.c
+
+ * fixed a bug in import: bin is wrongly calculated
+
+------------------------------------------------------------------------
+r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/misc/all2sam.pl
+
+nothing, really
+
+------------------------------------------------------------------------
+r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/Makefile
+ M /branches/dev/samtools/kseq.h
+ M /branches/dev/samtools/misc/Makefile
+ A /branches/dev/samtools/misc/md5.c
+ A /branches/dev/samtools/misc/md5.h
+ A /branches/dev/samtools/misc/md5fa.c
+
+ * fixed two warnings in kseq.h
+ * added md5sum utilities
+
+------------------------------------------------------------------------
+r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
+Changed paths:
+ M /branches/dev/samtools/Makefile
+ M /branches/dev/samtools/bam_import.c
+ M /branches/dev/samtools/bamtk.c
+ A /branches/dev/samtools/kseq.h
+ D /branches/dev/samtools/kstream.h
+
+ * samtools-0.1.0-52
+ * replace kstream with kseq. kseq is a superset of kstream. I need the
+ extra functions in kseq.h.
+ * also compile stand-alone faidx
+
+------------------------------------------------------------------------
+r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/bam_sort.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-51
+ * sorting by read names is available
+
+------------------------------------------------------------------------
+r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/bam.c
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/bam_import.c
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/bam_pileup.c
+ M /branches/dev/samtools/bam_sort.c
+ M /branches/dev/samtools/bam_tview.c
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/misc/maq2sam.c
+
+ * samtools-0.1.0-50
+ * format change to meet the latest specification
+
+------------------------------------------------------------------------
+r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/misc/maq2sam.c
+
+ * minor change in maqcns: special care when n==0
+ * change maq2sam to meet the latest specification
+
+------------------------------------------------------------------------
+r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/razf.c
+ M /branches/dev/samtools/razf.h
+
+considerable code clean up in razf
+
+------------------------------------------------------------------------
+r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/ChangeLog
+ M /branches/dev/samtools/Makefile
+ M /branches/dev/samtools/faidx.c
+
+make RAZF optional in faidx.c
+
+------------------------------------------------------------------------
+r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/Makefile
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/bam_aux.c
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-49
+ * added routines for retrieving aux data, NOT TESTED YET!
+
+------------------------------------------------------------------------
+r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
+Changed paths:
+ M /branches/dev/samtools/bam.c
+ M /branches/dev/samtools/bam_import.c
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/bgzf.c
+ M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-48
+ * bgzf: fixed a potential integer overflow on 32-it machines
+ * maqcns: set the minimum combined quality as 0
+ * supporting hex strings
+
+------------------------------------------------------------------------
+r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/bam_maqcns.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-47
+ * fixed the bug in maqcns
+
+------------------------------------------------------------------------
+r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/Makefile
+ M /branches/dev/samtools/bam.h
+ A /branches/dev/samtools/bam_maqcns.c
+ A /branches/dev/samtools/bam_maqcns.h
+ M /branches/dev/samtools/bam_tview.c
+ M /branches/dev/samtools/bamtk.c
+ A /branches/dev/samtools/glf.h
+
+ * samtools-0.1.0-46
+ * add MAQ consensus caller, currently BUGGY!
+
+------------------------------------------------------------------------
+r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
+Changed paths:
+ M /branches/dev/samtools/bam_pileup.c
+ M /branches/dev/samtools/bam_tview.c
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-45
+ * tview: display padded alignment (but not P operation)
+ * better coordinates and reference sequence
+
+------------------------------------------------------------------------
+r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
+Changed paths:
+ A /branches/dev/samtools/ChangeLog
+
+new ChangeLog
+
+------------------------------------------------------------------------
+r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+ D /branches/dev/samtools/ChangeLog
+ A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
+
+Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
+the log of my personal SVN repository.
+
+------------------------------------------------------------------------
+r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
+Changed paths:
+ M /branches/dev/samtools/Makefile
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/bgzf.c
+
+ * samtools-0.1.0-44
+ * declare fseeko and ftello as some Linux may not do this by default and
+ missing these declarations will make bgzf buggy
+ * get rid of some harmless warings
+ * use BGZF by default, now
+
+------------------------------------------------------------------------
+r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
+Changed paths:
+ M /branches/dev/samtools/bam_index.c
+ M /branches/dev/samtools/bamtk.c
+ M /branches/dev/samtools/razf.c
+
+ * samtools-0.1.0-43
+ * fixed a bug in razf_read()
+ * give more warnings when the file is truncated (or due to bugs in I/O library)
+
+------------------------------------------------------------------------
+r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/bgzf.c
+
+fixed a bug in bgzf.c at the end of the file
+
+------------------------------------------------------------------------
+r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
+Changed paths:
+ M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-42
+ * a lot happened to RAZF, although samtools itself is untouched. Better
+ also update the version number anyway to avoid confusion
+
+------------------------------------------------------------------------
+r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/razf.c
+
+a change from Jue, but I think it should not matter
+
+------------------------------------------------------------------------
+r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
+Changed paths:
+ M /branches/dev/samtools/razf.c
+
+fixed a potential bug in razf. However, it seems still buggy, just
+rarely happens, very rarely.
+
+------------------------------------------------------------------------
+r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/razf.c
+
+fixed a bug in razf, with the help of Jue
+
+------------------------------------------------------------------------
+r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/bam_index.c
+
+remove a comment
+
+------------------------------------------------------------------------
+r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+ M /branches/dev/samtools/Makefile
+ M /branches/dev/samtools/bam.h
+ M /branches/dev/samtools/razf.c
+ M /branches/dev/samtools/razf.h
+
+ * Jue has updated razf to realize Bob's scheme
+
+------------------------------------------------------------------------
+r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+ A /branches/dev/samtools/samtools.1
+
+the manual page
+
+------------------------------------------------------------------------
+r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
+Changed paths:
+ A /branches/dev/samtools/ChangeLog
+ A /branches/dev/samtools/Makefile
+ A /branches/dev/samtools/bam.c
+ A /branches/dev/samtools/bam.h
+ A /branches/dev/samtools/bam_aux.c
+ A /branches/dev/samtools/bam_endian.h
+ A /branches/dev/samtools/bam_import.c
+ A /branches/dev/samtools/bam_index.c
+ A /branches/dev/samtools/bam_lpileup.c
+ A /branches/dev/samtools/bam_pileup.c
+ A /branches/dev/samtools/bam_sort.c
+ A /branches/dev/samtools/bam_tview.c
+ A /branches/dev/samtools/bamtk.c
+ A /branches/dev/samtools/bgzf.c
+ A /branches/dev/samtools/bgzf.h
+ A /branches/dev/samtools/bgzip.c
+ A /branches/dev/samtools/faidx.c
+ A /branches/dev/samtools/faidx.h
+ A /branches/dev/samtools/khash.h
+ A /branches/dev/samtools/ksort.h
+ A /branches/dev/samtools/kstream.h
+ A /branches/dev/samtools/misc
+ A /branches/dev/samtools/misc/Makefile
+ A /branches/dev/samtools/misc/all2sam.pl
+ A /branches/dev/samtools/misc/maq2sam.c
+ A /branches/dev/samtools/razf.c
+ A /branches/dev/samtools/razf.h
+ A /branches/dev/samtools/razip.c
+ A /branches/dev/samtools/zutil.h
+
+The initial version of samtools, replicated from my local SVN repository.
+The current version is: 0.1.0-42. All future development will happen here.
+
+------------------------------------------------------------------------
+r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+ A /branches/dev/samtools
+
+samtools (C version)
+
+------------------------------------------------------------------------
diff --git a/src/samtools-0.1.18/INSTALL b/src/samtools-0.1.18/INSTALL
new file mode 100644
index 0000000..37d84a9
--- /dev/null
+++ b/src/samtools-0.1.18/INSTALL
@@ -0,0 +1,30 @@
+System Requirements
+===================
+
+SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
+preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
+file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
+diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.
+
+The text-based viewer (tview) requires the GNU ncurses library
+<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
+the modern Linux/Unix distributions. If you do not have this library installed,
+you can still compile the rest of SAMtools by manually changing:
+`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
+comment out the line starting with `LIBCURSES='.
+
+
+Compilation
+===========
+
+Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
+razip with `make razip'.
+
+
+Installation
+============
+
+Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to
+a location you want (e.g. a directory in your $PATH). You may also copy
+`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
+that the `man' command may find the manual.
diff --git a/src/samtools-0.1.18/Makefile b/src/samtools-0.1.18/Makefile
new file mode 100644
index 0000000..00927f8
--- /dev/null
+++ b/src/samtools-0.1.18/Makefile
@@ -0,0 +1,93 @@
+CC= gcc
+CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
+DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
+KNETFILE_O= knetfile.o
+LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
+ bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
+ $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
+ bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
+ bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
+ cut_target.o phase.o bam2depth.o
+PROG= samtools_0.1.18
+INCLUDES= -I.
+SUBDIRS= . bcftools
+LIBPATH=
+LIBCURSES= -lcurses
+
+.SUFFIXES:.c .o
+
+.c.o:
+ $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+ @target=`echo $@ | sed s/-recur//`; \
+ wdir=`pwd`; \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ cd $$subdir; \
+ $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+ cd $$wdir; \
+ done;
+
+all:$(PROG)
+
+.PHONY:all lib clean cleanlocal
+.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
+
+lib:libbam.a
+
+libbam.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
+
+samtools_0.1.18:lib-recur $(AOBJS)
+ $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz #$(LIBCURSES)
+
+razip:razip.o razf.o $(KNETFILE_O)
+ $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
+
+bgzip:bgzip.o bgzf.o $(KNETFILE_O)
+ $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz
+
+razip.o:razf.h
+bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
+sam.o:sam.h bam.h
+bam_import.o:bam.h kseq.h khash.h razf.h
+bam_pileup.o:bam.h razf.h ksort.h
+bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
+bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
+bam_lpileup.o:bam.h ksort.h
+bam_tview.o:bam.h faidx.h
+bam_sort.o:bam.h ksort.h razf.h
+bam_md.o:bam.h faidx.h
+sam_header.o:sam_header.h khash.h
+bcf.o:bcftools/bcf.h
+bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
+bam2bcf_indel.o:bam2bcf.h
+errmod.o:errmod.h
+phase.o:bam.h khash.h ksort.h
+bamtk.o:bam.h
+
+faidx.o:faidx.h razf.h khash.h
+faidx_main.o:faidx.h razf.h
+
+
+libbam.1.dylib-local:$(LOBJS)
+ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
+
+libbam.so.1-local:$(LOBJS)
+ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
+
+dylib:
+ @$(MAKE) cleanlocal; \
+ case `uname` in \
+ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
+ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
+ *) echo 'Unknown OS';; \
+ esac
+
+
+cleanlocal:
+ rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
+
+clean:cleanlocal-recur
diff --git a/src/samtools-0.1.18/Makefile.mingw b/src/samtools-0.1.18/Makefile.mingw
new file mode 100644
index 0000000..7a57ffc
--- /dev/null
+++ b/src/samtools-0.1.18/Makefile.mingw
@@ -0,0 +1,63 @@
+CC= gcc.exe
+AR= ar.exe
+CFLAGS= -g -Wall -O2
+DFLAGS= -D_USE_KNETFILE -D_CURSES_LIB=2
+KNETFILE_O= knetfile.o
+LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
+ bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \
+ $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bedidx.o
+AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
+ bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
+ bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
+ cut_target.o phase.o bam_cat.o bam2depth.o
+BCFOBJS= bcftools/bcf.o bcftools/fet.o bcftools/bcf2qcall.o bcftools/bcfutils.o \
+ bcftools/call1.o bcftools/index.o bcftools/kfunc.o bcftools/em.o \
+ bcftools/kmin.o bcftools/prob1.o bcftools/vcf.o bcftools/mut.o
+PROG= samtools.exe bcftools.exe
+INCLUDES= -I. -Iwin32
+SUBDIRS= .
+LIBPATH=
+
+.SUFFIXES:.c .o
+
+.c.o:
+ $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+.PHONY:all lib clean cleanlocal
+.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
+
+lib:libbam.a
+
+libbam.a:$(LOBJS)
+ $(AR) -cru $@ $(LOBJS)
+
+samtools.exe:$(AOBJS) libbam.a $(BCFOBJS)
+ $(CC) $(CFLAGS) -o $@ $(AOBJS) $(BCFOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz -lcurses -lws2_32
+
+bcftools.exe:$(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o
+ $(CC) $(CFLAGS) -o $@ $(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o -lm -Lwin32 -lz -lws2_32
+
+razip.o:razf.h
+bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
+sam.o:sam.h bam.h
+bam_import.o:bam.h kseq.h khash.h razf.h
+bam_pileup.o:bam.h razf.h ksort.h
+bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
+bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
+bam_lpileup.o:bam.h ksort.h
+bam_tview.o:bam.h faidx.h
+bam_sort.o:bam.h ksort.h razf.h
+bam_md.o:bam.h faidx.h
+sam_header.o:sam_header.h khash.h
+bcf.o:bcftools/bcf.h
+bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
+bam2bcf_indel.o:bam2bcf.h
+errmod.o:errmod.h
+
+faidx.o:faidx.h razf.h khash.h
+faidx_main.o:faidx.h razf.h
+
+clean:
+ rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
diff --git a/src/samtools-0.1.18/NEWS b/src/samtools-0.1.18/NEWS
new file mode 100644
index 0000000..41a6cc8
--- /dev/null
+++ b/src/samtools-0.1.18/NEWS
@@ -0,0 +1,806 @@
+Beta Release 0.1.18 (2 September, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in samtools:
+
+ * Support the new =/X CIGAR operators (by Peter Cock).
+
+ * Allow to subsample BAM while keeping the pairing intact (view -s).
+
+ * Implemented variant distance bias as a new filter (by Petr Danecek).
+
+ * Bugfix: huge memory usage during indexing
+
+ * Bugfix: use of uninitialized variable in mpileup (rare)
+
+ * Bugfix: wrong BAQ probability (rare)
+
+Notable changes in bcftools:
+
+ * Support indel in the contrast caller.
+
+ * Bugfix: LRT2=nan in rare cases
+
+(0.1.18: 2 September 2011, r982:295)
+
+
+
+Beta Release 0.1.17 (6 July, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+With the maturity of `mpileup' and the lack of update in the `pileup' command,
+the `pileup' command is now formally dropped. Most of the pileup functionality,
+such as outputting mapping quality and read positions, have been added
+`mpileup'.
+
+Since this release, `bcftools view' is able to perform contrast SNP calling
+(option -T) for discovering de novo and/or somatic mutations between a pair of
+samples or in a family trio. Potential mutations are scored by a log likelihood
+ratio, which is very simple in math, but should be comparable to more
+sophisticated methods. Note that getting the score is only the very first step.
+A lot more need to be done to reduce systematical errors due to mapping and
+reference errors and structural variations.
+
+Other notable changes in samtools:
+
+ * Improved sorting order checking during indexing.
+
+ * Improved region parsing. Colons in reference sequence names are parsed
+ properly.
+
+ * Fixed an issue where mpileup does not apply BAQ for the first few reads when
+ a region is specified.
+
+ * Fixed an issue where `faidx' does not work with FASTA files with long lines.
+
+ * Bugfix: wrong SP genotype information in the BCF output.
+
+Other notable changes in bcftools:
+
+ * Output the ML esitmate of the allele count.
+
+ * Added the HWE plus F<0 filter to varFilter. For multiple samples, it
+ effectively filters false heterozygous calls around centromeres.
+
+ * For association mapping, perform both 1-degree and 2-degree test. The
+ 2-degree test is conservative but more robust to HWE violation.
+
+(0.1.17: 6 July 2011, r973:277)
+
+
+
+Beta Release 0.1.16 (21 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in samtools:
+
+ * Support the new SAM/BAM type `B' in the latest SAM spec v1.4.
+
+ * When the output file of `samtools merge' exists, do not overwrite it unless
+ a new command-line option `-f' is applied.
+
+ * Bugfix: BED support is not working when the input BED is not sorted.
+
+ * Bugfix: some reads without coordinates but given on the reverse strand are
+ lost in merging.
+
+Notable changes in bcftools:
+
+ * Code cleanup: separated max-likelihood inference and Bayesian inference.
+
+ * Test Hardy-Weinberg equilibrium with a likelihood-ratio test.
+
+ * Provided another association test P-value by likelihood-ratio test.
+
+ * Use Brent's method to estimate the site allele frequency when EM converges
+ slowly. The resulting ML estimate of allele frequnecy is more accurate.
+
+ * Added the `ldpair' command, which computes r^2 between SNP pairs given in
+ an input file.
+
+Also, the `pileup' command, which has been deprecated by `mpileup' since
+version 0.1.10, will be dropped in the next release. The old `pileup' command
+is substandard and causing a lot of confusion.
+
+(0.1.16: 21 April 2011, r963:234)
+
+
+
+Beta Release 0.1.15 (10 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Noteable changes:
+
+ * Allow to perform variant calling or to extract information in multiple
+ regions specified by a BED file (`samtools mpileup -l', `samtools view -L'
+ and `bcftools view -l').
+
+ * Added the `depth' command to samtools to compute the per-base depth with a
+ simpler interface. File `bam2depth.c', which implements this command, is the
+ recommended example on how to use the mpileup APIs.
+
+ * Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg
+ test using this estimate.
+
+ * For `samtools view', when `-R' is specified, drop read groups in the header
+ that are not contained in the specified file.
+
+ * For `samtools flagstat', separate QC-pass and QC-fail reads.
+
+ * Improved the command line help of `samtools mpileup' and `bcftools view'.
+
+ * Use a global variable to control the verbose level of samtools stderr
+ output. Nonetheless, it has not been full utilized.
+
+ * Fixed an issue in association test which may report false associations,
+ possibly due to floating point underflow.
+
+(0.1.15: 10 April 2011, r949:203)
+
+
+
+Beta release 0.1.14 (21 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release implements a method for testing associations for case-control
+data. The method does not call genotypes but instead sums over all genotype
+configurations to compute a chi^2 based test statistics. It can be potentially
+applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
+has not been evaluated on real data.
+
+Another new feature is to make X chromosome variant calls when female and male
+samples are both present. The user needs to provide a file indicating the
+ploidy of each sample (see also manual bcftools/bcftools.1).
+
+Other notable changes:
+
+ * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
+ older which encodes PL in a different way.
+
+ * Changed the behavior of `bcftools view -s'. Now when a list of samples is
+ provided, the samples in the output will be reordered to match the ordering
+ in the sample list. This change is mainly designed for association test.
+
+ * Sped up `bcftools view -v' for target sequencing given thousands of samples.
+ Also added a new option `view -d' to skip loci where only a few samples are
+ covered by reads.
+
+ * Dropped HWE test. This feature has never been implemented properly. An EM
+ should be much better. To be implemented in future.
+
+ * Added the `cat' command to samtools. This command concatenate BAMs with
+ identical sequence dictionaries in an efficient way. Modified from bam_cat.c
+ written by Chris Saunders.
+
+ * Added `samtools view -1' to write BAMs at a low compression level but twice
+ faster to create. The `sort' command generates temporary files at a low
+ compression level as well.
+
+ * Added `samtools mpileup -6' to accept "BAM" with Illumina 1.3+ quality
+ strings (strictly speaking, such a file is not BAM).
+
+ * Added `samtools mpileup -L' to skip INDEL calling in regions with
+ excessively high coverage. Such regions dramatically slow down mpileup.
+
+ * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc.
+
+(0.1.14: 21 March 2011, r933:170)
+
+
+
+Beta release 0.1.13 (1 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The most important though largely invisible modification is the change of the
+order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
+spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
+generated by samtools older than r921 inclusive. VCF/BCF generated by the new
+samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
+version number.
+
+Single Individual Haplotyping (SIH) is added as an experimental feature. It
+originally aims to produce haploid consensus from fosmid pool sequencing, but
+also works with short-read data. For short reads, phased blocks are usually too
+short to be useful in many applications, but they can help to rule out part of
+SNPs close to INDELs or between copies of CNVs.
+
+
+Other notable changes in samtools:
+
+ * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
+ calling. This reduces the power but improves specificity.
+
+ * Improved sorting order checking in indexing. Now indexing is the preferred way
+ to check if a BAM is sorted.
+
+ * Added a switch `-E' to mpileup and calmd. This option uses an alternative way
+ to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
+ a little loss in specificity.
+
+ * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
+
+ * Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
+
+ * Added `mpileup -S' to compute per-sample strand bias P-value.
+
+ * Added `mpileup -G' to exclude read groups in variant calling.
+
+ * Fixed segfault in indel calling related to unmapped and refskip reads.
+
+ * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
+ genotypes for longer short INDELs, typically over 10bp.
+
+ * Fixed a bug in tview on big-endian machines.
+
+ * Fixed a very rare memory issue in bam_md.c
+
+ * Fixed an out-of-boundary bug in mpileup when the read base is `N'.
+
+ * Fixed a compiling error when the knetfile library is not used. Fixed a
+ library compiling error due to the lack of bam_nt16_nt4_table[] table.
+ Suppress a compiling warning related to the latest zlib.
+
+
+Other notable changes in bcftools:
+
+ * Updated the BCF spec.
+
+ * Added the `FQ' VCF INFO field, which gives the phred-scaled probability
+ of all samples being the same (identical to the reference or all homozygous
+ variants). Option `view -f' has been dropped.
+
+ * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
+ similar to "samtools.pl pileup2fq".
+
+ * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
+ spec. Drop bcf-fix.pl.
+
+ * Output bcftools specific INFO and FORMAT in the VCF header.
+
+ * Added `view -s' to call variants from a subset of samples.
+
+ * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
+ custom fields are still unparsed and will be stored as a missing value.
+
+ * Fixed a minor bug in Fisher's exact test; the results are rarely changed.
+
+
+(0.1.13: 1 March 2011, r926:134)
+
+
+
+Beta release 0.1.12a (2 December, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is another bug fix release:
+
+ * Fixed a memory violation in mpileup, which causes segfault. Release
+ 0.1.9 and above are affected.
+
+ * Fixed a memory violation in the indel caller, which does not causes
+ segfault, but may potentially affect deletion calls in an unexpected
+ way. Release 0.1.10 and above are affected.
+
+ * Fixed a bug in computing r-square in bcftools. Few are using this
+ functionality and it only has minor effect.
+
+ * Fixed a memory leak in bam_fetch().
+
+ * Fixed a bug in writing meta information to the BAM index for the last
+ sequence. This bug is invisible to most users, but it is a bug anyway.
+
+ * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
+
+(0.1.12: 2 December 2010, r862)
+
+
+
+Beta release 0.1.11 (21 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is mainly a bug fix release:
+
+ * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
+ are retrieved from a small region containing no reads.
+
+ * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
+ failure when the first CIGAR operation is a deletion.
+
+ * Improved fault tolerence in remote access.
+
+One minor feature has been implemented in bcftools:
+
+ * Added a reference-free variant calling mode. In this mode, a site is
+ regarded as a variat iff the sample(s) contains two or more alleles;
+ the meaning of the QUAL field in the VCF output is changed
+ accordingly. Effectively, the reference allele is irrelevant to the
+ result in the new mode, although the reference sequence has to be
+ used in realignment when SAMtools computes genotype likelihoods.
+
+In addition, since 0.1.10, the `pileup' command has been deprecated by
+`mpileup' which is more powerful and more accurate. The `pileup' command
+will not be removed in the next few releases, but new features will not
+be added.
+
+(0.1.11: 21 November 2010, r851)
+
+
+
+Beta Release 0.1.10 (16 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release is featured as the first major improvement to the indel
+caller. The method is similar to the old one implemented in the pileup
+command, but the details are handled more carefully both in theory and
+in practice. As a result, the new indel caller usually gives more
+accurate indel calls, though at the cost of sensitivity. The caller is
+implemented in the mpileup command and is invoked by default. It works
+with multiple samples.
+
+Other notable changes:
+
+ * With the -r option, the calmd command writes the difference between
+ the original base quality and the BAQ capped base quality at the BQ
+ tag but does not modify the base quality. Please use -Ar to overwrite
+ the original base quality (the 0.1.9 behavior).
+
+ * Allow to set a maximum per-sample read depth to reduce memory. In
+ 0.1.9, most of memory is wasted for the ultra high read depth in some
+ regions (e.g. the chr1 centromere).
+
+ * Optionally write per-sample read depth and per-sample strand bias
+ P-value.
+
+ * Compute equal-tail (Bayesian) credible interval of site allele
+ frequency at the CI95 VCF annotation.
+
+ * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
+ filtering.
+
+(0.1.10: 16 November 2010, r829)
+
+
+
+Beta Release 0.1.9 (27 October, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release is featured as the first major improvement to the samtools'
+SNP caller. It comes with a revised MAQ error model, the support of
+multi-sample SNP calling and the computation of base alignment quality
+(BAQ).
+
+The revised MAQ error model is based on the original model. It solves an
+issue of miscalling SNPs in repetitive regions. Althought such SNPs can
+usually be filtered at a later step, they mess up unfiltered calls. This
+is a theoretical flaw in the original model. The revised MAQ model
+deprecates the orginal MAQ model and the simplified SOAPsnp model.
+
+Multi-sample SNP calling is separated in two steps. The first is done by
+samtools mpileup and the second by a new program, bcftools, which is
+included in the samtools source code tree. Multi-sample SNP calling also
+works for single sample and has the advantage of enabling more powerful
+filtration. It is likely to deprecate pileup in future once a proper
+indel calling method is implemented.
+
+BAQ is the Phred-scaled probability of a read base being wrongly
+aligned. Capping base quality by BAQ has been shown to be very effective
+in suppressing false SNPs caused by misalignments around indels or in
+low-complexity regions with acceptable compromise on computation
+time. This strategy is highly recommended and can be used with other SNP
+callers as well.
+
+In addition to the three major improvements, other notable changes are:
+
+ * Changes to the pileup format. A reference skip (the N CIGAR operator)
+ is shown as '<' or '>' depending on the strand. Tview is also changed
+ accordingly.
+
+ * Accelerated pileup. The plain pileup is about 50% faster.
+
+ * Regional merge. The merge command now accepts a new option to merge
+ files in a specified region.
+
+ * Fixed a bug in bgzip and razip which causes source files to be
+ deleted even if option -c is applied.
+
+ * In APIs, propogate errors to downstream callers and make samtools
+ return non-zero values once errors occur.
+
+(0.1.9: 27 October 2010, r783)
+
+
+
+Beta Release 0.1.8 (11 July, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable functional changes:
+
+ * Added the `reheader' command which replaces a BAM header with a new
+ header. This command is much faster than replacing header by
+ BAM->SAM->BAM conversions.
+
+ * Added the `mpileup' command which computes the pileup of multiple
+ alignments.
+
+ * The `index' command now stores the number of mapped and unmapped
+ reads in the index file. This information can be retrieved quickly by
+ the new `idxstats' command.
+
+ * By default, pileup used the SOAPsnp model for SNP calling. This
+ avoids the floating overflow in the MAQ model which leads to spurious
+ calls in repetitive regions, although these calls will be immediately
+ filtered by varFilter.
+
+ * The `tview' command now correctly handles CIGARs like 7I10M and
+ 10M1P1I10M which cause assertion failure in earlier versions.
+
+ * Tview accepts a region like `=10,000' where `=' stands for the
+ current sequence name. This saves typing for long sequence names.
+
+ * Added the `-d' option to `pileup' which avoids slow indel calling
+ in ultradeep regions by subsampling reads locally.
+
+ * Added the `-R' option to `view' which retrieves alignments in read
+ groups listed in the specified file.
+
+Performance improvements:
+
+ * The BAM->SAM conversion is up to twice faster, depending on the
+ characteristic of the input.
+
+ * Parsing SAM headers with a lot of reference sequences is now much
+ faster.
+
+ * The number of lseek() calls per query is reduced when the query
+ region contains no read alignments.
+
+Bug fixes:
+
+ * Fixed an issue in the indel caller that leads to miscall of indels.
+ Note that this solution may not work well when the sequencing indel
+ error rate is higher than the rate of SNPs.
+
+ * Fixed another issue in the indel caller which may lead to incorrect
+ genotype.
+
+ * Fixed a bug in `sort' when option `-o' is applied.
+
+ * Fixed a bug in `view -r'.
+
+APIs and other changes:
+
+ * Added iterator interfaces to random access and pileup. The callback
+ interfaces directly call the iterator interfaces.
+
+ * The BGZF blocks holding the BAM header are indepedent of alignment
+ BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
+ fully contained in one BGZF block. This change is fully compatible
+ with the old version of samtools/picard.
+
+Changes in other utilities:
+
+ * Updated export2sam.pl by Chris Saunders.
+
+ * Improved the sam2vcf.pl script.
+
+ * Added a Python version of varfilter.py by Aylwyn Scally.
+
+(0.1.8: 11 July 2010, r613)
+
+
+
+Beta Release 0.1.7 (10 November, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Improved the indel caller in complex scenariors, in particular for
+ long reads. The indel caller is now able to make reasonable indel
+ calls from Craig Venter capillary reads.
+
+ * Rewrote single-end duplicate removal with improved
+ performance. Paired-end reads are not touched.
+
+ * Duplicate removal is now library aware. Samtools remove potential
+ PCR/optical dupliates inside a library rather than across libraries.
+
+ * SAM header is now fully parsed, although this functionality is not
+ used in merging and so on.
+
+ * In samtools merge, optionally take the input file name as RG-ID and
+ attach the RG tag to each alignment.
+
+ * Added FTP support in the RAZF library. RAZF-compressed reference
+ sequence can be retrieved remotely.
+
+ * Improved network support for Win32.
+
+ * Samtools sort and merge are now stable.
+
+Changes in other utilities:
+
+ * Implemented sam2vcf.pl that converts the pileup format to the VCF
+ format.
+
+ * This release of samtools is known to work with the latest
+ Bio-Samtools Perl module.
+
+(0.1.7: 10 November 2009, r510)
+
+
+
+Beta Release 0.1.6 (2 September, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * In tview, do not show a blank screen when no reads mapped to the
+ corresponding region.
+
+ * Implemented native HTTP support in the BGZF library. Samtools is now
+ able to directly open a BAM file on HTTP. HTTP proxy is also
+ supported via the "http_proxy" environmental variable.
+
+ * Samtools is now compitable with the MinGW (win32) compiler and the
+ PDCurses library.
+
+ * The calmd (or fillmd) command now calculates the NM tag and replaces
+ MD tags if they are wrong.
+
+ * The view command now recognizes and optionally prints FLAG in HEXs or
+ strings to make a SAM file more friendly to human eyes. This is a
+ samtools-C extension, not implemented in Picard for the time
+ being. Please type `samtools view -?' for more information.
+
+ * BAM files now have an end-of-file (EOF) marker to facilitate
+ truncation detection. A warning will be given if an on-disk BAM file
+ does not have this marker. The warning will be seen on BAM files
+ generated by an older version of samtools. It does NO harm.
+
+ * New key bindings in tview: `r' to show read names and `s' to show
+ reference skip (N operation) as deletions.
+
+ * Fixed a bug in `samtools merge -n'.
+
+ * Samtools merge now optionally copies the header of a user specified
+ SAM file to the resultant BAM output.
+
+ * Samtools pileup/tview works with a CIGAR with the first or the last
+ operation is an indel.
+
+ * Fixed a bug in bam_aux_get().
+
+
+Changes in other utilies:
+
+ * Fixed wrong FLAG in maq2sam.
+
+
+(0.1.6: 2 September 2009, r453)
+
+
+
+Beta Release 0.1.5 (7 July, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Support opening a BAM alignment on FTP. Users can now use "tview" to
+ view alignments at the NCBI ftp site. Please read manual for more
+ information.
+
+ * In library, propagate errors rather than exit or complain assertion
+ failure.
+
+ * Simplified the building system and fixed compiling errors caused by
+ zlib<1.2.2.1.
+
+ * Fixed an issue about lost header information when a SAM is imported
+ with "view -t".
+
+ * Implemented "samtool.pl varFilter" which filters both SNPs and short
+ indels. This command replaces "indelFilter".
+
+ * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
+ pileup output.
+
+ * In pileup, cap mapping quality at 60. This helps filtering when
+ different aligners are in use.
+
+ * In pileup, allow to output variant sites only.
+
+ * Made pileup generate correct calls in repetitive region. At the same
+ time, I am considering to implement a simplified model in SOAPsnp,
+ although this has not happened yet.
+
+ * In view, added '-u' option to output BAM without compression. This
+ option is preferred when the output is piped to other commands.
+
+ * In view, added '-l' and '-r' to get the alignments for one library or
+ read group. The "@RG" header lines are now partially parsed.
+
+ * Do not include command line utilities to libbam.a.
+
+ * Fixed memory leaks in pileup and bam_view1().
+
+ * Made faidx more tolerant to empty lines right before or after FASTA >
+ lines.
+
+
+Changes in other utilities:
+
+ * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
+
+
+This release involves several modifications to the key code base which
+may potentially introduce new bugs even though we have tried to minimize
+this by testing on several examples. Please let us know if you catch
+bugs.
+
+(0.1.5: 7 July 2009, r373)
+
+
+
+Beta Release 0.1.4 (21 May, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Added the 'rmdupse' command: removing duplicates for SE reads.
+
+ * Fixed a critical bug in the indel caller: clipped alignments are not
+ processed correctly.
+
+ * Fixed a bug in the tview: gapped alignment may be incorrectly
+ displayed.
+
+ * Unified the interface to BAM and SAM I/O. This is done by
+ implementing a wrapper on top of the old APIs and therefore old APIs
+ are still valid. The new I/O APIs also recognize the @SQ header
+ lines.
+
+ * Generate the MD tag.
+
+ * Generate "=" bases. However, the indel caller will not work when "="
+ bases are present.
+
+ * Enhanced support of color-read display (by Nils Homer).
+
+ * Implemented the GNU building system. However, currently the building
+ system does not generate libbam.a. We will improve this later. For
+ the time being, `make -f Makefile.generic' is preferred.
+
+ * Fixed a minor bug in pileup: the first read in a chromosome may be
+ skipped.
+
+ * Fixed bugs in bam_aux.c. These bugs do not affect other components as
+ they were not used previously.
+
+ * Output the 'SM' tag from maq2sam.
+
+(0.1.4: 21 May 2009, r297)
+
+
+
+Beta Release 0.1.3 (15 April, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in SAMtools:
+
+ * SAMtools is more consistent with the specification: a) '*' in the
+ QUAL field is allowed; b) the field separator is TAB only and SPACE
+ is treated as a character in a field; c) empty header is allowed.
+
+ * Implemented GLFv3 support in pileup.
+
+ * Fixed a severe bug in fixmate: strand information is wrongly
+ overwritten.
+
+ * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
+ not correctly retrieved sometimes.
+
+ * Fixed a bug in rmdup: segfault if unmapped reads are present.
+
+ * Move indel_filter.pl to samtools.pl and improved the filtering by
+ checking the actual number of alignments containing indels. The indel
+ pileup line is also changed a little to make this filtration easier.
+
+ * Fixed a minor bug in indexing: the bin number of an unmapped read is
+ wrongly calculated.
+
+ * Added `flagstat' command to show statistics on the FLAG field.
+
+ * Improved indel caller by setting the maximum window size in local
+ realignment.
+
+Changes in other utilities:
+
+ * Fixed a bug in maq2sam: a tag name is obsolete.
+
+ * Improvement to wgsim: a) added support for SOLiD read simulation; b)
+ show the number of substitutions/indels/errors in read name; c)
+ considerable code clean up.
+
+ * Various converters: improved functionality in general.
+
+ * Updated the example SAM due to the previous bug in fixmate.
+
+(0.1.3: 15 April 2009, r227)
+
+
+
+Beta Release 0.1.2 (28 January, 2008)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in SAMtools:
+
+ * Implemented a Bayesian indel caller. The new caller generate scores
+ and genotype and is potentially more accurate than Maq's indel
+ caller. The pileup format is also changed accordingly.
+
+ * Implemented rmdup command: remove potential PCR duplicates. Note that
+ this command ONLY works for FR orientation and requires ISIZE is
+ correctly set.
+
+ * Added fixmate command: fill in mate coordinates, ISIZE and mate
+ related flags from a name-sorted alignment.
+
+ * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
+
+ * Allow to select reads shown in the pileup output with a mask.
+
+ * Generate GLFv2 from pileup.
+
+ * Added two more flags for flagging PCR/optical duplicates and for QC
+ failure.
+
+ * Fixed a bug in sort command: name sorting for large alignment did not
+ work.
+
+ * Allow to completely disable RAZF (using Makefile.lite) as some people
+ have problem to compile it.
+
+ * Fixed a bug in import command when there are reads without
+ coordinates.
+
+ * Fixed a bug in tview: clipping broke the alignment viewer.
+
+ * Fixed a compiling error when _NO_CURSES is applied.
+
+ * Fixed a bug in merge command.
+
+Changes in other utilities:
+
+ * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
+ maq's reads simulator. Colin Hercus further improved it to allow
+ longer indels.
+
+ * Added wgsim_eval.pl, a script that evaluates the accuracy of
+ alignment on reads generated by wgsim.
+
+ * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
+ work properly when multiple hits are output.
+
+ * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
+ be retained when multiple hits are present.
+
+ * Fixed a bug in export2sam.pl for QC reads.
+
+ * Support RG tag at MAQ->SAM converter.
+
+ * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
+ indel are not properly handled, though.
+
+ * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
+ default Illumina output.
+
+(0.1.2: 28 January 2008; r116)
+
+
+
+Beta Release 0.1.1 (22 December, 2008)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The is the first public release of samtools. For more information,
+please check the manual page `samtools.1' and the samtools website
+http://samtools.sourceforge.net
diff --git a/src/samtools-0.1.18/bam.c b/src/samtools-0.1.18/bam.c
new file mode 100644
index 0000000..0055e84
--- /dev/null
+++ b/src/samtools-0.1.18/bam.c
@@ -0,0 +1,362 @@
+#include <stdio.h>
+#include <ctype.h>
+#include <errno.h>
+#include <assert.h>
+#include "bam.h"
+#include "bam_endian.h"
+#include "kstring.h"
+#include "sam_header.h"
+
+int bam_is_be = 0, bam_verbose = 2;
+char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
+
+/**************************
+ * CIGAR related routines *
+ **************************/
+
+uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
+{
+ uint32_t k, end;
+ end = c->pos;
+ for (k = 0; k < c->n_cigar; ++k) {
+ int op = cigar[k] & BAM_CIGAR_MASK;
+ if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
+ end += cigar[k] >> BAM_CIGAR_SHIFT;
+ }
+ return end;
+}
+
+int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
+{
+ uint32_t k;
+ int32_t l = 0;
+ for (k = 0; k < c->n_cigar; ++k) {
+ int op = cigar[k] & BAM_CIGAR_MASK;
+ if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP || op == BAM_CEQUAL || op == BAM_CDIFF)
+ l += cigar[k] >> BAM_CIGAR_SHIFT;
+ }
+ return l;
+}
+
+/********************
+ * BAM I/O routines *
+ ********************/
+
+bam_header_t *bam_header_init()
+{
+ bam_is_be = bam_is_big_endian();
+ return (bam_header_t*)calloc(1, sizeof(bam_header_t));
+}
+
+void bam_header_destroy(bam_header_t *header)
+{
+ int32_t i;
+ extern void bam_destroy_header_hash(bam_header_t *header);
+ if (header == 0) return;
+ if (header->target_name) {
+ for (i = 0; i < header->n_targets; ++i)
+ free(header->target_name[i]);
+ free(header->target_name);
+ free(header->target_len);
+ }
+ free(header->text);
+ if (header->dict) sam_header_free(header->dict);
+ if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
+ bam_destroy_header_hash(header);
+ free(header);
+}
+
+bam_header_t *bam_header_read(bamFile fp)
+{
+ bam_header_t *header;
+ char buf[4];
+ int magic_len;
+ int32_t i = 1, name_len;
+ // check EOF
+ i = bgzf_check_EOF(fp);
+ if (i < 0) {
+ // If the file is a pipe, checking the EOF marker will *always* fail
+ // with ESPIPE. Suppress the error message in this case.
+ if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
+ }
+ else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
+ // read "BAM1"
+ magic_len = bam_read(fp, buf, 4);
+ if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
+ fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
+ return 0;
+ }
+ header = bam_header_init();
+ // read plain text and the number of reference sequences
+ bam_read(fp, &header->l_text, 4);
+ if (bam_is_be) bam_swap_endian_4p(&header->l_text);
+ header->text = (char*)calloc(header->l_text + 1, 1);
+ bam_read(fp, header->text, header->l_text);
+ bam_read(fp, &header->n_targets, 4);
+ if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
+ // read reference sequence names and lengths
+ header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
+ header->target_len = (uint32_t*)calloc(header->n_targets, 4);
+ for (i = 0; i != header->n_targets; ++i) {
+ bam_read(fp, &name_len, 4);
+ if (bam_is_be) bam_swap_endian_4p(&name_len);
+ header->target_name[i] = (char*)calloc(name_len, 1);
+ bam_read(fp, header->target_name[i], name_len);
+ bam_read(fp, &header->target_len[i], 4);
+ if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
+ }
+ return header;
+}
+
+int bam_header_write(bamFile fp, const bam_header_t *header)
+{
+ char buf[4];
+ int32_t i, name_len, x;
+ // write "BAM1"
+ strncpy(buf, "BAM\001", 4);
+ bam_write(fp, buf, 4);
+ // write plain text and the number of reference sequences
+ if (bam_is_be) {
+ x = bam_swap_endian_4(header->l_text);
+ bam_write(fp, &x, 4);
+ if (header->l_text) bam_write(fp, header->text, header->l_text);
+ x = bam_swap_endian_4(header->n_targets);
+ bam_write(fp, &x, 4);
+ } else {
+ bam_write(fp, &header->l_text, 4);
+ if (header->l_text) bam_write(fp, header->text, header->l_text);
+ bam_write(fp, &header->n_targets, 4);
+ }
+ // write sequence names and lengths
+ for (i = 0; i != header->n_targets; ++i) {
+ char *p = header->target_name[i];
+ name_len = strlen(p) + 1;
+ if (bam_is_be) {
+ x = bam_swap_endian_4(name_len);
+ bam_write(fp, &x, 4);
+ } else bam_write(fp, &name_len, 4);
+ bam_write(fp, p, name_len);
+ if (bam_is_be) {
+ x = bam_swap_endian_4(header->target_len[i]);
+ bam_write(fp, &x, 4);
+ } else bam_write(fp, &header->target_len[i], 4);
+ }
+ bgzf_flush(fp);
+ return 0;
+}
+
+static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
+{
+ uint8_t *s;
+ uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
+ s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
+ for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
+ while (s < data + data_len) {
+ uint8_t type;
+ s += 2; // skip key
+ type = toupper(*s); ++s; // skip type
+ if (type == 'C' || type == 'A') ++s;
+ else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
+ else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
+ else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
+ else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+ else if (type == 'B') {
+ int32_t n, Bsize = bam_aux_type2size(*s);
+ memcpy(&n, s + 1, 4);
+ if (1 == Bsize) {
+ } else if (2 == Bsize) {
+ for (i = 0; i < n; i += 2)
+ bam_swap_endian_2p(s + 5 + i);
+ } else if (4 == Bsize) {
+ for (i = 0; i < n; i += 4)
+ bam_swap_endian_4p(s + 5 + i);
+ }
+ bam_swap_endian_4p(s+1);
+ }
+ }
+}
+
+int bam_read1(bamFile fp, bam1_t *b)
+{
+ bam1_core_t *c = &b->core;
+ int32_t block_len, ret, i;
+ uint32_t x[8];
+
+ assert(BAM_CORE_SIZE == 32);
+ if ((ret = bam_read(fp, &block_len, 4)) != 4) {
+ if (ret == 0) return -1; // normal end-of-file
+ else return -2; // truncated
+ }
+ if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
+ if (bam_is_be) {
+ bam_swap_endian_4p(&block_len);
+ for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
+ }
+ c->tid = x[0]; c->pos = x[1];
+ c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
+ c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
+ c->l_qseq = x[4];
+ c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
+ b->data_len = block_len - BAM_CORE_SIZE;
+ if (b->m_data < b->data_len) {
+ b->m_data = b->data_len;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
+ b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
+ if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
+ return 4 + block_len;
+}
+
+inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
+{
+ uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
+ int i;
+ assert(BAM_CORE_SIZE == 32);
+ x[0] = c->tid;
+ x[1] = c->pos;
+ x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
+ x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
+ x[4] = c->l_qseq;
+ x[5] = c->mtid;
+ x[6] = c->mpos;
+ x[7] = c->isize;
+ bgzf_flush_try(fp, 4 + block_len);
+ if (bam_is_be) {
+ for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
+ y = block_len;
+ bam_write(fp, bam_swap_endian_4p(&y), 4);
+ swap_endian_data(c, data_len, data);
+ } else bam_write(fp, &block_len, 4);
+ bam_write(fp, x, BAM_CORE_SIZE);
+ bam_write(fp, data, data_len);
+ if (bam_is_be) swap_endian_data(c, data_len, data);
+ return 4 + block_len;
+}
+
+int bam_write1(bamFile fp, const bam1_t *b)
+{
+ return bam_write1_core(fp, &b->core, b->data_len, b->data);
+}
+
+char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
+{
+ uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
+ int i;
+ const bam1_core_t *c = &b->core;
+ kstring_t str;
+ str.l = str.m = 0; str.s = 0;
+
+ kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str);
+ if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); }
+ else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
+ else { // BAM_OFSTR
+ for (i = 0; i < 16; ++i)
+ if ((c->flag & 1<<i) && bam_flag2char_table[i])
+ kputc(bam_flag2char_table[i], &str);
+ kputc('\t', &str);
+ }
+ if (c->tid < 0) kputsn("*\t", 2, &str);
+ else {
+ if (header) kputs(header->target_name[c->tid] , &str);
+ else kputw(c->tid, &str);
+ kputc('\t', &str);
+ }
+ kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
+ if (c->n_cigar == 0) kputc('*', &str);
+ else {
+ for (i = 0; i < c->n_cigar; ++i) {
+ kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
+ kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+ }
+ }
+ kputc('\t', &str);
+ if (c->mtid < 0) kputsn("*\t", 2, &str);
+ else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
+ else {
+ if (header) kputs(header->target_name[c->mtid], &str);
+ else kputw(c->mtid, &str);
+ kputc('\t', &str);
+ }
+ kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
+ if (c->l_qseq) {
+ for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
+ kputc('\t', &str);
+ if (t[0] == 0xff) kputc('*', &str);
+ else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
+ } else kputsn("*\t*", 3, &str);
+ s = bam1_aux(b);
+ while (s < b->data + b->data_len) {
+ uint8_t type, key[2];
+ key[0] = s[0]; key[1] = s[1];
+ s += 2; type = *s; ++s;
+ kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
+ if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
+ else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; }
+ else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; }
+ else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; }
+ else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; }
+ else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; }
+ else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
+ else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
+ else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
+ else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
+ else if (type == 'B') {
+ uint8_t sub_type = *(s++);
+ int32_t n;
+ memcpy(&n, s, 4);
+ s += 4; // no point to the start of the array
+ kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
+ for (i = 0; i < n; ++i) {
+ kputc(',', &str);
+ if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
+ else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
+ else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
+ else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
+ else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
+ else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
+ else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
+ }
+ }
+ }
+ return str.s;
+}
+
+char *bam_format1(const bam_header_t *header, const bam1_t *b)
+{
+ return bam_format1_core(header, b, BAM_OFDEC);
+}
+
+void bam_view1(const bam_header_t *header, const bam1_t *b)
+{
+ char *s = bam_format1(header, b);
+ puts(s);
+ free(s);
+}
+
+int bam_validate1(const bam_header_t *header, const bam1_t *b)
+{
+ char *s;
+
+ if (b->core.tid < -1 || b->core.mtid < -1) return 0;
+ if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;
+
+ if (b->data_len < b->core.l_qname) return 0;
+ s = memchr(bam1_qname(b), '\0', b->core.l_qname);
+ if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;
+
+ // FIXME: Other fields could also be checked, especially the auxiliary data
+
+ return 1;
+}
+
+// FIXME: we should also check the LB tag associated with each alignment
+const char *bam_get_library(bam_header_t *h, const bam1_t *b)
+{
+ const uint8_t *rg;
+ if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+ if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
+ rg = bam_aux_get(b, "RG");
+ return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
+}
diff --git a/src/samtools-0.1.18/bam.h b/src/samtools-0.1.18/bam.h
new file mode 100644
index 0000000..346c750
--- /dev/null
+++ b/src/samtools-0.1.18/bam.h
@@ -0,0 +1,763 @@
+/* The MIT License
+
+ Copyright (c) 2008-2010 Genome Research Ltd (GRL).
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3 at sanger.ac.uk> */
+
+#ifndef BAM_BAM_H
+#define BAM_BAM_H
+
+/*!
+ @header
+
+ BAM library provides I/O and various operations on manipulating files
+ in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
+ format. It now supports importing from or exporting to SAM, sorting,
+ merging, generating pileup, and quickly retrieval of reads overlapped
+ with a specified region.
+
+ @copyright Genome Research Ltd.
+ */
+
+#define BAM_VERSION "0.1.18 (r982:295)"
+
+#include <stdint.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+
+#ifndef BAM_LITE
+#define BAM_VIRTUAL_OFFSET16
+#include "bgzf.h"
+/*! @abstract BAM file handler */
+typedef BGZF *bamFile;
+#define bam_open(fn, mode) bgzf_open(fn, mode)
+#define bam_dopen(fd, mode) bgzf_fdopen(fd, mode)
+#define bam_close(fp) bgzf_close(fp)
+#define bam_read(fp, buf, size) bgzf_read(fp, buf, size)
+#define bam_write(fp, buf, size) bgzf_write(fp, buf, size)
+#define bam_tell(fp) bgzf_tell(fp)
+#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
+#else
+#define BAM_TRUE_OFFSET
+#include <zlib.h>
+typedef gzFile bamFile;
+#define bam_open(fn, mode) gzopen(fn, mode)
+#define bam_dopen(fd, mode) gzdopen(fd, mode)
+#define bam_close(fp) gzclose(fp)
+#define bam_read(fp, buf, size) gzread(fp, buf, size)
+/* no bam_write/bam_tell/bam_seek() here */
+#endif
+
+/*! @typedef
+ @abstract Structure for the alignment header.
+ @field n_targets number of reference sequences
+ @field target_name names of the reference sequences
+ @field target_len lengths of the referene sequences
+ @field dict header dictionary
+ @field hash hash table for fast name lookup
+ @field rg2lib hash table for @RG-ID -> LB lookup
+ @field l_text length of the plain text in the header
+ @field text plain text
+
+ @discussion Field hash points to null by default. It is a private
+ member.
+ */
+typedef struct {
+ int32_t n_targets;
+ char **target_name;
+ uint32_t *target_len;
+ void *dict, *hash, *rg2lib;
+ size_t l_text, n_text;
+ char *text;
+} bam_header_t;
+
+/*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
+#define BAM_FPAIRED 1
+/*! @abstract the read is mapped in a proper pair */
+#define BAM_FPROPER_PAIR 2
+/*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
+#define BAM_FUNMAP 4
+/*! @abstract the mate is unmapped */
+#define BAM_FMUNMAP 8
+/*! @abstract the read is mapped to the reverse strand */
+#define BAM_FREVERSE 16
+/*! @abstract the mate is mapped to the reverse strand */
+#define BAM_FMREVERSE 32
+/*! @abstract this is read1 */
+#define BAM_FREAD1 64
+/*! @abstract this is read2 */
+#define BAM_FREAD2 128
+/*! @abstract not primary alignment */
+#define BAM_FSECONDARY 256
+/*! @abstract QC failure */
+#define BAM_FQCFAIL 512
+/*! @abstract optical or PCR duplicate */
+#define BAM_FDUP 1024
+
+#define BAM_OFDEC 0
+#define BAM_OFHEX 1
+#define BAM_OFSTR 2
+
+/*! @abstract defautl mask for pileup */
+#define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
+
+#define BAM_CORE_SIZE sizeof(bam1_core_t)
+
+/**
+ * Describing how CIGAR operation/length is packed in a 32-bit integer.
+ */
+#define BAM_CIGAR_SHIFT 4
+#define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
+
+/*
+ CIGAR operations.
+ */
+/*! @abstract CIGAR: M = match or mismatch*/
+#define BAM_CMATCH 0
+/*! @abstract CIGAR: I = insertion to the reference */
+#define BAM_CINS 1
+/*! @abstract CIGAR: D = deletion from the reference */
+#define BAM_CDEL 2
+/*! @abstract CIGAR: N = skip on the reference (e.g. spliced alignment) */
+#define BAM_CREF_SKIP 3
+/*! @abstract CIGAR: S = clip on the read with clipped sequence
+ present in qseq */
+#define BAM_CSOFT_CLIP 4
+/*! @abstract CIGAR: H = clip on the read with clipped sequence trimmed off */
+#define BAM_CHARD_CLIP 5
+/*! @abstract CIGAR: P = padding */
+#define BAM_CPAD 6
+/*! @abstract CIGAR: equals = match */
+#define BAM_CEQUAL 7
+/*! @abstract CIGAR: X = mismatch */
+#define BAM_CDIFF 8
+
+/*! @typedef
+ @abstract Structure for core alignment information.
+ @field tid chromosome ID, defined by bam_header_t
+ @field pos 0-based leftmost coordinate
+ @field strand strand; 0 for forward and 1 otherwise
+ @field bin bin calculated by bam_reg2bin()
+ @field qual mapping quality
+ @field l_qname length of the query name
+ @field flag bitwise flag
+ @field n_cigar number of CIGAR operations
+ @field l_qseq length of the query sequence (read)
+ */
+typedef struct {
+ int32_t tid;
+ int32_t pos;
+ uint32_t bin:16, qual:8, l_qname:8;
+ uint32_t flag:16, n_cigar:16;
+ int32_t l_qseq;
+ int32_t mtid;
+ int32_t mpos;
+ int32_t isize;
+} bam1_core_t;
+
+/*! @typedef
+ @abstract Structure for one alignment.
+ @field core core information about the alignment
+ @field l_aux length of auxiliary data
+ @field data_len current length of bam1_t::data
+ @field m_data maximum length of bam1_t::data
+ @field data all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
+
+ @discussion Notes:
+
+ 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
+ 2. l_qseq is calculated from the total length of an alignment block
+ on reading or from CIGAR.
+ */
+typedef struct {
+ bam1_core_t core;
+ int l_aux, data_len, m_data;
+ uint8_t *data;
+} bam1_t;
+
+typedef struct __bam_iter_t *bam_iter_t;
+
+#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
+#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
+
+/*! @function
+ @abstract Get the CIGAR array
+ @param b pointer to an alignment
+ @return pointer to the CIGAR array
+
+ @discussion In the CIGAR array, each element is a 32-bit integer. The
+ lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
+ length of a CIGAR.
+ */
+#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
+
+/*! @function
+ @abstract Get the name of the query
+ @param b pointer to an alignment
+ @return pointer to the name string, null terminated
+ */
+#define bam1_qname(b) ((char*)((b)->data))
+
+/*! @function
+ @abstract Get query sequence
+ @param b pointer to an alignment
+ @return pointer to sequence
+
+ @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
+ 8 for T and 15 for N. Two bases are packed in one byte with the base
+ at the higher 4 bits having smaller coordinate on the read. It is
+ recommended to use bam1_seqi() macro to get the base.
+ */
+#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
+
+/*! @function
+ @abstract Get query quality
+ @param b pointer to an alignment
+ @return pointer to quality string
+ */
+#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
+
+/*! @function
+ @abstract Get a base on read
+ @param s Query sequence returned by bam1_seq()
+ @param i The i-th position, 0-based
+ @return 4-bit integer representing the base.
+ */
+#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+
+/*! @function
+ @abstract Get query sequence and quality
+ @param b pointer to an alignment
+ @return pointer to the concatenated auxiliary data
+ */
+#define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)
+
+#ifndef kroundup32
+/*! @function
+ @abstract Round an integer to the next closest power-2 integer.
+ @param x integer to be rounded (in place)
+ @discussion x will be modified.
+ */
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+/*!
+ @abstract Whether the machine is big-endian; modified only in
+ bam_header_init().
+ */
+extern int bam_is_be;
+
+/*!
+ @abstract Verbose level between 0 and 3; 0 is supposed to disable all
+ debugging information, though this may not have been implemented.
+ */
+extern int bam_verbose;
+
+/*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
+extern unsigned char bam_nt16_table[256];
+
+/*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */
+extern char *bam_nt16_rev_table;
+
+extern char bam_nt16_nt4_table[];
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ /*********************
+ * Low-level SAM I/O *
+ *********************/
+
+ /*! @abstract TAM file handler */
+ typedef struct __tamFile_t *tamFile;
+
+ /*!
+ @abstract Open a SAM file for reading, either uncompressed or compressed by gzip/zlib.
+ @param fn SAM file name
+ @return SAM file handler
+ */
+ tamFile sam_open(const char *fn);
+
+ /*!
+ @abstract Close a SAM file handler
+ @param fp SAM file handler
+ */
+ void sam_close(tamFile fp);
+
+ /*!
+ @abstract Read one alignment from a SAM file handler
+ @param fp SAM file handler
+ @param header header information (ordered names of chromosomes)
+ @param b read alignment; all members in b will be updated
+ @return 0 if successful; otherwise negative
+ */
+ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b);
+
+ /*!
+ @abstract Read header information from a TAB-delimited list file.
+ @param fn_list file name for the list
+ @return a pointer to the header structure
+
+ @discussion Each line in this file consists of chromosome name and
+ the length of chromosome.
+ */
+ bam_header_t *sam_header_read2(const char *fn_list);
+
+ /*!
+ @abstract Read header from a SAM file (if present)
+ @param fp SAM file handler
+ @return pointer to header struct; 0 if no @SQ lines available
+ */
+ bam_header_t *sam_header_read(tamFile fp);
+
+ /*!
+ @abstract Parse @SQ lines a update a header struct
+ @param h pointer to the header struct to be updated
+ @return number of target sequences
+
+ @discussion bam_header_t::{n_targets,target_len,target_name} will
+ be destroyed in the first place.
+ */
+ int sam_header_parse(bam_header_t *h);
+ int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
+
+ /*!
+ @abstract Parse @RG lines a update a header struct
+ @param h pointer to the header struct to be updated
+ @return number of @RG lines
+
+ @discussion bam_header_t::rg2lib will be destroyed in the first
+ place.
+ */
+ int sam_header_parse_rg(bam_header_t *h);
+
+#define sam_write1(header, b) bam_view1(header, b)
+
+
+ /********************************
+ * APIs for string dictionaries *
+ ********************************/
+
+ int bam_strmap_put(void *strmap, const char *rg, const char *lib);
+ const char *bam_strmap_get(const void *strmap, const char *rg);
+ void *bam_strmap_dup(const void*);
+ void *bam_strmap_init();
+ void bam_strmap_destroy(void *strmap);
+
+
+ /*********************
+ * Low-level BAM I/O *
+ *********************/
+
+ /*!
+ @abstract Initialize a header structure.
+ @return the pointer to the header structure
+
+ @discussion This function also modifies the global variable
+ bam_is_be.
+ */
+ bam_header_t *bam_header_init();
+
+ /*!
+ @abstract Destroy a header structure.
+ @param header pointer to the header
+ */
+ void bam_header_destroy(bam_header_t *header);
+
+ /*!
+ @abstract Read a header structure from BAM.
+ @param fp BAM file handler, opened by bam_open()
+ @return pointer to the header structure
+
+ @discussion The file position indicator must be placed at the
+ beginning of the file. Upon success, the position indicator will
+ be set at the start of the first alignment.
+ */
+ bam_header_t *bam_header_read(bamFile fp);
+
+ /*!
+ @abstract Write a header structure to BAM.
+ @param fp BAM file handler
+ @param header pointer to the header structure
+ @return always 0 currently
+ */
+ int bam_header_write(bamFile fp, const bam_header_t *header);
+
+ /*!
+ @abstract Read an alignment from BAM.
+ @param fp BAM file handler
+ @param b read alignment; all members are updated.
+ @return number of bytes read from the file
+
+ @discussion The file position indicator must be
+ placed right before an alignment. Upon success, this function
+ will set the position indicator to the start of the next
+ alignment. This function is not affected by the machine
+ endianness.
+ */
+ int bam_read1(bamFile fp, bam1_t *b);
+
+ /*!
+ @abstract Write an alignment to BAM.
+ @param fp BAM file handler
+ @param c pointer to the bam1_core_t structure
+ @param data_len total length of variable size data related to
+ the alignment
+ @param data pointer to the concatenated data
+ @return number of bytes written to the file
+
+ @discussion This function is not affected by the machine
+ endianness.
+ */
+ int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
+
+ /*!
+ @abstract Write an alignment to BAM.
+ @param fp BAM file handler
+ @param b alignment to write
+ @return number of bytes written to the file
+
+ @abstract It is equivalent to:
+ bam_write1_core(fp, &b->core, b->data_len, b->data)
+ */
+ int bam_write1(bamFile fp, const bam1_t *b);
+
+ /*! @function
+ @abstract Initiate a pointer to bam1_t struct
+ */
+#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
+
+ /*! @function
+ @abstract Free the memory allocated for an alignment.
+ @param b pointer to an alignment
+ */
+#define bam_destroy1(b) do { \
+ if (b) { free((b)->data); free(b); } \
+ } while (0)
+
+ /*!
+ @abstract Format a BAM record in the SAM format
+ @param header pointer to the header structure
+ @param b alignment to print
+ @return a pointer to the SAM string
+ */
+ char *bam_format1(const bam_header_t *header, const bam1_t *b);
+
+ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
+
+ /*!
+ @abstract Check whether a BAM record is plausibly valid
+ @param header associated header structure, or NULL if unavailable
+ @param b alignment to validate
+ @return 0 if the alignment is invalid; non-zero otherwise
+
+ @discussion Simple consistency check of some of the fields of the
+ alignment record. If the header is provided, several additional checks
+ are made. Not all fields are checked, so a non-zero result is not a
+ guarantee that the record is valid. However it is usually good enough
+ to detect when bam_seek() has been called with a virtual file offset
+ that is not the offset of an alignment record.
+ */
+ int bam_validate1(const bam_header_t *header, const bam1_t *b);
+
+ const char *bam_get_library(bam_header_t *header, const bam1_t *b);
+
+
+ /***************
+ * pileup APIs *
+ ***************/
+
+ /*! @typedef
+ @abstract Structure for one alignment covering the pileup position.
+ @field b pointer to the alignment
+ @field qpos position of the read base at the pileup site, 0-based
+ @field indel indel length; 0 for no indel, positive for ins and negative for del
+ @field is_del 1 iff the base on the padded read is a deletion
+ @field level the level of the read in the "viewer" mode
+
+ @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
+ difference between the two functions is that the former does not
+ set bam_pileup1_t::level, while the later does. Level helps the
+ implementation of alignment viewers, but calculating this has some
+ overhead.
+ */
+ typedef struct {
+ bam1_t *b;
+ int32_t qpos;
+ int indel, level;
+ uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28;
+ } bam_pileup1_t;
+
+ typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
+
+ struct __bam_plp_t;
+ typedef struct __bam_plp_t *bam_plp_t;
+
+ bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data);
+ int bam_plp_push(bam_plp_t iter, const bam1_t *b);
+ const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
+ const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
+ void bam_plp_set_mask(bam_plp_t iter, int mask);
+ void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt);
+ void bam_plp_reset(bam_plp_t iter);
+ void bam_plp_destroy(bam_plp_t iter);
+
+ struct __bam_mplp_t;
+ typedef struct __bam_mplp_t *bam_mplp_t;
+
+ bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
+ void bam_mplp_destroy(bam_mplp_t iter);
+ void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt);
+ int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
+
+ /*! @typedef
+ @abstract Type of function to be called by bam_plbuf_push().
+ @param tid chromosome ID as is defined in the header
+ @param pos start coordinate of the alignment, 0-based
+ @param n number of elements in pl array
+ @param pl array of alignments
+ @param data user provided data
+ @discussion See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.
+ */
+ typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
+
+ typedef struct {
+ bam_plp_t iter;
+ bam_pileup_f func;
+ void *data;
+ } bam_plbuf_t;
+
+ void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
+ void bam_plbuf_reset(bam_plbuf_t *buf);
+ bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
+ void bam_plbuf_destroy(bam_plbuf_t *buf);
+ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
+
+ int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
+
+ struct __bam_lplbuf_t;
+ typedef struct __bam_lplbuf_t bam_lplbuf_t;
+
+ void bam_lplbuf_reset(bam_lplbuf_t *buf);
+
+ /*! @abstract bam_plbuf_init() equivalent with level calculated. */
+ bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);
+
+ /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */
+ void bam_lplbuf_destroy(bam_lplbuf_t *tv);
+
+ /*! @abstract bam_plbuf_push() equivalent with level calculated. */
+ int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
+
+
+ /*********************
+ * BAM indexing APIs *
+ *********************/
+
+ struct __bam_index_t;
+ typedef struct __bam_index_t bam_index_t;
+
+ /*!
+ @abstract Build index for a BAM file.
+ @discussion Index file "fn.bai" will be created.
+ @param fn name of the BAM file
+ @return always 0 currently
+ */
+ int bam_index_build(const char *fn);
+
+ /*!
+ @abstract Load index from file "fn.bai".
+ @param fn name of the BAM file (NOT the index file)
+ @return pointer to the index structure
+ */
+ bam_index_t *bam_index_load(const char *fn);
+
+ /*!
+ @abstract Destroy an index structure.
+ @param idx pointer to the index structure
+ */
+ void bam_index_destroy(bam_index_t *idx);
+
+ /*! @typedef
+ @abstract Type of function to be called by bam_fetch().
+ @param b the alignment
+ @param data user provided data
+ */
+ typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
+
+ /*!
+ @abstract Retrieve the alignments that are overlapped with the
+ specified region.
+
+ @discussion A user defined function will be called for each
+ retrieved alignment ordered by its start position.
+
+ @param fp BAM file handler
+ @param idx pointer to the alignment index
+ @param tid chromosome ID as is defined in the header
+ @param beg start coordinate, 0-based
+ @param end end coordinate, 0-based
+ @param data user provided data (will be transferred to func)
+ @param func user defined function
+ */
+ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
+
+ bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end);
+ int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b);
+ void bam_iter_destroy(bam_iter_t iter);
+
+ /*!
+ @abstract Parse a region in the format: "chr2:100,000-200,000".
+ @discussion bam_header_t::hash will be initialized if empty.
+ @param header pointer to the header structure
+ @param str string to be parsed
+ @param ref_id the returned chromosome ID
+ @param begin the returned start coordinate
+ @param end the returned end coordinate
+ @return 0 on success; -1 on failure
+ */
+ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
+
+
+ /**************************
+ * APIs for optional tags *
+ **************************/
+
+ /*!
+ @abstract Retrieve data of a tag
+ @param b pointer to an alignment struct
+ @param tag two-character tag to be retrieved
+
+ @return pointer to the type and data. The first character is the
+ type that can be 'iIsScCdfAZH'.
+
+ @discussion Use bam_aux2?() series to convert the returned data to
+ the corresponding type.
+ */
+ uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
+
+ int32_t bam_aux2i(const uint8_t *s);
+ float bam_aux2f(const uint8_t *s);
+ double bam_aux2d(const uint8_t *s);
+ char bam_aux2A(const uint8_t *s);
+ char *bam_aux2Z(const uint8_t *s);
+
+ int bam_aux_del(bam1_t *b, uint8_t *s);
+ void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
+ uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
+
+
+ /*****************
+ * Miscellaneous *
+ *****************/
+
+ /*!
+ @abstract Calculate the rightmost coordinate of an alignment on the
+ reference genome.
+
+ @param c pointer to the bam1_core_t structure
+ @param cigar the corresponding CIGAR array (from bam1_t::cigar)
+ @return the rightmost coordinate, 0-based
+ */
+ uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar);
+
+ /*!
+ @abstract Calculate the length of the query sequence from CIGAR.
+ @param c pointer to the bam1_core_t structure
+ @param cigar the corresponding CIGAR array (from bam1_t::cigar)
+ @return length of the query sequence
+ */
+ int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
+
+#ifdef __cplusplus
+}
+#endif
+
+/*!
+ @abstract Calculate the minimum bin that contains a region [beg,end).
+ @param beg start of the region, 0-based
+ @param end end of the region, 0-based
+ @return bin
+ */
+static inline int bam_reg2bin(uint32_t beg, uint32_t end)
+{
+ --end;
+ if (beg>>14 == end>>14) return 4681 + (beg>>14);
+ if (beg>>17 == end>>17) return 585 + (beg>>17);
+ if (beg>>20 == end>>20) return 73 + (beg>>20);
+ if (beg>>23 == end>>23) return 9 + (beg>>23);
+ if (beg>>26 == end>>26) return 1 + (beg>>26);
+ return 0;
+}
+
+/*!
+ @abstract Copy an alignment
+ @param bdst destination alignment struct
+ @param bsrc source alignment struct
+ @return pointer to the destination alignment struct
+ */
+static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
+{
+ uint8_t *data = bdst->data;
+ int m_data = bdst->m_data; // backup data and m_data
+ if (m_data < bsrc->data_len) { // double the capacity
+ m_data = bsrc->data_len; kroundup32(m_data);
+ data = (uint8_t*)realloc(data, m_data);
+ }
+ memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
+ *bdst = *bsrc; // copy the rest
+ // restore the backup
+ bdst->m_data = m_data;
+ bdst->data = data;
+ return bdst;
+}
+
+/*!
+ @abstract Duplicate an alignment
+ @param src source alignment struct
+ @return pointer to the destination alignment struct
+ */
+static inline bam1_t *bam_dup1(const bam1_t *src)
+{
+ bam1_t *b;
+ b = bam_init1();
+ *b = *src;
+ b->m_data = b->data_len;
+ b->data = (uint8_t*)calloc(b->data_len, 1);
+ memcpy(b->data, src->data, b->data_len);
+ return b;
+}
+
+static inline int bam_aux_type2size(int x)
+{
+ if (x == 'C' || x == 'c' || x == 'A') return 1;
+ else if (x == 'S' || x == 's') return 2;
+ else if (x == 'I' || x == 'i' || x == 'f') return 4;
+ else return 0;
+}
+
+
+#endif
diff --git a/src/samtools-0.1.18/bam2bcf.c b/src/samtools-0.1.18/bam2bcf.c
new file mode 100644
index 0000000..dec3305
--- /dev/null
+++ b/src/samtools-0.1.18/bam2bcf.c
@@ -0,0 +1,351 @@
+#include <math.h>
+#include <stdint.h>
+#include "bam.h"
+#include "kstring.h"
+#include "bam2bcf.h"
+#include "errmod.h"
+#include "bcftools/bcf.h"
+
+extern void ks_introsort_uint32_t(size_t n, uint32_t a[]);
+
+#define CALL_ETA 0.03f
+#define CALL_MAX 256
+#define CALL_DEFTHETA 0.83f
+#define DEF_MAPQ 20
+
+#define CAP_DIST 25
+
+bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
+{
+ bcf_callaux_t *bca;
+ if (theta <= 0.) theta = CALL_DEFTHETA;
+ bca = calloc(1, sizeof(bcf_callaux_t));
+ bca->capQ = 60;
+ bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
+ bca->min_baseQ = min_baseQ;
+ bca->e = errmod_init(1. - theta);
+ bca->min_frac = 0.002;
+ bca->min_support = 1;
+ return bca;
+}
+
+void bcf_call_destroy(bcf_callaux_t *bca)
+{
+ if (bca == 0) return;
+ errmod_destroy(bca->e);
+ free(bca->bases); free(bca->inscns); free(bca);
+}
+/* ref_base is the 4-bit representation of the reference base. It is
+ * negative if we are looking at an indel. */
+int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
+{
+ static int *var_pos = NULL, nvar_pos = 0;
+ int i, n, ref4, is_indel, ori_depth = 0;
+ memset(r, 0, sizeof(bcf_callret1_t));
+ if (ref_base >= 0) {
+ ref4 = bam_nt16_nt4_table[ref_base];
+ is_indel = 0;
+ } else ref4 = 4, is_indel = 1;
+ if (_n == 0) return -1;
+ // enlarge the bases array if necessary
+ if (bca->max_bases < _n) {
+ bca->max_bases = _n;
+ kroundup32(bca->max_bases);
+ bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
+ }
+ // fill the bases array
+ memset(r, 0, sizeof(bcf_callret1_t));
+ for (i = n = 0; i < _n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
+ // set base
+ if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
+ ++ori_depth;
+ baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality
+ seqQ = is_indel? (p->aux>>8&0xff) : 99;
+ if (q < bca->min_baseQ) continue;
+ if (q > seqQ) q = seqQ;
+ mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+ mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
+ if (q > mapQ) q = mapQ;
+ if (q > 63) q = 63;
+ if (q < 4) q = 4;
+ if (!is_indel) {
+ b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
+ b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
+ is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
+ } else {
+ b = p->aux>>16&0x3f;
+ is_diff = (b != 0);
+ }
+ bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
+ // collect annotations
+ if (b < 4) r->qsum[b] += q;
+ ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
+ min_dist = p->b->core.l_qseq - 1 - p->qpos;
+ if (min_dist > p->qpos) min_dist = p->qpos;
+ if (min_dist > CAP_DIST) min_dist = CAP_DIST;
+ r->anno[1<<2|is_diff<<1|0] += baseQ;
+ r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
+ r->anno[2<<2|is_diff<<1|0] += mapQ;
+ r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
+ r->anno[3<<2|is_diff<<1|0] += min_dist;
+ r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
+ }
+ r->depth = n; r->ori_depth = ori_depth;
+ // glfgen
+ errmod_cal(bca->e, n, 5, bca->bases, r->p);
+
+ // Calculate the Variant Distance Bias (make it optional?)
+ if ( nvar_pos < _n ) {
+ nvar_pos = _n;
+ var_pos = realloc(var_pos,sizeof(int)*nvar_pos);
+ }
+ int alt_dp=0, read_len=0;
+ for (i=0; i<_n; i++) {
+ const bam_pileup1_t *p = pl + i;
+ if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base )
+ continue;
+
+ var_pos[alt_dp] = p->qpos;
+ if ( (bam1_cigar(p->b)[0]&BAM_CIGAR_MASK)==4 )
+ var_pos[alt_dp] -= bam1_cigar(p->b)[0]>>BAM_CIGAR_SHIFT;
+
+ alt_dp++;
+ read_len += p->b->core.l_qseq;
+ }
+ float mvd=0;
+ int j;
+ n=0;
+ for (i=0; i<alt_dp; i++) {
+ for (j=0; j<i; j++) {
+ mvd += abs(var_pos[i] - var_pos[j]);
+ n++;
+ }
+ }
+ r->mvd[0] = n ? mvd/n : 0;
+ r->mvd[1] = alt_dp;
+ r->mvd[2] = alt_dp ? read_len/alt_dp : 0;
+
+ return r->depth;
+}
+
+
+void calc_vdb(int n, const bcf_callret1_t *calls, bcf_call_t *call)
+{
+ // Variant distance bias. Samples merged by means of DP-weighted average.
+
+ float weight=0, tot_prob=0;
+
+ int i;
+ for (i=0; i<n; i++)
+ {
+ int mvd = calls[i].mvd[0];
+ int dp = calls[i].mvd[1];
+ int read_len = calls[i].mvd[2];
+
+ if ( dp<2 ) continue;
+
+ float prob = 0;
+ if ( dp==2 )
+ {
+ // Exact formula
+ prob = (mvd==0) ? 1.0/read_len : (read_len-mvd)*2.0/read_len/read_len;
+ }
+ else if ( dp==3 )
+ {
+ // Sin, quite accurate approximation
+ float mu = read_len/2.9;
+ prob = mvd>2*mu ? 0 : sin(mvd*3.14/2/mu) / (4*mu/3.14);
+ }
+ else
+ {
+ // Scaled gaussian curve, crude approximation, but behaves well. Using fixed depth for bigger depths.
+ if ( dp>5 )
+ dp = 5;
+ float sigma2 = (read_len/1.9/(dp+1)) * (read_len/1.9/(dp+1));
+ float norm = 1.125*sqrt(2*3.14*sigma2);
+ float mu = read_len/2.9;
+ if ( mvd < mu )
+ prob = exp(-(mvd-mu)*(mvd-mu)/2/sigma2)/norm;
+ else
+ prob = exp(-(mvd-mu)*(mvd-mu)/3.125/sigma2)/norm;
+ }
+
+ //fprintf(stderr,"dp=%d mvd=%d read_len=%d -> prob=%f\n", dp,mvd,read_len,prob);
+ tot_prob += prob*dp;
+ weight += dp;
+ }
+ tot_prob = weight ? tot_prob/weight : 1;
+ //fprintf(stderr,"prob=%f\n", tot_prob);
+ call->vdb = tot_prob;
+}
+
+int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
+{
+ int ref4, i, j, qsum[4];
+ int64_t tmp;
+ if (ref_base >= 0) {
+ call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
+ if (ref4 > 4) ref4 = 4;
+ } else call->ori_ref = -1, ref4 = 0;
+ // calculate qsum
+ memset(qsum, 0, 4 * sizeof(int));
+ for (i = 0; i < n; ++i)
+ for (j = 0; j < 4; ++j)
+ qsum[j] += calls[i].qsum[j];
+ for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
+ // find the top 2 alleles
+ for (i = 1; i < 4; ++i) // insertion sort
+ for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
+ tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
+ // set the reference allele and alternative allele(s)
+ for (i = 0; i < 5; ++i) call->a[i] = -1;
+ call->unseen = -1;
+ call->a[0] = ref4;
+ for (i = 3, j = 1; i >= 0; --i) {
+ if ((qsum[i]&3) != ref4) {
+ if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
+ else break;
+ }
+ }
+ if (ref_base >= 0) { // for SNPs, find the "unseen" base
+ if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
+ call->unseen = j, call->a[j++] = qsum[i]&3;
+ call->n_alleles = j;
+ } else {
+ call->n_alleles = j;
+ if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
+ }
+ // set the PL array
+ if (call->n < n) {
+ call->n = n;
+ call->PL = realloc(call->PL, 15 * n);
+ }
+ {
+ int x, g[15], z;
+ double sum_min = 0.;
+ x = call->n_alleles * (call->n_alleles + 1) / 2;
+ // get the possible genotypes
+ for (i = z = 0; i < call->n_alleles; ++i)
+ for (j = 0; j <= i; ++j)
+ g[z++] = call->a[j] * 5 + call->a[i];
+ for (i = 0; i < n; ++i) {
+ uint8_t *PL = call->PL + x * i;
+ const bcf_callret1_t *r = calls + i;
+ float min = 1e37;
+ for (j = 0; j < x; ++j)
+ if (min > r->p[g[j]]) min = r->p[g[j]];
+ sum_min += min;
+ for (j = 0; j < x; ++j) {
+ int y;
+ y = (int)(r->p[g[j]] - min + .499);
+ if (y > 255) y = 255;
+ PL[j] = y;
+ }
+ }
+// if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
+ call->shift = (int)(sum_min + .499);
+ }
+ // combine annotations
+ memset(call->anno, 0, 16 * sizeof(int));
+ for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) {
+ call->depth += calls[i].depth;
+ call->ori_depth += calls[i].ori_depth;
+ for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
+ }
+
+ calc_vdb(n, calls, call);
+
+ return 0;
+}
+
+int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+ const bcf_callaux_t *bca, const char *ref)
+{
+ extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+ kstring_t s;
+ int i, j;
+ b->n_smpl = bc->n;
+ b->tid = tid; b->pos = pos; b->qual = 0;
+ s.s = b->str; s.m = b->m_str; s.l = 0;
+ kputc('\0', &s);
+ if (bc->ori_ref < 0) { // an indel
+ // write REF
+ kputc(ref[pos], &s);
+ for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
+ kputc('\0', &s);
+ // write ALT
+ kputc(ref[pos], &s);
+ for (i = 1; i < 4; ++i) {
+ if (bc->a[i] < 0) break;
+ if (i > 1) {
+ kputc(',', &s); kputc(ref[pos], &s);
+ }
+ if (bca->indel_types[bc->a[i]] < 0) { // deletion
+ for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
+ kputc(ref[pos+1+j], &s);
+ } else { // insertion; cannot be a reference unless a bug
+ char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
+ for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
+ kputc("ACGTN"[(int)inscns[j]], &s);
+ for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
+ }
+ }
+ kputc('\0', &s);
+ } else { // a SNP
+ kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
+ for (i = 1; i < 5; ++i) {
+ if (bc->a[i] < 0) break;
+ if (i > 1) kputc(',', &s);
+ kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
+ }
+ kputc('\0', &s);
+ }
+ kputc('\0', &s);
+ // INFO
+ if (bc->ori_ref < 0) kputs("INDEL;", &s);
+ kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
+ for (i = 0; i < 16; ++i) {
+ if (i) kputc(',', &s);
+ kputw(bc->anno[i], &s);
+ }
+ if ( bc->vdb!=1 )
+ {
+ ksprintf(&s, ";VDB=%.4f", bc->vdb);
+ }
+ kputc('\0', &s);
+ // FMT
+ kputs("PL", &s);
+ if (bcr) {
+ kputs(":DP", &s);
+ if (is_SP) kputs(":SP", &s);
+ }
+ kputc('\0', &s);
+ b->m_str = s.m; b->str = s.s; b->l_str = s.l;
+ bcf_sync(b);
+ memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
+ if (bcr) {
+ uint16_t *dp = (uint16_t*)b->gi[1].data;
+ int32_t *sp = is_SP? b->gi[2].data : 0;
+ for (i = 0; i < bc->n; ++i) {
+ bcf_callret1_t *p = bcr + i;
+ dp[i] = p->depth < 0xffff? p->depth : 0xffff;
+ if (is_SP) {
+ if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
+ || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
+ {
+ sp[i] = 0;
+ } else {
+ double left, right, two;
+ int x;
+ kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two);
+ x = (int)(-4.343 * log(two) + .499);
+ if (x > 255) x = 255;
+ sp[i] = x;
+ }
+ }
+ }
+ }
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam2bcf.h b/src/samtools-0.1.18/bam2bcf.h
new file mode 100644
index 0000000..4af080c
--- /dev/null
+++ b/src/samtools-0.1.18/bam2bcf.h
@@ -0,0 +1,57 @@
+#ifndef BAM2BCF_H
+#define BAM2BCF_H
+
+#include <stdint.h>
+#include "errmod.h"
+#include "bcftools/bcf.h"
+
+#define B2B_INDEL_NULL 10000
+
+typedef struct __bcf_callaux_t {
+ int capQ, min_baseQ;
+ int openQ, extQ, tandemQ; // for indels
+ int min_support; // for collecting indel candidates
+ double min_frac; // for collecting indel candidates
+ // for internal uses
+ int max_bases;
+ int indel_types[4];
+ int maxins, indelreg;
+ char *inscns;
+ uint16_t *bases;
+ errmod_t *e;
+ void *rghash;
+} bcf_callaux_t;
+
+typedef struct {
+ int depth, ori_depth, qsum[4];
+ int anno[16];
+ float p[25];
+ int mvd[3]; // mean variant distance, number of variant reads, average read length
+} bcf_callret1_t;
+
+typedef struct {
+ int a[5]; // alleles: ref, alt, alt2, alt3
+ int n, n_alleles, shift, ori_ref, unseen;
+ int anno[16], depth, ori_depth;
+ uint8_t *PL;
+ float vdb; // variant distance bias
+} bcf_call_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
+ void bcf_call_destroy(bcf_callaux_t *bca);
+ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
+ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
+ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+ const bcf_callaux_t *bca, const char *ref);
+ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
+ const void *rghash);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/samtools-0.1.18/bam2bcf_indel.c b/src/samtools-0.1.18/bam2bcf_indel.c
new file mode 100644
index 0000000..5142b3e
--- /dev/null
+++ b/src/samtools-0.1.18/bam2bcf_indel.c
@@ -0,0 +1,475 @@
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include "bam.h"
+#include "bam2bcf.h"
+#include "kaln.h"
+#include "kprobaln.h"
+#include "khash.h"
+KHASH_SET_INIT_STR(rg)
+
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint32_t)
+
+#define MINUS_CONST 0x10000000
+#define INDEL_WINDOW_SIZE 50
+
+void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
+{
+ const char *s, *p, *q, *r, *t;
+ khash_t(rg) *hash;
+ if (list == 0 || hdtext == 0) return _hash;
+ if (_hash == 0) _hash = kh_init(rg);
+ hash = (khash_t(rg)*)_hash;
+ if ((s = strstr(hdtext, "@RG\t")) == 0) return hash;
+ do {
+ t = strstr(s + 4, "@RG\t"); // the next @RG
+ if ((p = strstr(s, "\tID:")) != 0) p += 4;
+ if ((q = strstr(s, "\tPL:")) != 0) q += 4;
+ if (p && q && (t == 0 || (p < t && q < t))) { // ID and PL are both present
+ int lp, lq;
+ char *x;
+ for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
+ for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
+ x = calloc((lp > lq? lp : lq) + 1, 1);
+ for (r = q; *r && *r != '\t' && *r != '\n'; ++r) x[r-q] = *r;
+ if (strstr(list, x)) { // insert ID to the hash table
+ khint_t k;
+ int ret;
+ for (r = p; *r && *r != '\t' && *r != '\n'; ++r) x[r-p] = *r;
+ x[r-p] = 0;
+ k = kh_get(rg, hash, x);
+ if (k == kh_end(hash)) k = kh_put(rg, hash, x, &ret);
+ else free(x);
+ } else free(x);
+ }
+ s = t;
+ } while (s);
+ return hash;
+}
+
+void bcf_call_del_rghash(void *_hash)
+{
+ khint_t k;
+ khash_t(rg) *hash = (khash_t(rg)*)_hash;
+ if (hash == 0) return;
+ for (k = kh_begin(hash); k < kh_end(hash); ++k)
+ if (kh_exist(hash, k))
+ free((char*)kh_key(hash, k));
+ kh_destroy(rg, hash);
+}
+
+static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
+{
+ int k, x = c->pos, y = 0, last_y = 0;
+ *_tpos = c->pos;
+ for (k = 0; k < c->n_cigar; ++k) {
+ int op = cigar[k] & BAM_CIGAR_MASK;
+ int l = cigar[k] >> BAM_CIGAR_SHIFT;
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ if (c->pos > tpos) return y;
+ if (x + l > tpos) {
+ *_tpos = tpos;
+ return y + (tpos - x);
+ }
+ x += l; y += l;
+ last_y = y;
+ } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+ else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+ if (x + l > tpos) {
+ *_tpos = is_left? x : x + l;
+ return y;
+ }
+ x += l;
+ }
+ }
+ *_tpos = x;
+ return last_y;
+}
+// FIXME: check if the inserted sequence is consistent with the homopolymer run
+// l is the relative gap length and l_run is the length of the homopolymer on the reference
+static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
+{
+ int q, qh;
+ q = bca->openQ + bca->extQ * (abs(l) - 1);
+ qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000;
+ return q < qh? q : qh;
+}
+
+static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
+{
+ int i, j, max = 0, max_i = pos, score = 0;
+ l = abs(l);
+ for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
+ if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
+ else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
+ if (score < 0) break;
+ if (max < score) max = score, max_i = i;
+ }
+ return max_i - pos;
+}
+
+int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
+ const void *rghash)
+{
+ int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
+ int N, K, l_run, ref_type, n_alt;
+ char *inscns = 0, *ref2, *query, **ref_sample;
+ khash_t(rg) *hash = (khash_t(rg)*)rghash;
+ if (ref == 0 || bca == 0) return -1;
+ // mark filtered reads
+ if (rghash) {
+ N = 0;
+ for (s = N = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ const uint8_t *rg = bam_aux_get(p->b, "RG");
+ p->aux = 1; // filtered by default
+ if (rg) {
+ khint_t k = kh_get(rg, hash, (const char*)(rg + 1));
+ if (k != kh_end(hash)) p->aux = 0, ++N; // not filtered
+ }
+ }
+ }
+ if (N == 0) return -1; // no reads left
+ }
+ // determine if there is a gap
+ for (s = N = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i)
+ if (plp[s][i].indel != 0) break;
+ if (i < n_plp[s]) break;
+ }
+ if (s == n) return -1; // there is no indel at this position.
+ for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads
+ { // find out how many types of indels are present
+ int m, n_alt = 0, n_tot = 0;
+ uint32_t *aux;
+ aux = calloc(N + 1, 4);
+ m = max_rd_len = 0;
+ aux[m++] = MINUS_CONST; // zero indel is always a type
+ for (s = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i) {
+ const bam_pileup1_t *p = plp[s] + i;
+ if (rghash == 0 || p->aux == 0) {
+ ++n_tot;
+ if (p->indel != 0) {
+ ++n_alt;
+ aux[m++] = MINUS_CONST + p->indel;
+ }
+ }
+ j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
+ if (j > max_rd_len) max_rd_len = j;
+ }
+ }
+ ks_introsort(uint32_t, m, aux);
+ // squeeze out identical types
+ for (i = 1, n_types = 1; i < m; ++i)
+ if (aux[i] != aux[i-1]) ++n_types;
+ if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
+ free(aux); return -1;
+ }
+ if (n_types >= 64) {
+ free(aux);
+ if (bam_verbose >= 2)
+ fprintf(stderr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1);
+ return -1;
+ }
+ types = (int*)calloc(n_types, sizeof(int));
+ t = 0;
+ types[t++] = aux[0] - MINUS_CONST;
+ for (i = 1; i < m; ++i)
+ if (aux[i] != aux[i-1])
+ types[t++] = aux[i] - MINUS_CONST;
+ free(aux);
+ for (t = 0; t < n_types; ++t)
+ if (types[t] == 0) break;
+ ref_type = t; // the index of the reference type (0)
+ }
+ { // calculate left and right boundary
+ left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
+ right = pos + INDEL_WINDOW_SIZE;
+ if (types[0] < 0) right -= types[0];
+ // in case the alignments stand out the reference
+ for (i = pos; i < right; ++i)
+ if (ref[i] == 0) break;
+ right = i;
+ }
+ /* The following block fixes a long-existing flaw in the INDEL
+ * calling model: the interference of nearby SNPs. However, it also
+ * reduces the power because sometimes, substitutions caused by
+ * indels are not distinguishable from true mutations. Multiple
+ * sequence realignment helps to increase the power.
+ */
+ { // construct per-sample consensus
+ int L = right - left + 1, max_i, max2_i;
+ uint32_t *cns, max, max2;
+ char *ref0, *r;
+ ref_sample = calloc(n, sizeof(void*));
+ cns = calloc(L, 4);
+ ref0 = calloc(L, 1);
+ for (i = 0; i < right - left; ++i)
+ ref0[i] = bam_nt16_table[(int)ref[i+left]];
+ for (s = 0; s < n; ++s) {
+ r = ref_sample[s] = calloc(L, 1);
+ memset(cns, 0, sizeof(int) * L);
+ // collect ref and non-ref counts
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ bam1_t *b = p->b;
+ uint32_t *cigar = bam1_cigar(b);
+ uint8_t *seq = bam1_seq(b);
+ int x = b->core.pos, y = 0;
+ for (k = 0; k < b->core.n_cigar; ++k) {
+ int op = cigar[k]&0xf;
+ int j, l = cigar[k]>>4;
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ for (j = 0; j < l; ++j)
+ if (x + j >= left && x + j < right)
+ cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;
+ x += l; y += l;
+ } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
+ else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+ }
+ }
+ // determine the consensus
+ for (i = 0; i < right - left; ++i) r[i] = ref0[i];
+ max = max2 = 0; max_i = max2_i = -1;
+ for (i = 0; i < right - left; ++i) {
+ if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i;
+ else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i;
+ }
+ if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1;
+ if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
+ if (max_i >= 0) r[max_i] = 15;
+ if (max2_i >= 0) r[max2_i] = 15;
+// for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
+ }
+ free(ref0); free(cns);
+ }
+ { // the length of the homopolymer run around the current position
+ int c = bam_nt16_table[(int)ref[pos + 1]];
+ if (c == 15) l_run = 1;
+ else {
+ for (i = pos + 2; ref[i]; ++i)
+ if (bam_nt16_table[(int)ref[i]] != c) break;
+ l_run = i;
+ for (i = pos; i >= 0; --i)
+ if (bam_nt16_table[(int)ref[i]] != c) break;
+ l_run -= i + 1;
+ }
+ }
+ // construct the consensus sequence
+ max_ins = types[n_types - 1]; // max_ins is at least 0
+ if (max_ins > 0) {
+ int *inscns_aux = calloc(4 * n_types * max_ins, sizeof(int));
+ // count the number of occurrences of each base at each position for each type of insertion
+ for (t = 0; t < n_types; ++t) {
+ if (types[t] > 0) {
+ for (s = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ if (p->indel == types[t]) {
+ uint8_t *seq = bam1_seq(p->b);
+ for (k = 1; k <= p->indel; ++k) {
+ int c = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos + k)];
+ if (c < 4) ++inscns_aux[(t*max_ins+(k-1))*4 + c];
+ }
+ }
+ }
+ }
+ }
+ }
+ // use the majority rule to construct the consensus
+ inscns = calloc(n_types * max_ins, 1);
+ for (t = 0; t < n_types; ++t) {
+ for (j = 0; j < types[t]; ++j) {
+ int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*4];
+ for (k = 0; k < 4; ++k)
+ if (ia[k] > max)
+ max = ia[k], max_k = k;
+ inscns[t*max_ins + j] = max? max_k : 4;
+ }
+ }
+ free(inscns_aux);
+ }
+ // compute the likelihood given each type of indel for each read
+ max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
+ ref2 = calloc(max_ref2, 1);
+ query = calloc(right - left + max_rd_len + max_ins + 2, 1);
+ 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 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]);
+ else ir = est_indelreg(pos, ref, -types[t], 0);
+ if (ir > bca->indelreg) bca->indelreg = ir;
+// fprintf(stderr, "%d, %d, %d\n", pos, types[t], ir);
+ // realignment
+ for (s = K = 0; s < n; ++s) {
+ // write ref2
+ for (k = 0, j = left; j <= pos; ++j)
+ ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
+ if (types[t] <= 0) j += -types[t];
+ else for (l = 0; l < types[t]; ++l)
+ ref2[k++] = inscns[t*max_ins + l];
+ for (; j < right && ref[j]; ++j)
+ ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
+ for (; k < max_ref2; ++k) ref2[k] = 4;
+ if (j < right) right = j;
+ // align each read to ref2
+ for (i = 0; i < n_plp[s]; ++i, ++K) {
+ bam_pileup1_t *p = plp[s] + i;
+ int qbeg, qend, tbeg, tend, sc, kk;
+ uint8_t *seq = bam1_seq(p->b);
+ uint32_t *cigar = bam1_cigar(p->b);
+ if (p->b->core.flag&4) continue; // unmapped reads
+ // FIXME: the following loop should be better moved outside; nonetheless, realignment should be much slower anyway.
+ for (kk = 0; kk < p->b->core.n_cigar; ++kk)
+ if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break;
+ if (kk < p->b->core.n_cigar) continue;
+ // FIXME: the following skips soft clips, but using them may be more sensitive.
+ // determine the start and end of sequences for alignment
+ qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg);
+ qend = tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
+ if (types[t] < 0) {
+ int l = -types[t];
+ tbeg = tbeg - l > left? tbeg - l : left;
+ }
+ // write the query sequence
+ for (l = qbeg; l < qend; ++l)
+ query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
+ { // do realignment; this is the bottleneck
+ const uint8_t *qual = bam1_qual(p->b), *bq;
+ uint8_t *qq;
+ qq = calloc(qend - qbeg, 1);
+ bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
+ if (bq) ++bq; // skip type
+ for (l = qbeg; l < qend; ++l) {
+ qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : 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, &apf1, 0, 0);
+ l = (int)(100. * sc / (qend - qbeg) + .499); // used for adjusting indelQ below
+ if (l > 255) l = 255;
+ score1[K*n_types + t] = score2[K*n_types + t] = sc<<8 | l;
+ if (sc > 5) {
+ sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+ (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0);
+ l = (int)(100. * sc / (qend - qbeg) + .499);
+ if (l > 255) l = 255;
+ score2[K*n_types + t] = sc<<8 | l;
+ }
+ free(qq);
+ }
+/*
+ for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
+ fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
+ fputc('\n', stderr);
+ for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], stderr);
+ fputc('\n', stderr);
+ fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam1_qname(p->b), qbeg, tbeg, sc);
+*/
+ }
+ }
+ }
+ free(ref2); free(query);
+ { // compute indelQ
+ int *sc, tmp, *sumq;
+ sc = alloca(n_types * sizeof(int));
+ sumq = alloca(n_types * sizeof(int));
+ memset(sumq, 0, sizeof(int) * n_types);
+ 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 = &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)
+ tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+ /* errmod_cal() assumes that if the call is wrong, the
+ * likelihoods of other events are equal. This is about
+ * right for substitutions, but is not desired for
+ * indels. To reuse errmod_cal(), I have to make
+ * compromise for multi-allelic indels.
+ */
+ if ((sc[0]&0x3f) == ref_type) {
+ indelQ1 = (sc[1]>>14) - (sc[0]>>14);
+ 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;
+ indelQ1 = (sc[t]>>14) - (sc[0]>>14);
+ seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
+ }
+ tmp = sc[0]>>6 & 0xff;
+ indelQ1 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ1 + .499); // reduce indelQ
+ 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]>>14) - (sc[0]>>14);
+ } else {
+ for (t = 0; t < n_types; ++t) // look for the reference type
+ if ((sc[t]&0x3f) == ref_type) break;
+ indelQ2 = (sc[t]>>14) - (sc[0]>>14);
+ }
+ tmp = sc[0]>>6 & 0xff;
+ indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499);
+ // pick the smaller between indelQ1 and indelQ2
+ indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
+ if (indelQ > 255) indelQ = 255;
+ if (seqQ > 255) seqQ = 255;
+ p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
+ sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
+// fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
+ }
+ }
+ // determine bca->indel_types[] and bca->inscns
+ bca->maxins = max_ins;
+ bca->inscns = realloc(bca->inscns, bca->maxins * 4);
+ for (t = 0; t < n_types; ++t)
+ sumq[t] = sumq[t]<<6 | t;
+ for (t = 1; t < n_types; ++t) // insertion sort
+ for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j)
+ tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp;
+ for (t = 0; t < n_types; ++t) // look for the reference type
+ if ((sumq[t]&0x3f) == ref_type) break;
+ if (t) { // then move the reference type to the first
+ tmp = sumq[t];
+ for (; t > 0; --t) sumq[t] = sumq[t-1];
+ sumq[0] = tmp;
+ }
+ for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
+ for (t = 0; t < 4 && t < n_types; ++t) {
+ bca->indel_types[t] = types[sumq[t]&0x3f];
+ memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
+ }
+ // update p->aux
+ for (s = n_alt = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ int x = types[p->aux>>16&0x3f];
+ for (j = 0; j < 4; ++j)
+ if (x == bca->indel_types[j]) break;
+ p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff));
+ if ((p->aux>>16&0x3f) > 0) ++n_alt;
+// fprintf(stderr, "X pos=%d read=%d:%d name=%s call=%d type=%d q=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), p->aux>>16&63, bca->indel_types[p->aux>>16&63], p->aux&0xff, p->aux>>8&0xff);
+ }
+ }
+ }
+ free(score1); free(score2);
+ // free
+ for (i = 0; i < n; ++i) free(ref_sample[i]);
+ free(ref_sample);
+ free(types); free(inscns);
+ return n_alt > 0? 0 : -1;
+}
diff --git a/src/samtools-0.1.18/bam2depth.c b/src/samtools-0.1.18/bam2depth.c
new file mode 100644
index 0000000..ca36b89
--- /dev/null
+++ b/src/samtools-0.1.18/bam2depth.c
@@ -0,0 +1,112 @@
+/* This program demonstrates how to generate pileup from multiple BAMs
+ * simutaneously, to achieve random access and to use the BED interface.
+ * To compile this program separately, you may:
+ *
+ * gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -L. -lbam -lz
+ */
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include "bam.h"
+
+typedef struct { // auxiliary data structure
+ bamFile fp; // the file handler
+ bam_iter_t iter; // NULL if a region not specified
+ int min_mapQ; // mapQ filter
+} aux_t;
+
+void *bed_read(const char *fn); // read a BED or position list file
+void bed_destroy(void *_h); // destroy the BED data structure
+int bed_overlap(const void *_h, const char *chr, int beg, int end); // test if chr:beg-end overlaps
+
+// This function reads a BAM alignment from one BAM file.
+static int read_bam(void *data, bam1_t *b) // read level filters better go here to avoid pileup
+{
+ aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
+ int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
+ if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+ return ret;
+}
+
+#ifdef _MAIN_BAM2DEPTH
+int main(int argc, char *argv[])
+#else
+int main_depth(int argc, char *argv[])
+#endif
+{
+ int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0;
+ const bam_pileup1_t **plp;
+ char *reg = 0; // specified region
+ void *bed = 0; // BED data structure
+ bam_header_t *h = 0; // BAM header of the 1st input
+ aux_t **data;
+ bam_mplp_t mplp;
+
+ // parse the command line
+ while ((n = getopt(argc, argv, "r:b:q:Q:")) >= 0) {
+ switch (n) {
+ case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header
+ case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
+ case 'q': baseQ = atoi(optarg); break; // base quality threshold
+ case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold
+ }
+ }
+ if (optind == argc) {
+ fprintf(stderr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-b in.bed] <in1.bam> [...]\n");
+ return 1;
+ }
+
+ // initialize the auxiliary data structures
+ n = argc - optind; // the number of BAMs on the command line
+ data = calloc(n, sizeof(void*)); // data[i] for the i-th input
+ beg = 0; end = 1<<30; tid = -1; // set the default region
+ for (i = 0; i < n; ++i) {
+ bam_header_t *htmp;
+ data[i] = calloc(1, sizeof(aux_t));
+ data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
+ data[i]->min_mapQ = mapQ; // set the mapQ filter
+ htmp = bam_header_read(data[i]->fp); // read the BAM header
+ if (i == 0) {
+ h = htmp; // keep the header of the 1st BAM
+ if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region
+ } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header
+ if (tid >= 0) { // if a region is specified and parsed successfully
+ bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index
+ data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator
+ bam_index_destroy(idx); // the index is not needed any more; phase out of the memory
+ }
+ }
+
+ // the core multi-pileup loop
+ mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
+ n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
+ plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp)
+ while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
+ if (pos < beg || pos >= end) continue; // out of range; skip
+ if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip
+ fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster
+ for (i = 0; i < n; ++i) { // base level filters have to go here
+ int j, m = 0;
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
+ if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos
+ else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality
+ }
+ printf("\t%d", n_plp[i] - m); // this the depth to output
+ }
+ putchar('\n');
+ }
+ free(n_plp); free(plp);
+ bam_mplp_destroy(mplp);
+
+ bam_header_destroy(h);
+ for (i = 0; i < n; ++i) {
+ bam_close(data[i]->fp);
+ if (data[i]->iter) bam_iter_destroy(data[i]->iter);
+ free(data[i]);
+ }
+ free(data); free(reg);
+ if (bed) bed_destroy(bed);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam_aux.c b/src/samtools-0.1.18/bam_aux.c
new file mode 100644
index 0000000..28b22e3
--- /dev/null
+++ b/src/samtools-0.1.18/bam_aux.c
@@ -0,0 +1,213 @@
+#include <ctype.h>
+#include "bam.h"
+#include "khash.h"
+typedef char *str_p;
+KHASH_MAP_INIT_STR(s, int)
+KHASH_MAP_INIT_STR(r2l, str_p)
+
+void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
+{
+ int ori_len = b->data_len;
+ b->data_len += 3 + len;
+ b->l_aux += 3 + len;
+ if (b->m_data < b->data_len) {
+ b->m_data = b->data_len;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
+ b->data[ori_len + 2] = type;
+ memcpy(b->data + ori_len + 3, data, len);
+}
+
+uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
+{
+ return bam_aux_get(b, tag);
+}
+
+#define __skip_tag(s) do { \
+ int type = toupper(*(s)); \
+ ++(s); \
+ if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
+ else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
+ else (s) += bam_aux_type2size(type); \
+ } while(0)
+
+uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
+{
+ uint8_t *s;
+ int y = tag[0]<<8 | tag[1];
+ s = bam1_aux(b);
+ while (s < b->data + b->data_len) {
+ int x = (int)s[0]<<8 | s[1];
+ s += 2;
+ if (x == y) return s;
+ __skip_tag(s);
+ }
+ return 0;
+}
+// s MUST BE returned by bam_aux_get()
+int bam_aux_del(bam1_t *b, uint8_t *s)
+{
+ uint8_t *p, *aux;
+ aux = bam1_aux(b);
+ p = s - 2;
+ __skip_tag(s);
+ memmove(p, s, b->l_aux - (s - aux));
+ b->data_len -= s - p;
+ b->l_aux -= s - p;
+ return 0;
+}
+
+int bam_aux_drop_other(bam1_t *b, uint8_t *s)
+{
+ if (s) {
+ uint8_t *p, *aux;
+ aux = bam1_aux(b);
+ p = s - 2;
+ __skip_tag(s);
+ memmove(aux, p, s - p);
+ b->data_len -= b->l_aux - (s - p);
+ b->l_aux = s - p;
+ } else {
+ b->data_len -= b->l_aux;
+ b->l_aux = 0;
+ }
+ return 0;
+}
+
+void bam_init_header_hash(bam_header_t *header)
+{
+ if (header->hash == 0) {
+ int ret, i;
+ khiter_t iter;
+ khash_t(s) *h;
+ header->hash = h = kh_init(s);
+ for (i = 0; i < header->n_targets; ++i) {
+ iter = kh_put(s, h, header->target_name[i], &ret);
+ kh_value(h, iter) = i;
+ }
+ }
+}
+
+void bam_destroy_header_hash(bam_header_t *header)
+{
+ if (header->hash)
+ kh_destroy(s, (khash_t(s)*)header->hash);
+}
+
+int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
+{
+ khint_t k;
+ khash_t(s) *h = (khash_t(s)*)header->hash;
+ k = kh_get(s, h, seq_name);
+ return k == kh_end(h)? -1 : kh_value(h, k);
+}
+
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
+{
+ char *s;
+ int i, l, k, name_end;
+ khiter_t iter;
+ khash_t(s) *h;
+
+ bam_init_header_hash(header);
+ h = (khash_t(s)*)header->hash;
+
+ *ref_id = *beg = *end = -1;
+ name_end = l = strlen(str);
+ s = (char*)malloc(l+1);
+ // remove space
+ for (i = k = 0; i < l; ++i)
+ if (!isspace(str[i])) s[k++] = str[i];
+ s[k] = 0; l = k;
+ // determine the sequence name
+ for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+ if (i >= 0) name_end = i;
+ if (name_end < l) { // check if this is really the end
+ int n_hyphen = 0;
+ for (i = name_end + 1; i < l; ++i) {
+ if (s[i] == '-') ++n_hyphen;
+ else if (!isdigit(s[i]) && s[i] != ',') break;
+ }
+ if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+ s[name_end] = 0;
+ iter = kh_get(s, h, s);
+ if (iter == kh_end(h)) { // cannot find the sequence name
+ iter = kh_get(s, h, str); // try str as the name
+ if (iter == kh_end(h)) {
+ if (bam_verbose >= 2) fprintf(stderr, "[%s] fail to determine the sequence name.\n", __func__);
+ free(s); return -1;
+ } else s[name_end] = ':', name_end = l;
+ }
+ } else iter = kh_get(s, h, str);
+ *ref_id = kh_val(h, iter);
+ // parse the interval
+ if (name_end < l) {
+ for (i = k = name_end + 1; i < l; ++i)
+ if (s[i] != ',') s[k++] = s[i];
+ s[k] = 0;
+ *beg = atoi(s + name_end + 1);
+ for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+ *end = i < k? atoi(s + i + 1) : 1<<29;
+ if (*beg > 0) --*beg;
+ } else *beg = 0, *end = 1<<29;
+ free(s);
+ return *beg <= *end? 0 : -1;
+}
+
+int32_t bam_aux2i(const uint8_t *s)
+{
+ int type;
+ if (s == 0) return 0;
+ type = *s++;
+ if (type == 'c') return (int32_t)*(int8_t*)s;
+ else if (type == 'C') return (int32_t)*(uint8_t*)s;
+ else if (type == 's') return (int32_t)*(int16_t*)s;
+ else if (type == 'S') return (int32_t)*(uint16_t*)s;
+ else if (type == 'i' || type == 'I') return *(int32_t*)s;
+ else return 0;
+}
+
+float bam_aux2f(const uint8_t *s)
+{
+ int type;
+ type = *s++;
+ if (s == 0) return 0.0;
+ if (type == 'f') return *(float*)s;
+ else return 0.0;
+}
+
+double bam_aux2d(const uint8_t *s)
+{
+ int type;
+ type = *s++;
+ if (s == 0) return 0.0;
+ if (type == 'd') return *(double*)s;
+ else return 0.0;
+}
+
+char bam_aux2A(const uint8_t *s)
+{
+ int type;
+ type = *s++;
+ if (s == 0) return 0;
+ if (type == 'A') return *(char*)s;
+ else return 0;
+}
+
+char *bam_aux2Z(const uint8_t *s)
+{
+ int type;
+ type = *s++;
+ if (s == 0) return 0;
+ if (type == 'Z' || type == 'H') return (char*)s;
+ else return 0;
+}
+
+#ifdef _WIN32
+double drand48()
+{
+ return (double)rand() / RAND_MAX;
+}
+#endif
diff --git a/src/samtools-0.1.18/bam_cat.c b/src/samtools-0.1.18/bam_cat.c
new file mode 100644
index 0000000..0fde045
--- /dev/null
+++ b/src/samtools-0.1.18/bam_cat.c
@@ -0,0 +1,184 @@
+/*
+
+bam_cat -- efficiently concatenates bam files
+
+bam_cat can be used to concatenate BAM files. Under special
+circumstances, it can be used as an alternative to 'samtools merge' to
+concatenate multiple sorted files into a single sorted file. For this
+to work each file must be sorted, and the sorted files must be given
+as command line arguments in order such that the final read in file i
+is less than or equal to the first read in file i+1.
+
+This code is derived from the bam_reheader function in samtools 0.1.8
+and modified to perform concatenation by Chris Saunders on behalf of
+Illumina.
+
+
+########## License:
+
+The MIT License
+
+Original SAMtools work copyright (c) 2008-2009 Genome Research Ltd.
+Modified SAMtools work copyright (c) 2010 Illumina, Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+*/
+
+
+/*
+makefile:
+"""
+CC=gcc
+CFLAGS+=-g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I$(SAMTOOLS_DIR)
+LDFLAGS+=-L$(SAMTOOLS_DIR)
+LDLIBS+=-lbam -lz
+
+all:bam_cat
+"""
+*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#include "bgzf.h"
+#include "bam.h"
+
+#define BUF_SIZE 0x10000
+
+#define GZIPID1 31
+#define GZIPID2 139
+
+#define BGZF_EMPTY_BLOCK_SIZE 28
+
+
+int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam)
+{
+ BGZF *fp;
+ FILE* fp_file;
+ uint8_t *buf;
+ uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE];
+ const int es=BGZF_EMPTY_BLOCK_SIZE;
+ int i;
+
+ fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(stdout), "w");
+ if (fp == 0) {
+ fprintf(stderr, "[%s] ERROR: fail to open output file '%s'.\n", __func__, outbam);
+ return 1;
+ }
+ if (h) bam_header_write(fp, h);
+
+ buf = (uint8_t*) malloc(BUF_SIZE);
+ for(i = 0; i < nfn; ++i){
+ BGZF *in;
+ bam_header_t *old;
+ int len,j;
+
+ in = strcmp(fn[i], "-")? bam_open(fn[i], "r") : bam_dopen(fileno(stdin), "r");
+ if (in == 0) {
+ fprintf(stderr, "[%s] ERROR: fail to open file '%s'.\n", __func__, fn[i]);
+ return -1;
+ }
+ if (in->open_mode != 'r') return -1;
+
+ old = bam_header_read(in);
+ if (h == 0 && i == 0) bam_header_write(fp, old);
+
+ if (in->block_offset < in->block_length) {
+ bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
+ bgzf_flush(fp);
+ }
+
+ j=0;
+#ifdef _USE_KNETFILE
+ fp_file=fp->x.fpw;
+ while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0) {
+#else
+ fp_file=fp->file;
+ while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) {
+#endif
+ if(len<es){
+ int diff=es-len;
+ if(j==0) {
+ fprintf(stderr, "[%s] ERROR: truncated file?: '%s'.\n", __func__, fn[i]);
+ return -1;
+ }
+ fwrite(ebuf, 1, len, fp_file);
+ memcpy(ebuf,ebuf+len,diff);
+ memcpy(ebuf+diff,buf,len);
+ } else {
+ if(j!=0) fwrite(ebuf, 1, es, fp_file);
+ len-= es;
+ memcpy(ebuf,buf+len,es);
+ fwrite(buf, 1, len, fp_file);
+ }
+ j=1;
+ }
+
+ /* check final gzip block */
+ {
+ const uint8_t gzip1=ebuf[0];
+ const uint8_t gzip2=ebuf[1];
+ const uint32_t isize=*((uint32_t*)(ebuf+es-4));
+ if(((gzip1!=GZIPID1) || (gzip2!=GZIPID2)) || (isize!=0)) {
+ fprintf(stderr, "[%s] WARNING: Unexpected block structure in file '%s'.", __func__, fn[i]);
+ fprintf(stderr, " Possible output corruption.\n");
+ fwrite(ebuf, 1, es, fp_file);
+ }
+ }
+ bam_header_destroy(old);
+ bgzf_close(in);
+ }
+ free(buf);
+ bgzf_close(fp);
+ return 0;
+}
+
+
+
+int main_cat(int argc, char *argv[])
+{
+ bam_header_t *h = 0;
+ char *outfn = 0;
+ int c, ret;
+ while ((c = getopt(argc, argv, "h:o:")) >= 0) {
+ switch (c) {
+ case 'h': {
+ tamFile fph = sam_open(optarg);
+ if (fph == 0) {
+ fprintf(stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, argv[1]);
+ return 1;
+ }
+ h = sam_header_read(fph);
+ sam_close(fph);
+ break;
+ }
+ case 'o': outfn = strdup(optarg); break;
+ }
+ }
+ if (argc - optind < 2) {
+ fprintf(stderr, "Usage: samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [...]\n");
+ return 1;
+ }
+ ret = bam_cat(argc - optind, argv + optind, h, outfn? outfn : "-");
+ free(outfn);
+ return ret;
+}
diff --git a/src/samtools-0.1.18/bam_color.c b/src/samtools-0.1.18/bam_color.c
new file mode 100644
index 0000000..ce637f7
--- /dev/null
+++ b/src/samtools-0.1.18/bam_color.c
@@ -0,0 +1,127 @@
+#include <ctype.h>
+#include "bam.h"
+
+/*!
+ @abstract Get the color encoding the previous and current base
+ @param b pointer to an alignment
+ @param i The i-th position, 0-based
+ @return color
+
+ @discussion Returns 0 no color information is found.
+ */
+char bam_aux_getCSi(bam1_t *b, int i)
+{
+ uint8_t *c = bam_aux_get(b, "CS");
+ char *cs = NULL;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cs = bam_aux2Z(c);
+ // adjust for strandedness and leading adaptor
+ if(bam1_strand(b)) i = strlen(cs) - 1 - i;
+ else i++;
+ return cs[i];
+}
+
+/*!
+ @abstract Get the color quality of the color encoding the previous and current base
+ @param b pointer to an alignment
+ @param i The i-th position, 0-based
+ @return color quality
+
+ @discussion Returns 0 no color information is found.
+ */
+char bam_aux_getCQi(bam1_t *b, int i)
+{
+ uint8_t *c = bam_aux_get(b, "CQ");
+ char *cq = NULL;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cq = bam_aux2Z(c);
+ // adjust for strandedness
+ if(bam1_strand(b)) i = strlen(cq) - 1 - i;
+ return cq[i];
+}
+
+char bam_aux_nt2int(char a)
+{
+ switch(toupper(a)) {
+ case 'A':
+ return 0;
+ break;
+ case 'C':
+ return 1;
+ break;
+ case 'G':
+ return 2;
+ break;
+ case 'T':
+ return 3;
+ break;
+ default:
+ return 4;
+ break;
+ }
+}
+
+char bam_aux_ntnt2cs(char a, char b)
+{
+ a = bam_aux_nt2int(a);
+ b = bam_aux_nt2int(b);
+ if(4 == a || 4 == b) return '4';
+ return "0123"[(int)(a ^ b)];
+}
+
+/*!
+ @abstract Get the color error profile at the give position
+ @param b pointer to an alignment
+ @return the original color if the color was an error, '-' (dash) otherwise
+
+ @discussion Returns 0 no color information is found.
+ */
+char bam_aux_getCEi(bam1_t *b, int i)
+{
+ int cs_i;
+ uint8_t *c = bam_aux_get(b, "CS");
+ char *cs = NULL;
+ char prev_b, cur_b;
+ char cur_color, cor_color;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cs = bam_aux2Z(c);
+
+ // adjust for strandedness and leading adaptor
+ if(bam1_strand(b)) { //reverse strand
+ cs_i = strlen(cs) - 1 - i;
+ // get current color
+ cur_color = cs[cs_i];
+ // get previous base. Note: must rc adaptor
+ prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
+ // get current base
+ cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
+ }
+ else {
+ cs_i=i+1;
+ // get current color
+ cur_color = cs[cs_i];
+ // get previous base
+ prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)];
+ // get current base
+ cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
+ }
+
+ // corrected color
+ cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
+
+ if(cur_color == cor_color) {
+ return '-';
+ }
+ else {
+ return cur_color;
+ }
+}
diff --git a/src/samtools-0.1.18/bam_endian.h b/src/samtools-0.1.18/bam_endian.h
new file mode 100644
index 0000000..0fc74a8
--- /dev/null
+++ b/src/samtools-0.1.18/bam_endian.h
@@ -0,0 +1,42 @@
+#ifndef BAM_ENDIAN_H
+#define BAM_ENDIAN_H
+
+#include <stdint.h>
+
+static inline int bam_is_big_endian()
+{
+ long one= 1;
+ return !(*((char *)(&one)));
+}
+static inline uint16_t bam_swap_endian_2(uint16_t v)
+{
+ return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
+}
+static inline void *bam_swap_endian_2p(void *x)
+{
+ *(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x);
+ return x;
+}
+static inline uint32_t bam_swap_endian_4(uint32_t v)
+{
+ v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
+ return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
+}
+static inline void *bam_swap_endian_4p(void *x)
+{
+ *(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x);
+ return x;
+}
+static inline uint64_t bam_swap_endian_8(uint64_t v)
+{
+ v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
+ v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
+ return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
+}
+static inline void *bam_swap_endian_8p(void *x)
+{
+ *(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x);
+ return x;
+}
+
+#endif
diff --git a/src/samtools-0.1.18/bam_import.c b/src/samtools-0.1.18/bam_import.c
new file mode 100644
index 0000000..5518a9c
--- /dev/null
+++ b/src/samtools-0.1.18/bam_import.c
@@ -0,0 +1,485 @@
+#include <zlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <assert.h>
+#ifdef _WIN32
+#include <fcntl.h>
+#endif
+#include "kstring.h"
+#include "bam.h"
+#include "sam_header.h"
+#include "kseq.h"
+#include "khash.h"
+
+KSTREAM_INIT(gzFile, gzread, 16384)
+KHASH_MAP_INIT_STR(ref, uint64_t)
+
+void bam_init_header_hash(bam_header_t *header);
+void bam_destroy_header_hash(bam_header_t *header);
+int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
+
+unsigned char bam_nt16_table[256] = {
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
+ 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+ 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
+ 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+ 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+ 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
+};
+
+unsigned short bam_char2flag_table[256] = {
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
+ BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
+};
+
+char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
+
+struct __tamFile_t {
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t *str;
+ uint64_t n_lines;
+ int is_first;
+};
+
+char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
+{
+ char **list = 0, *s;
+ int n = 0, dret, m = 0;
+ gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+ kstream_t *ks;
+ kstring_t *str;
+ str = (kstring_t*)calloc(1, sizeof(kstring_t));
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, '\n', str, &dret) > 0) {
+ if (n == m) {
+ m = m? m << 1 : 16;
+ list = (char**)realloc(list, m * sizeof(char*));
+ }
+ if (str->s[str->l-1] == '\r')
+ str->s[--str->l] = '\0';
+ s = list[n++] = (char*)calloc(str->l + 1, 1);
+ strcpy(s, str->s);
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(str->s); free(str);
+ *_n = n;
+ return list;
+}
+
+static bam_header_t *hash2header(const kh_ref_t *hash)
+{
+ bam_header_t *header;
+ khiter_t k;
+ header = bam_header_init();
+ header->n_targets = kh_size(hash);
+ header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
+ header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
+ for (k = kh_begin(hash); k != kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ int i = (int)kh_value(hash, k);
+ header->target_name[i] = (char*)kh_key(hash, k);
+ header->target_len[i] = kh_value(hash, k)>>32;
+ }
+ }
+ bam_init_header_hash(header);
+ return header;
+}
+bam_header_t *sam_header_read2(const char *fn)
+{
+ bam_header_t *header;
+ int c, dret, ret, error = 0;
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t *str;
+ kh_ref_t *hash;
+ khiter_t k;
+ if (fn == 0) return 0;
+ fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+ if (fp == 0) return 0;
+ hash = kh_init(ref);
+ ks = ks_init(fp);
+ str = (kstring_t*)calloc(1, sizeof(kstring_t));
+ while (ks_getuntil(ks, 0, str, &dret) > 0) {
+ char *s = strdup(str->s);
+ int len, i;
+ i = kh_size(hash);
+ ks_getuntil(ks, 0, str, &dret);
+ len = atoi(str->s);
+ k = kh_put(ref, hash, s, &ret);
+ if (ret == 0) {
+ fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
+ error = 1;
+ }
+ kh_value(hash, k) = (uint64_t)len<<32 | i;
+ if (dret != '\n')
+ while ((c = ks_getc(ks)) != '\n' && c != -1);
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(str->s); free(str);
+ fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
+ if (error) return 0;
+ header = hash2header(hash);
+ kh_destroy(ref, hash);
+ return header;
+}
+static inline uint8_t *alloc_data(bam1_t *b, int size)
+{
+ if (b->m_data < size) {
+ b->m_data = size;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ return b->data;
+}
+static inline void parse_error(int64_t n_lines, const char * __restrict msg)
+{
+ fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
+ abort();
+}
+static inline void append_text(bam_header_t *header, kstring_t *str)
+{
+ size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
+ kroundup32(x); kroundup32(y);
+ if (x < y)
+ {
+ header->n_text = y;
+ header->text = (char*)realloc(header->text, y);
+ if ( !header->text )
+ {
+ fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
+ abort();
+ }
+ }
+ // Sanity check
+ if ( header->l_text+str->l+1 >= header->n_text )
+ {
+ fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y);
+ abort();
+ }
+ strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
+ header->l_text += str->l + 1;
+ header->text[header->l_text] = 0;
+}
+
+int sam_header_parse(bam_header_t *h)
+{
+ char **tmp;
+ int i;
+ free(h->target_len); free(h->target_name);
+ h->n_targets = 0; h->target_len = 0; h->target_name = 0;
+ if (h->l_text < 3) return 0;
+ if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+ tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
+ if (h->n_targets == 0) return 0;
+ h->target_name = calloc(h->n_targets, sizeof(void*));
+ for (i = 0; i < h->n_targets; ++i)
+ h->target_name[i] = strdup(tmp[i]);
+ free(tmp);
+ tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
+ h->target_len = calloc(h->n_targets, 4);
+ for (i = 0; i < h->n_targets; ++i)
+ h->target_len[i] = atoi(tmp[i]);
+ free(tmp);
+ return h->n_targets;
+}
+
+bam_header_t *sam_header_read(tamFile fp)
+{
+ int ret, dret;
+ bam_header_t *header = bam_header_init();
+ kstring_t *str = fp->str;
+ while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
+ str->s[str->l] = dret; // note that str->s is NOT null terminated!!
+ append_text(header, str);
+ if (dret != '\n') {
+ ret = ks_getuntil(fp->ks, '\n', str, &dret);
+ str->s[str->l] = '\n'; // NOT null terminated!!
+ append_text(header, str);
+ }
+ ++fp->n_lines;
+ }
+ sam_header_parse(header);
+ bam_init_header_hash(header);
+ fp->is_first = 1;
+ return header;
+}
+
+int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
+{
+ int ret, doff, doff0, dret, z = 0;
+ bam1_core_t *c = &b->core;
+ kstring_t *str = fp->str;
+ kstream_t *ks = fp->ks;
+
+ if (fp->is_first) {
+ fp->is_first = 0;
+ ret = str->l;
+ } else {
+ do { // special consideration for empty lines
+ ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
+ if (ret >= 0) z += str->l + 1;
+ } while (ret == 0);
+ }
+ if (ret < 0) return -1;
+ ++fp->n_lines;
+ doff = 0;
+
+ { // name
+ c->l_qname = strlen(str->s) + 1;
+ memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
+ doff += c->l_qname;
+ }
+ { // flag
+ long flag;
+ char *s;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+ flag = strtol((char*)str->s, &s, 0);
+ if (*s) { // not the end of the string
+ flag = 0;
+ for (s = str->s; *s; ++s)
+ flag |= bam_char2flag_table[(int)*s];
+ }
+ c->flag = flag;
+ }
+ { // tid, pos, qual
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
+ if (c->tid < 0 && strcmp(str->s, "*")) {
+ if (header->n_targets == 0) {
+ fprintf(stderr, "[sam_read1] missing header? Abort!\n");
+ exit(1);
+ } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
+ }
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
+ if (ret < 0) return -2;
+ }
+ { // cigar
+ char *s, *t;
+ int i, op;
+ long x;
+ c->n_cigar = 0;
+ if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
+ z += str->l + 1;
+ if (str->s[0] != '*') {
+ for (s = str->s; *s; ++s) {
+ if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar;
+ else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
+ }
+ b->data = alloc_data(b, doff + c->n_cigar * 4);
+ for (i = 0, s = str->s; i != c->n_cigar; ++i) {
+ x = strtol(s, &t, 10);
+ op = toupper(*t);
+ if (op == 'M') op = BAM_CMATCH;
+ else if (op == 'I') op = BAM_CINS;
+ else if (op == 'D') op = BAM_CDEL;
+ else if (op == 'N') op = BAM_CREF_SKIP;
+ else if (op == 'S') op = BAM_CSOFT_CLIP;
+ else if (op == 'H') op = BAM_CHARD_CLIP;
+ else if (op == 'P') op = BAM_CPAD;
+ else if (op == '=') op = BAM_CEQUAL;
+ else if (op == 'X') op = BAM_CDIFF;
+ else parse_error(fp->n_lines, "invalid CIGAR operation");
+ s = t + 1;
+ bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
+ }
+ if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
+ c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
+ doff += c->n_cigar * 4;
+ } else {
+ if (!(c->flag&BAM_FUNMAP)) {
+ fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
+ c->flag |= BAM_FUNMAP;
+ }
+ c->bin = bam_reg2bin(c->pos, c->pos + 1);
+ }
+ }
+ { // mtid, mpos, isize
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+ c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+ c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+ c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
+ if (ret < 0) return -4;
+ }
+ { // seq and qual
+ int i;
+ uint8_t *p = 0;
+ if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
+ z += str->l + 1;
+ if (strcmp(str->s, "*")) {
+ c->l_qseq = strlen(str->s);
+ if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) {
+ fprintf(stderr, "Line %ld, sequence length %i vs %i from CIGAR\n",
+ (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
+ parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+ }
+ p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
+ memset(p, 0, (c->l_qseq+1)/2);
+ for (i = 0; i < c->l_qseq; ++i)
+ p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
+ } else c->l_qseq = 0;
+ if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
+ z += str->l + 1;
+ if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
+ parse_error(fp->n_lines, "sequence and quality are inconsistent");
+ p += (c->l_qseq+1)/2;
+ if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
+ else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
+ doff += c->l_qseq + (c->l_qseq+1)/2;
+ }
+ doff0 = doff;
+ if (dret != '\n' && dret != '\r') { // aux
+ while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
+ uint8_t *s, type, key[2];
+ z += str->l + 1;
+ if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
+ parse_error(fp->n_lines, "missing colon in auxiliary data");
+ key[0] = str->s[0]; key[1] = str->s[1];
+ type = str->s[3];
+ s = alloc_data(b, doff + 3) + doff;
+ s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
+ if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
+ s = alloc_data(b, doff + 2) + doff;
+ *s++ = 'A'; *s = str->s[5];
+ doff += 2;
+ } else if (type == 'I' || type == 'i') {
+ long long x;
+ s = alloc_data(b, doff + 5) + doff;
+ x = (long long)atoll(str->s + 5);
+ if (x < 0) {
+ if (x >= -127) {
+ *s++ = 'c'; *(int8_t*)s = (int8_t)x;
+ s += 1; doff += 2;
+ } else if (x >= -32767) {
+ *s++ = 's'; *(int16_t*)s = (int16_t)x;
+ s += 2; doff += 3;
+ } else {
+ *s++ = 'i'; *(int32_t*)s = (int32_t)x;
+ s += 4; doff += 5;
+ if (x < -2147483648ll)
+ fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
+ (long long)fp->n_lines, x);
+ }
+ } else {
+ if (x <= 255) {
+ *s++ = 'C'; *s++ = (uint8_t)x;
+ doff += 2;
+ } else if (x <= 65535) {
+ *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
+ s += 2; doff += 3;
+ } else {
+ *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
+ s += 4; doff += 5;
+ if (x > 4294967295ll)
+ fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
+ (long long)fp->n_lines, x);
+ }
+ }
+ } else if (type == 'f') {
+ s = alloc_data(b, doff + 5) + doff;
+ *s++ = 'f';
+ *(float*)s = (float)atof(str->s + 5);
+ s += 4; doff += 5;
+ } else if (type == 'd') {
+ s = alloc_data(b, doff + 9) + doff;
+ *s++ = 'd';
+ *(float*)s = (float)atof(str->s + 9);
+ s += 8; doff += 9;
+ } else if (type == 'Z' || type == 'H') {
+ int size = 1 + (str->l - 5) + 1;
+ if (type == 'H') { // check whether the hex string is valid
+ int i;
+ if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
+ for (i = 0; i < str->l - 5; ++i) {
+ int c = toupper(str->s[5 + i]);
+ if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
+ parse_error(fp->n_lines, "invalid hex character");
+ }
+ }
+ s = alloc_data(b, doff + size) + doff;
+ *s++ = type;
+ memcpy(s, str->s + 5, str->l - 5);
+ s[str->l - 5] = 0;
+ doff += size;
+ } else if (type == 'B') {
+ int32_t n = 0, Bsize, k = 0, size;
+ char *p;
+ if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
+ Bsize = bam_aux_type2size(str->s[5]); // the size of each element
+ for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
+ if (*p == ',') ++n;
+ p = str->s + 7; // now p points to the first number in the array
+ size = 6 + Bsize * n; // total number of bytes allocated to this tag
+ s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
+ *s++ = 'B'; *s++ = str->s[5];
+ memcpy(s, &n, 4); s += 4; // write the number of elements
+ if (str->s[5] == 'c') while (p < str->s + str->l) ((int8_t*)s)[k++] = (int8_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++] = (uint8_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++] = (int16_t)strtol(p, &p, 0), ++p; // FIXME: avoid unaligned memory
+ else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++] = (int32_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++] = (float)strtod(p, &p), ++p;
+ else parse_error(fp->n_lines, "unrecognized array type");
+ s += Bsize * n; doff += size;
+ } else parse_error(fp->n_lines, "unrecognized type");
+ if (dret == '\n' || dret == '\r') break;
+ }
+ }
+ b->l_aux = doff - doff0;
+ b->data_len = doff;
+ return z;
+}
+
+tamFile sam_open(const char *fn)
+{
+ tamFile fp;
+ gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
+ if (gzfp == 0) return 0;
+ fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
+ fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
+ fp->fp = gzfp;
+ fp->ks = ks_init(fp->fp);
+ return fp;
+}
+
+void sam_close(tamFile fp)
+{
+ if (fp) {
+ ks_destroy(fp->ks);
+ gzclose(fp->fp);
+ free(fp->str->s); free(fp->str);
+ free(fp);
+ }
+}
diff --git a/src/samtools-0.1.18/bam_index.c b/src/samtools-0.1.18/bam_index.c
new file mode 100644
index 0000000..9610a26
--- /dev/null
+++ b/src/samtools-0.1.18/bam_index.c
@@ -0,0 +1,719 @@
+#include <ctype.h>
+#include <assert.h>
+#include "bam.h"
+#include "khash.h"
+#include "ksort.h"
+#include "bam_endian.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+/*!
+ @header
+
+ Alignment indexing. Before indexing, BAM must be sorted based on the
+ leftmost coordinate of alignments. In indexing, BAM uses two indices:
+ a UCSC binning index and a simple linear index. The binning index is
+ efficient for alignments spanning long distance, while the auxiliary
+ linear index helps to reduce unnecessary seek calls especially for
+ short alignments.
+
+ The UCSC binning scheme was suggested by Richard Durbin and Lincoln
+ Stein and is explained by Kent et al. (2002). In this scheme, each bin
+ represents a contiguous genomic region which can be fully contained in
+ another bin; each alignment is associated with a bin which represents
+ the smallest region containing the entire alignment. The binning
+ scheme is essentially another representation of R-tree. A distinct bin
+ uniquely corresponds to a distinct internal node in a R-tree. Bin A is
+ a child of Bin B if region A is contained in B.
+
+ In BAM, each bin may span 2^29, 2^26, 2^23, 2^20, 2^17 or 2^14 bp. Bin
+ 0 spans a 512Mbp region, bins 1-8 span 64Mbp, 9-72 8Mbp, 73-584 1Mbp,
+ 585-4680 128Kbp and bins 4681-37449 span 16Kbp regions. If we want to
+ find the alignments overlapped with a region [rbeg,rend), we need to
+ calculate the list of bins that may be overlapped the region and test
+ the alignments in the bins to confirm the overlaps. If the specified
+ region is short, typically only a few alignments in six bins need to
+ be retrieved. The overlapping alignments can be quickly fetched.
+
+ */
+
+#define BAM_MIN_CHUNK_GAP 32768
+// 1<<14 is the size of minimum bin.
+#define BAM_LIDX_SHIFT 14
+
+#define BAM_MAX_BIN 37450 // =(8^6-1)/7+1
+
+typedef struct {
+ uint64_t u, v;
+} pair64_t;
+
+#define pair64_lt(a,b) ((a).u < (b).u)
+KSORT_INIT(off, pair64_t, pair64_lt)
+
+typedef struct {
+ uint32_t m, n;
+ pair64_t *list;
+} bam_binlist_t;
+
+typedef struct {
+ int32_t n, m;
+ uint64_t *offset;
+} bam_lidx_t;
+
+KHASH_MAP_INIT_INT(i, bam_binlist_t)
+
+struct __bam_index_t {
+ int32_t n;
+ uint64_t n_no_coor; // unmapped reads without coordinate
+ khash_t(i) **index;
+ bam_lidx_t *index2;
+};
+
+// requirement: len <= LEN_MASK
+static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
+{
+ khint_t k;
+ bam_binlist_t *l;
+ int ret;
+ k = kh_put(i, h, bin, &ret);
+ l = &kh_value(h, k);
+ if (ret) { // not present
+ l->m = 1; l->n = 0;
+ l->list = (pair64_t*)calloc(l->m, 16);
+ }
+ if (l->n == l->m) {
+ l->m <<= 1;
+ l->list = (pair64_t*)realloc(l->list, l->m * 16);
+ }
+ l->list[l->n].u = beg; l->list[l->n++].v = end;
+}
+
+static inline void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset)
+{
+ int i, beg, end;
+ beg = b->core.pos >> BAM_LIDX_SHIFT;
+ end = (bam_calend(&b->core, bam1_cigar(b)) - 1) >> BAM_LIDX_SHIFT;
+ if (index2->m < end + 1) {
+ int old_m = index2->m;
+ index2->m = end + 1;
+ kroundup32(index2->m);
+ index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
+ memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
+ }
+ if (beg == end) {
+ if (index2->offset[beg] == 0) index2->offset[beg] = offset;
+ } else {
+ for (i = beg; i <= end; ++i)
+ if (index2->offset[i] == 0) index2->offset[i] = offset;
+ }
+ index2->n = end + 1;
+}
+
+static void merge_chunks(bam_index_t *idx)
+{
+#if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
+ khash_t(i) *index;
+ int i, l, m;
+ khint_t k;
+ for (i = 0; i < idx->n; ++i) {
+ index = idx->index[i];
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ bam_binlist_t *p;
+ if (!kh_exist(index, k) || kh_key(index, k) == BAM_MAX_BIN) continue;
+ p = &kh_value(index, k);
+ m = 0;
+ for (l = 1; l < p->n; ++l) {
+#ifdef BAM_TRUE_OFFSET
+ if (p->list[m].v + BAM_MIN_CHUNK_GAP > p->list[l].u) p->list[m].v = p->list[l].v;
+#else
+ if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
+#endif
+ else p->list[++m] = p->list[l];
+ } // ~for(l)
+ p->n = m + 1;
+ } // ~for(k)
+ } // ~for(i)
+#endif // defined(BAM_TRUE_OFFSET) || defined(BAM_BGZF)
+}
+
+static void fill_missing(bam_index_t *idx)
+{
+ int i, j;
+ for (i = 0; i < idx->n; ++i) {
+ bam_lidx_t *idx2 = &idx->index2[i];
+ for (j = 1; j < idx2->n; ++j)
+ if (idx2->offset[j] == 0)
+ idx2->offset[j] = idx2->offset[j-1];
+ }
+}
+
+bam_index_t *bam_index_core(bamFile fp)
+{
+ bam1_t *b;
+ bam_header_t *h;
+ int i, ret;
+ bam_index_t *idx;
+ uint32_t last_bin, save_bin;
+ int32_t last_coor, last_tid, save_tid;
+ bam1_core_t *c;
+ uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
+
+ idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
+ b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ h = bam_header_read(fp);
+ c = &b->core;
+
+ idx->n = h->n_targets;
+ bam_header_destroy(h);
+ idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
+ for (i = 0; i < idx->n; ++i) idx->index[i] = kh_init(i);
+ idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
+
+ save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
+ save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
+ n_mapped = n_unmapped = n_no_coor = off_end = 0;
+ off_beg = off_end = bam_tell(fp);
+ while ((ret = bam_read1(fp, b)) >= 0) {
+ if (c->tid < 0) ++n_no_coor;
+ if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
+ last_tid = c->tid;
+ last_bin = 0xffffffffu;
+ } else if ((uint32_t)last_tid > (uint32_t)c->tid) {
+ fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
+ bam1_qname(b), last_tid+1, c->tid+1);
+ return NULL;
+ } else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
+ fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
+ bam1_qname(b), last_coor, c->pos, c->tid+1);
+ return NULL;
+ }
+ if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+ if (c->bin != last_bin) { // then possibly write the binning index
+ if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
+ insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
+ if (last_bin == 0xffffffffu && save_tid != 0xffffffffu) { // write the meta element
+ off_end = last_off;
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end);
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
+ n_mapped = n_unmapped = 0;
+ off_beg = off_end;
+ }
+ save_off = last_off;
+ save_bin = last_bin = c->bin;
+ save_tid = c->tid;
+ if (save_tid < 0) break;
+ }
+ if (bam_tell(fp) <= last_off) {
+ fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
+ (unsigned long long)bam_tell(fp), (unsigned long long)last_off);
+ return NULL;
+ }
+ if (c->flag & BAM_FUNMAP) ++n_unmapped;
+ else ++n_mapped;
+ last_off = bam_tell(fp);
+ last_coor = b->core.pos;
+ }
+ if (save_tid >= 0) {
+ insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
+ }
+ merge_chunks(idx);
+ fill_missing(idx);
+ if (ret >= 0) {
+ while ((ret = bam_read1(fp, b)) >= 0) {
+ ++n_no_coor;
+ if (c->tid >= 0 && n_no_coor) {
+ fprintf(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+ return NULL;
+ }
+ }
+ }
+ if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
+ free(b->data); free(b);
+ idx->n_no_coor = n_no_coor;
+ return idx;
+}
+
+void bam_index_destroy(bam_index_t *idx)
+{
+ khint_t k;
+ int i;
+ if (idx == 0) return;
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index = idx->index[i];
+ bam_lidx_t *index2 = idx->index2 + i;
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ if (kh_exist(index, k))
+ free(kh_value(index, k).list);
+ }
+ kh_destroy(i, index);
+ free(index2->offset);
+ }
+ free(idx->index); free(idx->index2);
+ free(idx);
+}
+
+void bam_index_save(const bam_index_t *idx, FILE *fp)
+{
+ int32_t i, size;
+ khint_t k;
+ fwrite("BAI\1", 1, 4, fp);
+ if (bam_is_be) {
+ uint32_t x = idx->n;
+ fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ } else fwrite(&idx->n, 4, 1, fp);
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index = idx->index[i];
+ bam_lidx_t *index2 = idx->index2 + i;
+ // write binning index
+ size = kh_size(index);
+ if (bam_is_be) { // big endian
+ uint32_t x = size;
+ fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ } else fwrite(&size, 4, 1, fp);
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ if (kh_exist(index, k)) {
+ bam_binlist_t *p = &kh_value(index, k);
+ if (bam_is_be) { // big endian
+ uint32_t x;
+ x = kh_key(index, k); fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ x = p->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ for (x = 0; (int)x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ fwrite(p->list, 16, p->n, fp);
+ for (x = 0; (int)x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ } else {
+ fwrite(&kh_key(index, k), 4, 1, fp);
+ fwrite(&p->n, 4, 1, fp);
+ fwrite(p->list, 16, p->n, fp);
+ }
+ }
+ }
+ // write linear index (index2)
+ if (bam_is_be) {
+ int x = index2->n;
+ fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ } else fwrite(&index2->n, 4, 1, fp);
+ if (bam_is_be) { // big endian
+ int x;
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ fwrite(index2->offset, 8, index2->n, fp);
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ } else fwrite(index2->offset, 8, index2->n, fp);
+ }
+ { // write the number of reads coor-less records.
+ uint64_t x = idx->n_no_coor;
+ if (bam_is_be) bam_swap_endian_8p(&x);
+ fwrite(&x, 8, 1, fp);
+ }
+ fflush(fp);
+}
+
+static bam_index_t *bam_index_load_core(FILE *fp)
+{
+ int i;
+ char magic[4];
+ bam_index_t *idx;
+ if (fp == 0) {
+ fprintf(stderr, "[bam_index_load_core] fail to load index.\n");
+ return 0;
+ }
+ fread(magic, 1, 4, fp);
+ if (strncmp(magic, "BAI\1", 4)) {
+ fprintf(stderr, "[bam_index_load] wrong magic number.\n");
+ fclose(fp);
+ return 0;
+ }
+ idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
+ fread(&idx->n, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&idx->n);
+ idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
+ idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index;
+ bam_lidx_t *index2 = idx->index2 + i;
+ uint32_t key, size;
+ khint_t k;
+ int j, ret;
+ bam_binlist_t *p;
+ index = idx->index[i] = kh_init(i);
+ // load binning index
+ fread(&size, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&size);
+ for (j = 0; j < (int)size; ++j) {
+ fread(&key, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&key);
+ k = kh_put(i, index, key, &ret);
+ p = &kh_value(index, k);
+ fread(&p->n, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&p->n);
+ p->m = p->n;
+ p->list = (pair64_t*)malloc(p->m * 16);
+ fread(p->list, 16, p->n, fp);
+ if (bam_is_be) {
+ int x;
+ for (x = 0; x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ }
+ }
+ // load linear index
+ fread(&index2->n, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&index2->n);
+ index2->m = index2->n;
+ index2->offset = (uint64_t*)calloc(index2->m, 8);
+ fread(index2->offset, index2->n, 8, fp);
+ if (bam_is_be)
+ for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
+ }
+ if (fread(&idx->n_no_coor, 8, 1, fp) == 0) idx->n_no_coor = 0;
+ if (bam_is_be) bam_swap_endian_8p(&idx->n_no_coor);
+ return idx;
+}
+
+bam_index_t *bam_index_load_local(const char *_fn)
+{
+ FILE *fp;
+ char *fnidx, *fn;
+
+ if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) {
+ const char *p;
+ int l = strlen(_fn);
+ for (p = _fn + l - 1; p >= _fn; --p)
+ if (*p == '/') break;
+ fn = strdup(p + 1);
+ } else fn = strdup(_fn);
+ fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcpy(fnidx, fn); strcat(fnidx, ".bai");
+ fp = fopen(fnidx, "rb");
+ if (fp == 0) { // try "{base}.bai"
+ char *s = strstr(fn, "bam");
+ if (s == fn + strlen(fn) - 3) {
+ strcpy(fnidx, fn);
+ fnidx[strlen(fn)-1] = 'i';
+ fp = fopen(fnidx, "rb");
+ }
+ }
+ free(fnidx); free(fn);
+ if (fp) {
+ bam_index_t *idx = bam_index_load_core(fp);
+ fclose(fp);
+ return idx;
+ } else return 0;
+}
+
+#ifdef _USE_KNETFILE
+static void download_from_remote(const char *url)
+{
+ const int buf_size = 1 * 1024 * 1024;
+ char *fn;
+ FILE *fp;
+ uint8_t *buf;
+ knetFile *fp_remote;
+ int l;
+ if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
+ l = strlen(url);
+ for (fn = (char*)url + l - 1; fn >= url; --fn)
+ if (*fn == '/') break;
+ ++fn; // fn now points to the file name
+ fp_remote = knet_open(url, "r");
+ if (fp_remote == 0) {
+ fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
+ return;
+ }
+ if ((fp = fopen(fn, "wb")) == 0) {
+ fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
+ knet_close(fp_remote);
+ return;
+ }
+ buf = (uint8_t*)calloc(buf_size, 1);
+ while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+ fwrite(buf, 1, l, fp);
+ free(buf);
+ fclose(fp);
+ knet_close(fp_remote);
+}
+#else
+static void download_from_remote(const char *url)
+{
+ return;
+}
+#endif
+
+bam_index_t *bam_index_load(const char *fn)
+{
+ bam_index_t *idx;
+ idx = bam_index_load_local(fn);
+ if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
+ char *fnidx = calloc(strlen(fn) + 5, 1);
+ strcat(strcpy(fnidx, fn), ".bai");
+ fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
+ download_from_remote(fnidx);
+ idx = bam_index_load_local(fn);
+ }
+ if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
+ return idx;
+}
+
+int bam_index_build2(const char *fn, const char *_fnidx)
+{
+ char *fnidx;
+ FILE *fpidx;
+ bamFile fp;
+ bam_index_t *idx;
+ if ((fp = bam_open(fn, "r")) == 0) {
+ fprintf(stderr, "[bam_index_build2] fail to open the BAM file.\n");
+ return -1;
+ }
+ idx = bam_index_core(fp);
+ bam_close(fp);
+ if(idx == 0) {
+ fprintf(stderr, "[bam_index_build2] fail to index the BAM file.\n");
+ return -1;
+ }
+ if (_fnidx == 0) {
+ fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcpy(fnidx, fn); strcat(fnidx, ".bai");
+ } else fnidx = strdup(_fnidx);
+ fpidx = fopen(fnidx, "wb");
+ if (fpidx == 0) {
+ fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
+ free(fnidx);
+ return -1;
+ }
+ bam_index_save(idx, fpidx);
+ bam_index_destroy(idx);
+ fclose(fpidx);
+ free(fnidx);
+ return 0;
+}
+
+int bam_index_build(const char *fn)
+{
+ return bam_index_build2(fn, 0);
+}
+
+int bam_index(int argc, char *argv[])
+{
+ if (argc < 2) {
+ fprintf(stderr, "Usage: samtools index <in.bam> [out.index]\n");
+ return 1;
+ }
+ if (argc >= 3) bam_index_build2(argv[1], argv[2]);
+ else bam_index_build(argv[1]);
+ return 0;
+}
+
+int bam_idxstats(int argc, char *argv[])
+{
+ bam_index_t *idx;
+ bam_header_t *header;
+ bamFile fp;
+ int i;
+ if (argc < 2) {
+ fprintf(stderr, "Usage: samtools idxstats <in.bam>\n");
+ return 1;
+ }
+ fp = bam_open(argv[1], "r");
+ if (fp == 0) { fprintf(stderr, "[%s] fail to open BAM.\n", __func__); return 1; }
+ header = bam_header_read(fp);
+ bam_close(fp);
+ idx = bam_index_load(argv[1]);
+ if (idx == 0) { fprintf(stderr, "[%s] fail to load the index.\n", __func__); return 1; }
+ for (i = 0; i < idx->n; ++i) {
+ khint_t k;
+ khash_t(i) *h = idx->index[i];
+ printf("%s\t%d", header->target_name[i], header->target_len[i]);
+ k = kh_get(i, h, BAM_MAX_BIN);
+ if (k != kh_end(h))
+ printf("\t%llu\t%llu", (long long)kh_val(h, k).list[1].u, (long long)kh_val(h, k).list[1].v);
+ else printf("\t0\t0");
+ putchar('\n');
+ }
+ printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor);
+ bam_header_destroy(header);
+ bam_index_destroy(idx);
+ return 0;
+}
+
+static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[BAM_MAX_BIN])
+{
+ int i = 0, k;
+ if (beg >= end) return 0;
+ if (end >= 1u<<29) end = 1u<<29;
+ --end;
+ list[i++] = 0;
+ for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
+ for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
+ for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
+ for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
+ for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
+ return i;
+}
+
+static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
+{
+ uint32_t rbeg = b->core.pos;
+ uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
+ return (rend > beg && rbeg < end);
+}
+
+struct __bam_iter_t {
+ int from_first; // read from the first record; no random access
+ int tid, beg, end, n_off, i, finished;
+ uint64_t curr_off;
+ pair64_t *off;
+};
+
+// bam_fetch helper function retrieves
+bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
+{
+ uint16_t *bins;
+ int i, n_bins, n_off;
+ pair64_t *off;
+ khint_t k;
+ khash_t(i) *index;
+ uint64_t min_off;
+ bam_iter_t iter = 0;
+
+ if (beg < 0) beg = 0;
+ if (end < beg) return 0;
+ // initialize iter
+ iter = calloc(1, sizeof(struct __bam_iter_t));
+ iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
+ //
+ bins = (uint16_t*)calloc(BAM_MAX_BIN, 2);
+ n_bins = reg2bins(beg, end, bins);
+ index = idx->index[tid];
+ if (idx->index2[tid].n > 0) {
+ min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
+ : idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT];
+ if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
+ int n = beg>>BAM_LIDX_SHIFT;
+ if (n > idx->index2[tid].n) n = idx->index2[tid].n;
+ for (i = n - 1; i >= 0; --i)
+ if (idx->index2[tid].offset[i] != 0) break;
+ if (i >= 0) min_off = idx->index2[tid].offset[i];
+ }
+ } else min_off = 0; // tabix 0.1.2 may produce such index files
+ for (i = n_off = 0; i < n_bins; ++i) {
+ if ((k = kh_get(i, index, bins[i])) != kh_end(index))
+ n_off += kh_value(index, k).n;
+ }
+ if (n_off == 0) {
+ free(bins); return iter;
+ }
+ off = (pair64_t*)calloc(n_off, 16);
+ for (i = n_off = 0; i < n_bins; ++i) {
+ if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
+ int j;
+ bam_binlist_t *p = &kh_value(index, k);
+ for (j = 0; j < p->n; ++j)
+ if (p->list[j].v > min_off) off[n_off++] = p->list[j];
+ }
+ }
+ free(bins);
+ if (n_off == 0) {
+ free(off); return iter;
+ }
+ {
+ bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ int l;
+ ks_introsort(off, n_off, off);
+ // resolve completely contained adjacent blocks
+ for (i = 1, l = 0; i < n_off; ++i)
+ if (off[l].v < off[i].v)
+ off[++l] = off[i];
+ n_off = l + 1;
+ // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
+ for (i = 1; i < n_off; ++i)
+ if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
+ { // merge adjacent blocks
+#if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
+ for (i = 1, l = 0; i < n_off; ++i) {
+#ifdef BAM_TRUE_OFFSET
+ if (off[l].v + BAM_MIN_CHUNK_GAP > off[i].u) off[l].v = off[i].v;
+#else
+ if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
+#endif
+ else off[++l] = off[i];
+ }
+ n_off = l + 1;
+#endif
+ }
+ bam_destroy1(b);
+ }
+ iter->n_off = n_off; iter->off = off;
+ return iter;
+}
+
+pair64_t *get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int *cnt_off)
+{ // for pysam compatibility
+ bam_iter_t iter;
+ pair64_t *off;
+ iter = bam_iter_query(idx, tid, beg, end);
+ off = iter->off; *cnt_off = iter->n_off;
+ free(iter);
+ return off;
+}
+
+void bam_iter_destroy(bam_iter_t iter)
+{
+ if (iter) { free(iter->off); free(iter); }
+}
+
+int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
+{
+ int ret;
+ if (iter && iter->finished) return -1;
+ if (iter == 0 || iter->from_first) {
+ ret = bam_read1(fp, b);
+ if (ret < 0 && iter) iter->finished = 1;
+ return ret;
+ }
+ if (iter->off == 0) return -1;
+ for (;;) {
+ if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
+ if (iter->i == iter->n_off - 1) { ret = -1; break; } // no more chunks
+ if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
+ if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
+ bam_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
+ iter->curr_off = bam_tell(fp);
+ }
+ ++iter->i;
+ }
+ if ((ret = bam_read1(fp, b)) >= 0) {
+ iter->curr_off = bam_tell(fp);
+ if (b->core.tid != iter->tid || b->core.pos >= iter->end) { // no need to proceed
+ ret = bam_validate1(NULL, b)? -1 : -5; // determine whether end of region or error
+ break;
+ }
+ else if (is_overlap(iter->beg, iter->end, b)) return ret;
+ } else break; // end of file or error
+ }
+ iter->finished = 1;
+ return ret;
+}
+
+int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+{
+ int ret;
+ bam_iter_t iter;
+ bam1_t *b;
+ b = bam_init1();
+ iter = bam_iter_query(idx, tid, beg, end);
+ while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+ bam_iter_destroy(iter);
+ bam_destroy1(b);
+ return (ret == -1)? 0 : ret;
+}
diff --git a/src/samtools-0.1.18/bam_lpileup.c b/src/samtools-0.1.18/bam_lpileup.c
new file mode 100644
index 0000000..d4dd63b
--- /dev/null
+++ b/src/samtools-0.1.18/bam_lpileup.c
@@ -0,0 +1,198 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+#include "bam.h"
+#include "ksort.h"
+
+#define TV_GAP 2
+
+typedef struct __freenode_t {
+ uint32_t level:28, cnt:4;
+ struct __freenode_t *next;
+} freenode_t, *freenode_p;
+
+#define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level))
+KSORT_INIT(node, freenode_p, freenode_lt)
+
+/* Memory pool, similar to the one in bam_pileup.c */
+typedef struct {
+ int cnt, n, max;
+ freenode_t **buf;
+} mempool_t;
+
+static mempool_t *mp_init()
+{
+ return (mempool_t*)calloc(1, sizeof(mempool_t));
+}
+static void mp_destroy(mempool_t *mp)
+{
+ int k;
+ for (k = 0; k < mp->n; ++k) free(mp->buf[k]);
+ free(mp->buf); free(mp);
+}
+static inline freenode_t *mp_alloc(mempool_t *mp)
+{
+ ++mp->cnt;
+ if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t));
+ else return mp->buf[--mp->n];
+}
+static inline void mp_free(mempool_t *mp, freenode_t *p)
+{
+ --mp->cnt; p->next = 0; p->cnt = TV_GAP;
+ if (mp->n == mp->max) {
+ mp->max = mp->max? mp->max<<1 : 256;
+ mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max);
+ }
+ mp->buf[mp->n++] = p;
+}
+
+/* core part */
+struct __bam_lplbuf_t {
+ int max, n_cur, n_pre;
+ int max_level, *cur_level, *pre_level;
+ mempool_t *mp;
+ freenode_t **aux, *head, *tail;
+ int n_nodes, m_aux;
+ bam_pileup_f func;
+ void *user_data;
+ bam_plbuf_t *plbuf;
+};
+
+void bam_lplbuf_reset(bam_lplbuf_t *buf)
+{
+ freenode_t *p, *q;
+ bam_plbuf_reset(buf->plbuf);
+ for (p = buf->head; p->next;) {
+ q = p->next;
+ mp_free(buf->mp, p);
+ p = q;
+ }
+ buf->head = buf->tail;
+ buf->max_level = 0;
+ buf->n_cur = buf->n_pre = 0;
+ buf->n_nodes = 0;
+}
+
+static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
+{
+ bam_lplbuf_t *tv = (bam_lplbuf_t*)data;
+ freenode_t *p;
+ int i, l, max_level;
+ // allocate memory if necessary
+ if (tv->max < n) { // enlarge
+ tv->max = n;
+ kroundup32(tv->max);
+ tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max);
+ tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max);
+ }
+ tv->n_cur = n;
+ // update cnt
+ for (p = tv->head; p->next; p = p->next)
+ if (p->cnt > 0) --p->cnt;
+ // calculate cur_level[]
+ max_level = 0;
+ for (i = l = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (p->is_head) {
+ if (tv->head->next && tv->head->cnt == 0) { // then take a free slot
+ freenode_t *p = tv->head->next;
+ tv->cur_level[i] = tv->head->level;
+ mp_free(tv->mp, tv->head);
+ tv->head = p;
+ --tv->n_nodes;
+ } else tv->cur_level[i] = ++tv->max_level;
+ } else {
+ tv->cur_level[i] = tv->pre_level[l++];
+ if (p->is_tail) { // then return a free slot
+ tv->tail->level = tv->cur_level[i];
+ tv->tail->next = mp_alloc(tv->mp);
+ tv->tail = tv->tail->next;
+ ++tv->n_nodes;
+ }
+ }
+ if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i];
+ ((bam_pileup1_t*)p)->level = tv->cur_level[i];
+ }
+ assert(l == tv->n_pre);
+ tv->func(tid, pos, n, pl, tv->user_data);
+ // sort the linked list
+ if (tv->n_nodes) {
+ freenode_t *q;
+ if (tv->n_nodes + 1 > tv->m_aux) { // enlarge
+ tv->m_aux = tv->n_nodes + 1;
+ kroundup32(tv->m_aux);
+ tv->aux = (freenode_t**)realloc(tv->aux, sizeof(void*) * tv->m_aux);
+ }
+ for (p = tv->head, i = l = 0; p->next;) {
+ if (p->level > max_level) { // then discard this entry
+ q = p->next;
+ mp_free(tv->mp, p);
+ p = q;
+ } else {
+ tv->aux[i++] = p;
+ p = p->next;
+ }
+ }
+ tv->aux[i] = tv->tail; // add a proper tail for the loop below
+ tv->n_nodes = i;
+ if (tv->n_nodes) {
+ ks_introsort(node, tv->n_nodes, tv->aux);
+ for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1];
+ tv->head = tv->aux[0];
+ } else tv->head = tv->tail;
+ }
+ // clean up
+ tv->max_level = max_level;
+ memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4);
+ // squeeze out terminated levels
+ for (i = l = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (!p->is_tail)
+ tv->pre_level[l++] = tv->pre_level[i];
+ }
+ tv->n_pre = l;
+/*
+ fprintf(stderr, "%d\t", pos+1);
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (p->is_head) fprintf(stderr, "^");
+ if (p->is_tail) fprintf(stderr, "$");
+ fprintf(stderr, "%d,", p->level);
+ }
+ fprintf(stderr, "\n");
+*/
+ return 0;
+}
+
+bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data)
+{
+ bam_lplbuf_t *tv;
+ tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t));
+ tv->mp = mp_init();
+ tv->head = tv->tail = mp_alloc(tv->mp);
+ tv->func = func;
+ tv->user_data = data;
+ tv->plbuf = bam_plbuf_init(tview_func, tv);
+ return (bam_lplbuf_t*)tv;
+}
+
+void bam_lplbuf_destroy(bam_lplbuf_t *tv)
+{
+ freenode_t *p, *q;
+ free(tv->cur_level); free(tv->pre_level);
+ bam_plbuf_destroy(tv->plbuf);
+ free(tv->aux);
+ for (p = tv->head; p->next;) {
+ q = p->next;
+ mp_free(tv->mp, p); p = q;
+ }
+ mp_free(tv->mp, p);
+ assert(tv->mp->cnt == 0);
+ mp_destroy(tv->mp);
+ free(tv);
+}
+
+int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv)
+{
+ return bam_plbuf_push(b, tv->plbuf);
+}
diff --git a/src/samtools-0.1.18/bam_mate.c b/src/samtools-0.1.18/bam_mate.c
new file mode 100644
index 0000000..61f808a
--- /dev/null
+++ b/src/samtools-0.1.18/bam_mate.c
@@ -0,0 +1,70 @@
+#include <stdlib.h>
+#include <string.h>
+#include "bam.h"
+
+// currently, this function ONLY works if each read has one hit
+void bam_mating_core(bamFile in, bamFile out)
+{
+ bam_header_t *header;
+ bam1_t *b[2];
+ int curr, has_prev;
+
+ header = bam_header_read(in);
+ bam_header_write(out, header);
+
+ b[0] = bam_init1();
+ b[1] = bam_init1();
+ curr = 0; has_prev = 0;
+ while (bam_read1(in, b[curr]) >= 0) {
+ bam1_t *cur = b[curr], *pre = b[1-curr];
+ if (has_prev) {
+ if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
+ cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
+ pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
+ if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
+ && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
+ {
+ uint32_t cur5, pre5;
+ cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
+ pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
+ cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
+ } else cur->core.isize = pre->core.isize = 0;
+ if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
+ else cur->core.flag &= ~BAM_FMREVERSE;
+ if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
+ else pre->core.flag &= ~BAM_FMREVERSE;
+ if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
+ if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
+ bam_write1(out, pre);
+ bam_write1(out, cur);
+ has_prev = 0;
+ } else { // unpaired or singleton
+ pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
+ if (pre->core.flag & BAM_FPAIRED) {
+ pre->core.flag |= BAM_FMUNMAP;
+ pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
+ }
+ bam_write1(out, pre);
+ }
+ } else has_prev = 1;
+ curr = 1 - curr;
+ }
+ if (has_prev) bam_write1(out, b[1-curr]);
+ bam_header_destroy(header);
+ bam_destroy1(b[0]);
+ bam_destroy1(b[1]);
+}
+
+int bam_mating(int argc, char *argv[])
+{
+ bamFile in, out;
+ if (argc < 3) {
+ fprintf(stderr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
+ return 1;
+ }
+ in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
+ out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
+ bam_mating_core(in, out);
+ bam_close(in); bam_close(out);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam_md.c b/src/samtools-0.1.18/bam_md.c
new file mode 100644
index 0000000..d42aa8f
--- /dev/null
+++ b/src/samtools-0.1.18/bam_md.c
@@ -0,0 +1,384 @@
+#include <unistd.h>
+#include <assert.h>
+#include <string.h>
+#include <ctype.h>
+#include <math.h>
+#include "faidx.h"
+#include "sam.h"
+#include "kstring.h"
+#include "kaln.h"
+#include "kprobaln.h"
+
+#define USE_EQUAL 1
+#define DROP_TAG 2
+#define BIN_QUAL 4
+#define UPDATE_NM 8
+#define UPDATE_MD 16
+#define HASH_QNM 32
+
+char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+
+int bam_aux_drop_other(bam1_t *b, uint8_t *s);
+
+void bam_fillmd1_core(bam1_t *b, char *ref, int flag, int max_nm)
+{
+ uint8_t *seq = bam1_seq(b);
+ uint32_t *cigar = bam1_cigar(b);
+ bam1_core_t *c = &b->core;
+ int i, x, y, u = 0;
+ kstring_t *str;
+ int32_t old_nm_i = -1, nm = 0;
+
+ str = (kstring_t*)calloc(1, sizeof(kstring_t));
+ for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
+ int j, l = cigar[i]>>4, op = cigar[i]&0xf;
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ for (j = 0; j < l; ++j) {
+ int z = y + j;
+ int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
+ if (ref[x+j] == 0) break; // out of boundary
+ if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
+ if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
+ ++u;
+ } else {
+ kputw(u, str); kputc(ref[x+j], str);
+ u = 0; ++nm;
+ }
+ }
+ if (j < l) break;
+ x += l; y += l;
+ } else if (op == BAM_CDEL) {
+ kputw(u, str); kputc('^', str);
+ for (j = 0; j < l; ++j) {
+ if (ref[x+j] == 0) break;
+ kputc(ref[x+j], str);
+ }
+ u = 0;
+ if (j < l) break;
+ x += l; nm += l;
+ } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
+ y += l;
+ if (op == BAM_CINS) nm += l;
+ } else if (op == BAM_CREF_SKIP) {
+ x += l;
+ }
+ }
+ kputw(u, str);
+ // apply max_nm
+ if (max_nm > 0 && nm >= max_nm) {
+ for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
+ int j, l = cigar[i]>>4, op = cigar[i]&0xf;
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ for (j = 0; j < l; ++j) {
+ int z = y + j;
+ int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
+ if (ref[x+j] == 0) break; // out of boundary
+ if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
+ seq[z/2] |= (z&1)? 0x0f : 0xf0;
+ bam1_qual(b)[z] = 0;
+ }
+ }
+ if (j < l) break;
+ x += l; y += l;
+ } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
+ else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+ }
+ }
+ // update NM
+ if (flag & UPDATE_NM) {
+ uint8_t *old_nm = bam_aux_get(b, "NM");
+ if (c->flag & BAM_FUNMAP) return;
+ if (old_nm) old_nm_i = bam_aux2i(old_nm);
+ if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
+ else if (nm != old_nm_i) {
+ fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
+ bam_aux_del(b, old_nm);
+ bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
+ }
+ }
+ // update MD
+ if (flag & UPDATE_MD) {
+ uint8_t *old_md = bam_aux_get(b, "MD");
+ if (c->flag & BAM_FUNMAP) return;
+ if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
+ else {
+ int is_diff = 0;
+ if (strlen((char*)old_md+1) == str->l) {
+ for (i = 0; i < str->l; ++i)
+ if (toupper(old_md[i+1]) != toupper(str->s[i]))
+ break;
+ if (i < str->l) is_diff = 1;
+ } else is_diff = 1;
+ if (is_diff) {
+ fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
+ bam_aux_del(b, old_md);
+ bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
+ }
+ }
+ }
+ // drop all tags but RG
+ if (flag&DROP_TAG) {
+ uint8_t *q = bam_aux_get(b, "RG");
+ bam_aux_drop_other(b, q);
+ }
+ // reduce the resolution of base quality
+ if (flag&BIN_QUAL) {
+ uint8_t *qual = bam1_qual(b);
+ for (i = 0; i < b->core.l_qseq; ++i)
+ if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7;
+ }
+ free(str->s); free(str);
+}
+
+void bam_fillmd1(bam1_t *b, char *ref, int flag)
+{
+ bam_fillmd1_core(b, ref, flag, 0);
+}
+
+int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
+{
+ uint8_t *seq = bam1_seq(b), *qual = bam1_qual(b);
+ uint32_t *cigar = bam1_cigar(b);
+ bam1_core_t *c = &b->core;
+ int i, x, y, mm, q, len, clip_l, clip_q;
+ double t;
+ if (thres < 0) thres = 40; // set the default
+ mm = q = len = clip_l = clip_q = 0;
+ for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
+ int j, l = cigar[i]>>4, op = cigar[i]&0xf;
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ for (j = 0; j < l; ++j) {
+ int z = y + j;
+ int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
+ if (ref[x+j] == 0) break; // out of boundary
+ if (c2 != 15 && c1 != 15 && qual[z] >= 13) { // not ambiguous
+ ++len;
+ if (c1 && c1 != c2 && qual[z] >= 13) { // mismatch
+ ++mm;
+ q += qual[z] > 33? 33 : qual[z];
+ }
+ }
+ }
+ if (j < l) break;
+ x += l; y += l; len += l;
+ } else if (op == BAM_CDEL) {
+ for (j = 0; j < l; ++j)
+ if (ref[x+j] == 0) break;
+ if (j < l) break;
+ x += l;
+ } else if (op == BAM_CSOFT_CLIP) {
+ for (j = 0; j < l; ++j) clip_q += qual[y+j];
+ clip_l += l;
+ y += l;
+ } else if (op == BAM_CHARD_CLIP) {
+ clip_q += 13 * l;
+ clip_l += l;
+ } else if (op == BAM_CINS) y += l;
+ else if (op == BAM_CREF_SKIP) x += l;
+ }
+ for (i = 0, t = 1; i < mm; ++i)
+ t *= (double)len / (i+1);
+ t = q - 4.343 * log(t) + clip_q / 5.;
+ if (t > thres) return -1;
+ if (t < 0) t = 0;
+ t = sqrt((thres - t) / thres) * thres;
+// fprintf(stderr, "%s %lf %d\n", bam1_qname(b), t, q);
+ return (int)(t + .499);
+}
+
+int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
+{
+ int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1;
+ uint32_t *cigar = bam1_cigar(b);
+ bam1_core_t *c = &b->core;
+ kpa_par_t conf = kpa_par_def;
+ uint8_t *bq = 0, *zq = 0, *qual = bam1_qual(b);
+ if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0) return -1; // do nothing
+ // test if BQ or ZQ is present
+ if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
+ if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
+ if (bq && zq) { // remove the ZQ tag
+ bam_aux_del(b, zq-1);
+ zq = 0;
+ }
+ if (bq || zq) {
+ if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing
+ if (bq && apply_baq) { // then convert BQ to ZQ
+ for (i = 0; i < c->l_qseq; ++i)
+ qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64);
+ *(bq - 3) = 'Z';
+ } else if (zq && !apply_baq) { // then convert ZQ to BQ
+ for (i = 0; i < c->l_qseq; ++i)
+ qual[i] += (int)zq[i] - 64;
+ *(zq - 3) = 'B';
+ }
+ return 0;
+ }
+ // find the start and end of the alignment
+ x = c->pos, y = 0, yb = ye = xb = xe = -1;
+ for (k = 0; k < c->n_cigar; ++k) {
+ int op, l;
+ op = cigar[k]&0xf; l = cigar[k]>>4;
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ if (yb < 0) yb = y;
+ if (xb < 0) xb = x;
+ ye = y + l; xe = x + l;
+ x += l; y += l;
+ } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+ else if (op == BAM_CDEL) x += l;
+ else if (op == BAM_CREF_SKIP) return -1; // do nothing if there is a reference skip
+ }
+ // set bandwidth and the start and the end
+ bw = 7;
+ if (abs((xe - xb) - (ye - yb)) > bw)
+ bw = abs((xe - xb) - (ye - yb)) + 3;
+ conf.bw = bw;
+ xb -= yb + bw/2; if (xb < 0) xb = 0;
+ xe += c->l_qseq - ye + bw/2;
+ if (xe - xb - c->l_qseq > bw)
+ xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2;
+ { // glocal
+ uint8_t *s, *r, *q, *seq = bam1_seq(b), *bq;
+ int *state;
+ bq = calloc(c->l_qseq + 1, 1);
+ memcpy(bq, qual, c->l_qseq);
+ s = calloc(c->l_qseq, 1);
+ for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
+ r = calloc(xe - xb, 1);
+ for (i = xb; i < xe; ++i) {
+ if (ref[i] == 0) { xe = i; break; }
+ r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
+ }
+ state = calloc(c->l_qseq, sizeof(int));
+ q = calloc(c->l_qseq, 1);
+ kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
+ if (!extend_baq) { // in this block, bq[] is capped by base quality qual[]
+ for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
+ int op = cigar[k]&0xf, l = cigar[k]>>4;
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ for (i = y; i < y + l; ++i) {
+ if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
+ else bq[i] = bq[i] < q[i]? bq[i] : q[i];
+ }
+ x += l; y += l;
+ } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+ else if (op == BAM_CDEL) x += l;
+ }
+ for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
+ } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!)
+ uint8_t *left, *rght;
+ left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
+ for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
+ int op = cigar[k]&0xf, l = cigar[k]>>4;
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ for (i = y; i < y + l; ++i)
+ bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i];
+ for (left[y] = bq[y], i = y + 1; i < y + l; ++i)
+ left[i] = bq[i] > left[i-1]? bq[i] : left[i-1];
+ for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i)
+ rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1];
+ for (i = y; i < y + l; ++i)
+ bq[i] = left[i] < rght[i]? left[i] : rght[i];
+ x += l; y += l;
+ } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+ else if (op == BAM_CDEL) x += l;
+ }
+ for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ
+ free(left); free(rght);
+ }
+ if (apply_baq) {
+ for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual
+ bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq);
+ } else bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq);
+ free(bq); free(s); free(r); free(q); free(state);
+ }
+ return 0;
+}
+
+int bam_prob_realn(bam1_t *b, const char *ref)
+{
+ return bam_prob_realn_core(b, ref, 1);
+}
+
+int bam_fillmd(int argc, char *argv[])
+{
+ int c, flt_flag, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag;
+ samfile_t *fp, *fpout = 0;
+ faidx_t *fai;
+ char *ref = 0, mode_w[8], mode_r[8];
+ bam1_t *b;
+
+ flt_flag = UPDATE_NM | UPDATE_MD;
+ is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0;
+ mode_w[0] = mode_r[0] = 0;
+ strcpy(mode_r, "r"); strcpy(mode_w, "w");
+ while ((c = getopt(argc, argv, "EqreuNhbSC:n:Ad")) >= 0) {
+ switch (c) {
+ case 'r': is_realn = 1; break;
+ case 'e': flt_flag |= USE_EQUAL; break;
+ case 'd': flt_flag |= DROP_TAG; break;
+ case 'q': flt_flag |= BIN_QUAL; break;
+ case 'h': flt_flag |= HASH_QNM; break;
+ case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); break;
+ case 'b': is_bam_out = 1; break;
+ case 'u': is_uncompressed = is_bam_out = 1; break;
+ case 'S': is_sam_in = 1; break;
+ case 'n': max_nm = atoi(optarg); break;
+ case 'C': capQ = atoi(optarg); break;
+ case 'A': baq_flag |= 1; break;
+ case 'E': baq_flag |= 2; break;
+ default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
+ }
+ }
+ if (!is_sam_in) strcat(mode_r, "b");
+ if (is_bam_out) strcat(mode_w, "b");
+ else strcat(mode_w, "h");
+ if (is_uncompressed) strcat(mode_w, "u");
+ if (optind + 1 >= argc) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools fillmd [-eubrS] <aln.bam> <ref.fasta>\n\n");
+ fprintf(stderr, "Options: -e change identical bases to '='\n");
+ fprintf(stderr, " -u uncompressed BAM output (for piping)\n");
+ fprintf(stderr, " -b compressed BAM output\n");
+ fprintf(stderr, " -S the input is SAM with header\n");
+ fprintf(stderr, " -A modify the quality string\n");
+ fprintf(stderr, " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n");
+ fprintf(stderr, " -E extended BAQ for better sensitivity but lower specificity\n\n");
+ return 1;
+ }
+ fp = samopen(argv[optind], mode_r, 0);
+ if (fp == 0) return 1;
+ if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) {
+ fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");
+ return 1;
+ }
+ fpout = samopen("-", mode_w, fp->header);
+ fai = fai_load(argv[optind+1]);
+
+ b = bam_init1();
+ while ((ret = samread(fp, b)) >= 0) {
+ if (b->core.tid >= 0) {
+ if (tid != b->core.tid) {
+ free(ref);
+ ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
+ tid = b->core.tid;
+ if (ref == 0)
+ fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
+ fp->header->target_name[tid]);
+ }
+ if (is_realn) bam_prob_realn_core(b, ref, baq_flag);
+ if (capQ > 10) {
+ int q = bam_cap_mapQ(b, ref, capQ);
+ if (b->core.qual > q) b->core.qual = q;
+ }
+ if (ref) bam_fillmd1_core(b, ref, flt_flag, max_nm);
+ }
+ samwrite(fpout, b);
+ }
+ bam_destroy1(b);
+
+ free(ref);
+ fai_destroy(fai);
+ samclose(fp); samclose(fpout);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam_pileup.c b/src/samtools-0.1.18/bam_pileup.c
new file mode 100644
index 0000000..57434e0
--- /dev/null
+++ b/src/samtools-0.1.18/bam_pileup.c
@@ -0,0 +1,437 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <assert.h>
+#include "sam.h"
+
+typedef struct {
+ int k, x, y, end;
+} cstate_t;
+
+static cstate_t g_cstate_null = { -1, 0, 0, 0 };
+
+typedef struct __linkbuf_t {
+ bam1_t b;
+ uint32_t beg, end;
+ cstate_t s;
+ struct __linkbuf_t *next;
+} lbnode_t;
+
+/* --- BEGIN: Memory pool */
+
+typedef struct {
+ int cnt, n, max;
+ lbnode_t **buf;
+} mempool_t;
+
+static mempool_t *mp_init()
+{
+ mempool_t *mp;
+ mp = (mempool_t*)calloc(1, sizeof(mempool_t));
+ return mp;
+}
+static void mp_destroy(mempool_t *mp)
+{
+ int k;
+ for (k = 0; k < mp->n; ++k) {
+ free(mp->buf[k]->b.data);
+ free(mp->buf[k]);
+ }
+ free(mp->buf);
+ free(mp);
+}
+static inline lbnode_t *mp_alloc(mempool_t *mp)
+{
+ ++mp->cnt;
+ if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
+ else return mp->buf[--mp->n];
+}
+static inline void mp_free(mempool_t *mp, lbnode_t *p)
+{
+ --mp->cnt; p->next = 0; // clear lbnode_t::next here
+ if (mp->n == mp->max) {
+ mp->max = mp->max? mp->max<<1 : 256;
+ mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
+ }
+ mp->buf[mp->n++] = p;
+}
+
+/* --- END: Memory pool */
+
+/* --- BEGIN: Auxiliary functions */
+
+/* s->k: the index of the CIGAR operator that has just been processed.
+ s->x: the reference coordinate of the start of s->k
+ s->y: the query coordiante of the start of s->k
+ */
+static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
+{
+#define _cop(c) ((c)&BAM_CIGAR_MASK)
+#define _cln(c) ((c)>>BAM_CIGAR_SHIFT)
+
+ bam1_t *b = p->b;
+ bam1_core_t *c = &b->core;
+ uint32_t *cigar = bam1_cigar(b);
+ int k, is_head = 0;
+ // determine the current CIGAR operation
+// fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam1_qname(b), pos, s->end, s->k, s->x, s->y);
+ if (s->k == -1) { // never processed
+ is_head = 1;
+ if (c->n_cigar == 1) { // just one operation, save a loop
+ if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0;
+ } else { // find the first match or deletion
+ for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
+ int op = _cop(cigar[k]);
+ int l = _cln(cigar[k]);
+ if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break;
+ else if (op == BAM_CREF_SKIP) s->x += l;
+ else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
+ }
+ assert(k < c->n_cigar);
+ s->k = k;
+ }
+ } else { // the read has been processed before
+ int op, l = _cln(cigar[s->k]);
+ if (pos - s->x >= l) { // jump to the next operation
+ assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
+ op = _cop(cigar[s->k+1]);
+ if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop
+ if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
+ s->x += l;
+ ++s->k;
+ } else { // find the next M/D/N/=/X
+ if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
+ s->x += l;
+ for (k = s->k + 1; k < c->n_cigar; ++k) {
+ op = _cop(cigar[k]), l = _cln(cigar[k]);
+ if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break;
+ else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
+ }
+ s->k = k;
+ }
+ assert(s->k < c->n_cigar); // otherwise a bug
+ } // else, do nothing
+ }
+ { // collect pileup information
+ int op, l;
+ op = _cop(cigar[s->k]); l = _cln(cigar[s->k]);
+ p->is_del = p->indel = p->is_refskip = 0;
+ if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
+ int op2 = _cop(cigar[s->k+1]);
+ int l2 = _cln(cigar[s->k+1]);
+ if (op2 == BAM_CDEL) p->indel = -(int)l2;
+ else if (op2 == BAM_CINS) p->indel = l2;
+ else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
+ int l3 = 0;
+ for (k = s->k + 2; k < c->n_cigar; ++k) {
+ op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
+ if (op2 == BAM_CINS) l3 += l2;
+ else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break;
+ }
+ if (l3 > 0) p->indel = l3;
+ }
+ }
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ p->qpos = s->y + (pos - s->x);
+ } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+ p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
+ p->is_refskip = (op == BAM_CREF_SKIP);
+ } // cannot be other operations; otherwise a bug
+ p->is_head = (pos == c->pos); p->is_tail = (pos == s->end);
+ }
+ return 1;
+}
+
+/* --- END: Auxiliary functions */
+
+/*******************
+ * pileup iterator *
+ *******************/
+
+struct __bam_plp_t {
+ mempool_t *mp;
+ lbnode_t *head, *tail, *dummy;
+ int32_t tid, pos, max_tid, max_pos;
+ int is_eof, flag_mask, max_plp, error, maxcnt;
+ bam_pileup1_t *plp;
+ // for the "auto" interface only
+ bam1_t *b;
+ bam_plp_auto_f func;
+ void *data;
+};
+
+bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
+{
+ bam_plp_t iter;
+ iter = calloc(1, sizeof(struct __bam_plp_t));
+ iter->mp = mp_init();
+ iter->head = iter->tail = mp_alloc(iter->mp);
+ iter->dummy = mp_alloc(iter->mp);
+ iter->max_tid = iter->max_pos = -1;
+ iter->flag_mask = BAM_DEF_MASK;
+ iter->maxcnt = 8000;
+ if (func) {
+ iter->func = func;
+ iter->data = data;
+ iter->b = bam_init1();
+ }
+ return iter;
+}
+
+void bam_plp_destroy(bam_plp_t iter)
+{
+ mp_free(iter->mp, iter->dummy);
+ mp_free(iter->mp, iter->head);
+ if (iter->mp->cnt != 0)
+ fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
+ mp_destroy(iter->mp);
+ if (iter->b) bam_destroy1(iter->b);
+ free(iter->plp);
+ free(iter);
+}
+
+const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+{
+ if (iter->error) { *_n_plp = -1; return 0; }
+ *_n_plp = 0;
+ if (iter->is_eof && iter->head->next == 0) return 0;
+ while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
+ int n_plp = 0;
+ lbnode_t *p, *q;
+ // write iter->plp at iter->pos
+ iter->dummy->next = iter->head;
+ for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) {
+ if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
+ q->next = p->next; mp_free(iter->mp, p); p = q;
+ } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
+ if (n_plp == iter->max_plp) { // then double the capacity
+ iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
+ iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
+ }
+ iter->plp[n_plp].b = &p->b;
+ if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true...
+ }
+ }
+ iter->head = iter->dummy->next; // dummy->next may be changed
+ *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
+ // update iter->tid and iter->pos
+ if (iter->head->next) {
+ if (iter->tid > iter->head->b.core.tid) {
+ fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
+ iter->error = 1;
+ *_n_plp = -1;
+ return 0;
+ }
+ }
+ if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
+ iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
+ } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
+ iter->pos = iter->head->beg; // jump to the next position
+ } else ++iter->pos; // scan contiguously
+ // return
+ if (n_plp) return iter->plp;
+ if (iter->is_eof && iter->head->next == 0) break;
+ }
+ return 0;
+}
+
+int bam_plp_push(bam_plp_t iter, const bam1_t *b)
+{
+ if (iter->error) return -1;
+ if (b) {
+ if (b->core.tid < 0) return 0;
+ if (b->core.flag & iter->flag_mask) return 0;
+ if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) return 0;
+ bam_copy1(&iter->tail->b, b);
+ iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
+ iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
+ if (b->core.tid < iter->max_tid) {
+ fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
+ iter->error = 1;
+ return -1;
+ }
+ if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
+ fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
+ iter->error = 1;
+ return -1;
+ }
+ iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
+ if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
+ iter->tail->next = mp_alloc(iter->mp);
+ iter->tail = iter->tail->next;
+ }
+ } else iter->is_eof = 1;
+ return 0;
+}
+
+const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+{
+ const bam_pileup1_t *plp;
+ if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
+ if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+ else { // no pileup line can be obtained; read alignments
+ *_n_plp = 0;
+ if (iter->is_eof) return 0;
+ while (iter->func(iter->data, iter->b) >= 0) {
+ if (bam_plp_push(iter, iter->b) < 0) {
+ *_n_plp = -1;
+ return 0;
+ }
+ if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+ // otherwise no pileup line can be returned; read the next alignment.
+ }
+ bam_plp_push(iter, 0);
+ if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+ return 0;
+ }
+}
+
+void bam_plp_reset(bam_plp_t iter)
+{
+ lbnode_t *p, *q;
+ iter->max_tid = iter->max_pos = -1;
+ iter->tid = iter->pos = 0;
+ iter->is_eof = 0;
+ for (p = iter->head; p->next;) {
+ q = p->next;
+ mp_free(iter->mp, p);
+ p = q;
+ }
+ iter->head = iter->tail;
+}
+
+void bam_plp_set_mask(bam_plp_t iter, int mask)
+{
+ iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
+}
+
+void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
+{
+ iter->maxcnt = maxcnt;
+}
+
+/*****************
+ * callback APIs *
+ *****************/
+
+int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
+{
+ bam_plbuf_t *buf;
+ int ret;
+ bam1_t *b;
+ b = bam_init1();
+ buf = bam_plbuf_init(func, func_data);
+ bam_plbuf_set_mask(buf, mask);
+ while ((ret = bam_read1(fp, b)) >= 0)
+ bam_plbuf_push(b, buf);
+ bam_plbuf_push(0, buf);
+ bam_plbuf_destroy(buf);
+ bam_destroy1(b);
+ return 0;
+}
+
+void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
+{
+ bam_plp_set_mask(buf->iter, mask);
+}
+
+void bam_plbuf_reset(bam_plbuf_t *buf)
+{
+ bam_plp_reset(buf->iter);
+}
+
+bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
+{
+ bam_plbuf_t *buf;
+ buf = calloc(1, sizeof(bam_plbuf_t));
+ buf->iter = bam_plp_init(0, 0);
+ buf->func = func;
+ buf->data = data;
+ return buf;
+}
+
+void bam_plbuf_destroy(bam_plbuf_t *buf)
+{
+ bam_plp_destroy(buf->iter);
+ free(buf);
+}
+
+int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
+{
+ int ret, n_plp, tid, pos;
+ const bam_pileup1_t *plp;
+ ret = bam_plp_push(buf->iter, b);
+ if (ret < 0) return ret;
+ while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
+ buf->func(tid, pos, n_plp, plp, buf->data);
+ return 0;
+}
+
+/***********
+ * mpileup *
+ ***********/
+
+struct __bam_mplp_t {
+ int n;
+ uint64_t min, *pos;
+ bam_plp_t *iter;
+ int *n_plp;
+ const bam_pileup1_t **plp;
+};
+
+bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
+{
+ int i;
+ bam_mplp_t iter;
+ iter = calloc(1, sizeof(struct __bam_mplp_t));
+ iter->pos = calloc(n, 8);
+ iter->n_plp = calloc(n, sizeof(int));
+ iter->plp = calloc(n, sizeof(void*));
+ iter->iter = calloc(n, sizeof(void*));
+ iter->n = n;
+ iter->min = (uint64_t)-1;
+ for (i = 0; i < n; ++i) {
+ iter->iter[i] = bam_plp_init(func, data[i]);
+ iter->pos[i] = iter->min;
+ }
+ return iter;
+}
+
+void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt)
+{
+ int i;
+ for (i = 0; i < iter->n; ++i)
+ iter->iter[i]->maxcnt = maxcnt;
+}
+
+void bam_mplp_destroy(bam_mplp_t iter)
+{
+ int i;
+ for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
+ free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
+ free(iter);
+}
+
+int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
+{
+ int i, ret = 0;
+ uint64_t new_min = (uint64_t)-1;
+ for (i = 0; i < iter->n; ++i) {
+ if (iter->pos[i] == iter->min) {
+ int tid, pos;
+ iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
+ iter->pos[i] = (uint64_t)tid<<32 | pos;
+ }
+ if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
+ }
+ iter->min = new_min;
+ if (new_min == (uint64_t)-1) return 0;
+ *_tid = new_min>>32; *_pos = (uint32_t)new_min;
+ for (i = 0; i < iter->n; ++i) {
+ if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line"
+ n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
+ ++ret;
+ } else n_plp[i] = 0, plp[i] = 0;
+ }
+ return ret;
+}
diff --git a/src/samtools-0.1.18/bam_plcmd.c b/src/samtools-0.1.18/bam_plcmd.c
new file mode 100644
index 0000000..cbf6ae8
--- /dev/null
+++ b/src/samtools-0.1.18/bam_plcmd.c
@@ -0,0 +1,546 @@
+#include <math.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include "sam.h"
+#include "faidx.h"
+#include "kstring.h"
+
+static inline int printw(int c, FILE *fp)
+{
+ char buf[16];
+ int l, x;
+ if (c == 0) return fputc('0', fp);
+ for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+ if (c < 0) buf[l++] = '-';
+ buf[l] = 0;
+ for (x = 0; x < l/2; ++x) {
+ int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
+ }
+ fputs(buf, fp);
+ return 0;
+}
+
+static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
+{
+ int j;
+ if (p->is_head) {
+ putchar('^');
+ putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
+ }
+ if (!p->is_del) {
+ int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+ if (ref) {
+ int rb = pos < ref_len? ref[pos] : 'N';
+ if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.';
+ else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+ } else {
+ if (c == '=') c = bam1_strand(p->b)? ',' : '.';
+ else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+ }
+ putchar(c);
+ } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
+ if (p->indel > 0) {
+ putchar('+'); printw(p->indel, stdout);
+ for (j = 1; j <= p->indel; ++j) {
+ int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
+ putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
+ }
+ } else if (p->indel < 0) {
+ printw(p->indel, stdout);
+ for (j = 1; j <= -p->indel; ++j) {
+ int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
+ putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
+ }
+ }
+ if (p->is_tail) putchar('$');
+}
+
+#include <assert.h>
+#include "bam2bcf.h"
+#include "sample.h"
+
+#define MPLP_GLF 0x10
+#define MPLP_NO_COMP 0x20
+#define MPLP_NO_ORPHAN 0x40
+#define MPLP_REALN 0x80
+#define MPLP_FMT_DP 0x100
+#define MPLP_FMT_SP 0x200
+#define MPLP_NO_INDEL 0x400
+#define MPLP_EXT_BAQ 0x800
+#define MPLP_ILLUMINA13 0x1000
+#define MPLP_IGNORE_RG 0x2000
+#define MPLP_PRINT_POS 0x4000
+#define MPLP_PRINT_MAPQ 0x8000
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
+
+typedef struct {
+ int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth;
+ int openQ, extQ, tandemQ, min_support; // for indels
+ double min_frac; // for indels
+ char *reg, *pl_list;
+ faidx_t *fai;
+ void *bed, *rghash;
+} mplp_conf_t;
+
+typedef struct {
+ bamFile fp;
+ bam_iter_t iter;
+ bam_header_t *h;
+ int ref_id;
+ char *ref;
+ const mplp_conf_t *conf;
+} mplp_aux_t;
+
+typedef struct {
+ int n;
+ int *n_plp, *m_plp;
+ bam_pileup1_t **plp;
+} mplp_pileup_t;
+
+static int mplp_func(void *data, bam1_t *b)
+{
+ extern int bam_realn(bam1_t *b, const char *ref);
+ extern int bam_prob_realn_core(bam1_t *b, const char *ref, int);
+ extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
+ mplp_aux_t *ma = (mplp_aux_t*)data;
+ int ret, skip = 0;
+ do {
+ int has_ref;
+ ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
+ if (ret < 0) break;
+ if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
+ skip = 1;
+ continue;
+ }
+ if (ma->conf->bed) { // test overlap
+ skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
+ if (skip) continue;
+ }
+ if (ma->conf->rghash) { // exclude read groups
+ uint8_t *rg = bam_aux_get(b, "RG");
+ skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
+ if (skip) continue;
+ }
+ if (ma->conf->flag & MPLP_ILLUMINA13) {
+ int i;
+ uint8_t *qual = bam1_qual(b);
+ for (i = 0; i < b->core.l_qseq; ++i)
+ qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+ }
+ has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
+ skip = 0;
+ if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
+ if (has_ref && ma->conf->capQ_thres > 10) {
+ int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres);
+ if (q < 0) skip = 1;
+ else if (b->core.qual > q) b->core.qual = q;
+ }
+ else if (b->core.qual < ma->conf->min_mq) skip = 1;
+ else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
+ } while (skip);
+ return ret;
+}
+
+static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
+ int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
+{
+ int i, j;
+ memset(m->n_plp, 0, m->n * sizeof(int));
+ for (i = 0; i < n; ++i) {
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j;
+ uint8_t *q;
+ int id = -1;
+ q = ignore_rg? 0 : bam_aux_get(p->b, "RG");
+ if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
+ if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
+ if (id < 0 || id >= m->n) {
+ assert(q); // otherwise a bug
+ fprintf(stderr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
+ exit(1);
+ }
+ if (m->n_plp[id] == m->m_plp[id]) {
+ m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
+ m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
+ }
+ m->plp[id][m->n_plp[id]++] = *p;
+ }
+ }
+}
+
+static int mpileup(mplp_conf_t *conf, int n, char **fn)
+{
+ extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
+ extern void bcf_call_del_rghash(void *rghash);
+ mplp_aux_t **data;
+ int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
+ const bam_pileup1_t **plp;
+ bam_mplp_t iter;
+ bam_header_t *h = 0;
+ char *ref;
+ void *rghash = 0;
+
+ bcf_callaux_t *bca = 0;
+ bcf_callret1_t *bcr = 0;
+ bcf_call_t bc;
+ bcf_t *bp = 0;
+ bcf_hdr_t *bh = 0;
+
+ bam_sample_t *sm = 0;
+ kstring_t buf;
+ mplp_pileup_t gplp;
+
+ memset(&gplp, 0, sizeof(mplp_pileup_t));
+ memset(&buf, 0, sizeof(kstring_t));
+ memset(&bc, 0, sizeof(bcf_call_t));
+ data = calloc(n, sizeof(void*));
+ plp = calloc(n, sizeof(void*));
+ n_plp = calloc(n, sizeof(int*));
+ sm = bam_smpl_init();
+
+ // read the header and initialize data
+ for (i = 0; i < n; ++i) {
+ bam_header_t *h_tmp;
+ data[i] = calloc(1, sizeof(mplp_aux_t));
+ data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
+ data[i]->conf = conf;
+ h_tmp = bam_header_read(data[i]->fp);
+ data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
+ bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
+ rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
+ if (conf->reg) {
+ int beg, end;
+ bam_index_t *idx;
+ idx = bam_index_load(fn[i]);
+ if (idx == 0) {
+ fprintf(stderr, "[%s] fail to load index for %d-th input.\n", __func__, i+1);
+ exit(1);
+ }
+ if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
+ fprintf(stderr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
+ exit(1);
+ }
+ if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
+ data[i]->iter = bam_iter_query(idx, tid, beg, end);
+ bam_index_destroy(idx);
+ }
+ if (i == 0) h = h_tmp;
+ else {
+ // FIXME: to check consistency
+ bam_header_destroy(h_tmp);
+ }
+ }
+ gplp.n = sm->n;
+ gplp.n_plp = calloc(sm->n, sizeof(int));
+ gplp.m_plp = calloc(sm->n, sizeof(int));
+ gplp.plp = calloc(sm->n, sizeof(void*));
+
+ fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
+ // write the VCF header
+ if (conf->flag & MPLP_GLF) {
+ kstring_t s;
+ bh = calloc(1, sizeof(bcf_hdr_t));
+ s.l = s.m = 0; s.s = 0;
+ bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
+ for (i = 0; i < h->n_targets; ++i) {
+ kputs(h->target_name[i], &s);
+ kputc('\0', &s);
+ }
+ bh->l_nm = s.l;
+ bh->name = malloc(s.l);
+ memcpy(bh->name, s.s, s.l);
+ s.l = 0;
+ for (i = 0; i < sm->n; ++i) {
+ kputs(sm->smpl[i], &s); kputc('\0', &s);
+ }
+ bh->l_smpl = s.l;
+ bh->sname = malloc(s.l);
+ memcpy(bh->sname, s.s, s.l);
+ bh->txt = malloc(strlen(BAM_VERSION) + 64);
+ bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
+ free(s.s);
+ bcf_hdr_sync(bh);
+ bcf_hdr_write(bp, bh);
+ bca = bcf_call_init(-1., conf->min_baseQ);
+ bcr = calloc(sm->n, sizeof(bcf_callret1_t));
+ bca->rghash = rghash;
+ bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
+ bca->min_frac = conf->min_frac;
+ bca->min_support = conf->min_support;
+ }
+ if (tid0 >= 0 && conf->fai) { // region is set
+ ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
+ ref_tid = tid0;
+ for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
+ } else ref_tid = -1, ref = 0;
+ iter = bam_mplp_init(n, mplp_func, (void**)data);
+ max_depth = conf->max_depth;
+ if (max_depth * sm->n > 1<<20)
+ fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
+ if (max_depth * sm->n < 8000) {
+ max_depth = 8000 / sm->n;
+ fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
+ }
+ max_indel_depth = conf->max_indel_depth * sm->n;
+ bam_mplp_set_maxcnt(iter, max_depth);
+ while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
+ if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
+ if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
+ if (tid != ref_tid) {
+ free(ref); ref = 0;
+ if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
+ for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
+ ref_tid = tid;
+ }
+ if (conf->flag & MPLP_GLF) {
+ int total_depth, _ref0, ref16;
+ bcf1_t *b = calloc(1, sizeof(bcf1_t));
+ for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
+ group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
+ _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+ ref16 = bam_nt16_table[_ref0];
+ for (i = 0; i < gplp.n; ++i)
+ bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
+ bcf_call_combine(gplp.n, bcr, ref16, &bc);
+ bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
+ (conf->flag&MPLP_FMT_SP), 0, 0);
+ bcf_write(bp, bh, b);
+ bcf_destroy(b);
+ // call indels
+ if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
+ for (i = 0; i < gplp.n; ++i)
+ bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
+ if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
+ b = calloc(1, sizeof(bcf1_t));
+ bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
+ (conf->flag&MPLP_FMT_SP), bca, ref);
+ bcf_write(bp, bh, b);
+ bcf_destroy(b);
+ }
+ }
+ } else {
+ printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
+ for (i = 0; i < n; ++i) {
+ int j;
+ printf("\t%d\t", n_plp[i]);
+ if (n_plp[i] == 0) {
+ printf("*\t*"); // FIXME: printf() is very slow...
+ if (conf->flag & MPLP_PRINT_POS) printf("\t*");
+ } else {
+ for (j = 0; j < n_plp[i]; ++j)
+ pileup_seq(plp[i] + j, pos, ref_len, ref);
+ putchar('\t');
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j;
+ int c = bam1_qual(p->b)[p->qpos] + 33;
+ if (c > 126) c = 126;
+ putchar(c);
+ }
+ if (conf->flag & MPLP_PRINT_MAPQ) {
+ putchar('\t');
+ for (j = 0; j < n_plp[i]; ++j) {
+ int c = plp[i][j].b->core.qual + 33;
+ if (c > 126) c = 126;
+ putchar(c);
+ }
+ }
+ if (conf->flag & MPLP_PRINT_POS) {
+ putchar('\t');
+ for (j = 0; j < n_plp[i]; ++j) {
+ if (j > 0) putchar(',');
+ printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
+ }
+ }
+ }
+ }
+ putchar('\n');
+ }
+ }
+
+ bcf_close(bp);
+ bam_smpl_destroy(sm); free(buf.s);
+ for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
+ free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
+ bcf_call_del_rghash(rghash);
+ bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
+ bam_mplp_destroy(iter);
+ bam_header_destroy(h);
+ for (i = 0; i < n; ++i) {
+ bam_close(data[i]->fp);
+ if (data[i]->iter) bam_iter_destroy(data[i]->iter);
+ free(data[i]);
+ }
+ free(data); free(plp); free(ref); free(n_plp);
+ return 0;
+}
+
+#define MAX_PATH_LEN 1024
+static int read_file_list(const char *file_list,int *n,char **argv[])
+{
+ char buf[MAX_PATH_LEN];
+ int len, nfiles;
+ char **files;
+
+ FILE *fh = fopen(file_list,"r");
+ if ( !fh )
+ {
+ fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
+ return 1;
+ }
+
+ // Speed is not an issue here, determine the number of files by reading the file twice
+ nfiles = 0;
+ while ( fgets(buf,MAX_PATH_LEN,fh) ) nfiles++;
+
+ if ( fseek(fh, 0L, SEEK_SET) )
+ {
+ fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
+ return 1;
+ }
+
+ files = calloc(nfiles,sizeof(char*));
+ nfiles = 0;
+ while ( fgets(buf,MAX_PATH_LEN,fh) )
+ {
+ len = strlen(buf);
+ while ( len>0 && isspace(buf[len-1]) ) len--;
+ if ( !len ) continue;
+
+ files[nfiles] = malloc(sizeof(char)*(len+1));
+ strncpy(files[nfiles],buf,len);
+ files[nfiles][len] = 0;
+ nfiles++;
+ }
+ fclose(fh);
+ if ( !nfiles )
+ {
+ fprintf(stderr,"No files read from %s\n", file_list);
+ return 1;
+ }
+ *argv = files;
+ *n = nfiles;
+ return 0;
+}
+#undef MAX_PATH_LEN
+
+int bam_mpileup(int argc, char *argv[])
+{
+ int c;
+ const char *file_list = NULL;
+ char **fn = NULL;
+ int nfiles = 0, use_orphan = 0;
+ mplp_conf_t mplp;
+ memset(&mplp, 0, sizeof(mplp_conf_t));
+ #define MPLP_PRINT_POS 0x4000
+ mplp.max_mq = 60;
+ mplp.min_baseQ = 13;
+ mplp.capQ_thres = 0;
+ mplp.max_depth = 250; mplp.max_indel_depth = 250;
+ mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
+ mplp.min_frac = 0.002; mplp.min_support = 1;
+ mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
+ while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6Os")) >= 0) {
+ switch (c) {
+ case 'f':
+ mplp.fai = fai_load(optarg);
+ if (mplp.fai == 0) return 1;
+ break;
+ case 'd': mplp.max_depth = atoi(optarg); break;
+ case 'r': mplp.reg = strdup(optarg); break;
+ case 'l': mplp.bed = bed_read(optarg); break;
+ case 'P': mplp.pl_list = strdup(optarg); break;
+ case 'g': mplp.flag |= MPLP_GLF; break;
+ case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
+ case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
+ case 'B': mplp.flag &= ~MPLP_REALN; break;
+ case 'D': mplp.flag |= MPLP_FMT_DP; break;
+ case 'S': mplp.flag |= MPLP_FMT_SP; break;
+ case 'I': mplp.flag |= MPLP_NO_INDEL; break;
+ case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
+ case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+ case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
+ case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
+ case 'O': mplp.flag |= MPLP_PRINT_POS; break;
+ case 'C': mplp.capQ_thres = atoi(optarg); break;
+ case 'M': mplp.max_mq = atoi(optarg); break;
+ case 'q': mplp.min_mq = atoi(optarg); break;
+ case 'Q': mplp.min_baseQ = atoi(optarg); break;
+ case 'b': file_list = optarg; break;
+ case 'o': mplp.openQ = atoi(optarg); break;
+ case 'e': mplp.extQ = atoi(optarg); break;
+ case 'h': mplp.tandemQ = atoi(optarg); break;
+ case 'A': use_orphan = 1; break;
+ case 'F': mplp.min_frac = atof(optarg); break;
+ case 'm': mplp.min_support = atoi(optarg); break;
+ case 'L': mplp.max_indel_depth = atoi(optarg); break;
+ case 'G': {
+ FILE *fp_rg;
+ char buf[1024];
+ mplp.rghash = bcf_str2id_init();
+ if ((fp_rg = fopen(optarg, "r")) == 0)
+ fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
+ while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
+ bcf_str2id_add(mplp.rghash, strdup(buf));
+ fclose(fp_rg);
+ }
+ break;
+ }
+ }
+ if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
+ if (argc == 1) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+ fprintf(stderr, "Input options:\n\n");
+ fprintf(stderr, " -6 assume the quality is in the Illumina-1.3+ encoding\n");
+ fprintf(stderr, " -A count anomalous read pairs\n");
+ fprintf(stderr, " -B disable BAQ computation\n");
+ fprintf(stderr, " -b FILE list of input BAM files [null]\n");
+ fprintf(stderr, " -C INT parameter for adjusting mapQ; 0 to disable [0]\n");
+ fprintf(stderr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
+ fprintf(stderr, " -E extended BAQ for higher sensitivity but lower specificity\n");
+ fprintf(stderr, " -f FILE faidx indexed reference sequence file [null]\n");
+ fprintf(stderr, " -G FILE exclude read groups listed in FILE [null]\n");
+ fprintf(stderr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n");
+ fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
+ fprintf(stderr, " -r STR region in which pileup is generated [null]\n");
+ fprintf(stderr, " -R ignore RG tags\n");
+ fprintf(stderr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
+ fprintf(stderr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
+ fprintf(stderr, "\nOutput options:\n\n");
+ fprintf(stderr, " -D output per-sample DP in BCF (require -g/-u)\n");
+ fprintf(stderr, " -g generate BCF output (genotype likelihoods)\n");
+ fprintf(stderr, " -O output base positions on reads (disabled by -g/-u)\n");
+ fprintf(stderr, " -s output mapping quality (disabled by -g/-u)\n");
+ fprintf(stderr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n");
+ fprintf(stderr, " -u generate uncompress BCF output\n");
+ fprintf(stderr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
+ fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
+ fprintf(stderr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
+ fprintf(stderr, " -h INT coefficient for homopolymer errors [%d]\n", mplp.tandemQ);
+ fprintf(stderr, " -I do not perform indel calling\n");
+ fprintf(stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
+ fprintf(stderr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
+ fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
+ fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
+ return 1;
+ }
+ if (file_list) {
+ if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+ mpileup(&mplp,nfiles,fn);
+ for (c=0; c<nfiles; c++) free(fn[c]);
+ free(fn);
+ } else mpileup(&mplp, argc - optind, argv + optind);
+ if (mplp.rghash) bcf_str2id_thorough_destroy(mplp.rghash);
+ free(mplp.reg); free(mplp.pl_list);
+ if (mplp.fai) fai_destroy(mplp.fai);
+ if (mplp.bed) bed_destroy(mplp.bed);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam_reheader.c b/src/samtools-0.1.18/bam_reheader.c
new file mode 100644
index 0000000..0b52267
--- /dev/null
+++ b/src/samtools-0.1.18/bam_reheader.c
@@ -0,0 +1,61 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include "bgzf.h"
+#include "bam.h"
+
+#define BUF_SIZE 0x10000
+
+int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
+{
+ BGZF *fp;
+ bam_header_t *old;
+ int len;
+ uint8_t *buf;
+ if (in->open_mode != 'r') return -1;
+ buf = malloc(BUF_SIZE);
+ old = bam_header_read(in);
+ fp = bgzf_fdopen(fd, "w");
+ bam_header_write(fp, h);
+ if (in->block_offset < in->block_length) {
+ bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
+ bgzf_flush(fp);
+ }
+#ifdef _USE_KNETFILE
+ while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
+ fwrite(buf, 1, len, fp->x.fpw);
+#else
+ while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
+ fwrite(buf, 1, len, fp->file);
+#endif
+ free(buf);
+ fp->block_offset = in->block_offset = 0;
+ bgzf_close(fp);
+ return 0;
+}
+
+int main_reheader(int argc, char *argv[])
+{
+ bam_header_t *h;
+ BGZF *in;
+ if (argc != 3) {
+ fprintf(stderr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
+ return 1;
+ }
+ { // read the header
+ tamFile fph = sam_open(argv[1]);
+ if (fph == 0) {
+ fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
+ return 1;
+ }
+ h = sam_header_read(fph);
+ sam_close(fph);
+ }
+ in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
+ if (in == 0) {
+ fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
+ return 1;
+ }
+ bam_reheader(in, h, fileno(stdout));
+ bgzf_close(in);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam_rmdup.c b/src/samtools-0.1.18/bam_rmdup.c
new file mode 100644
index 0000000..f0d2b5d
--- /dev/null
+++ b/src/samtools-0.1.18/bam_rmdup.c
@@ -0,0 +1,206 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+#include <unistd.h>
+#include "sam.h"
+
+typedef bam1_t *bam1_p;
+
+#include "khash.h"
+KHASH_SET_INIT_STR(name)
+KHASH_MAP_INIT_INT64(pos, bam1_p)
+
+#define BUFFER_SIZE 0x40000
+
+typedef struct {
+ uint64_t n_checked, n_removed;
+ khash_t(pos) *best_hash;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
+typedef struct {
+ int n, max;
+ bam1_t **a;
+} tmp_stack_t;
+
+static inline void stack_insert(tmp_stack_t *stack, bam1_t *b)
+{
+ if (stack->n == stack->max) {
+ stack->max = stack->max? stack->max<<1 : 0x10000;
+ stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max);
+ }
+ stack->a[stack->n++] = b;
+}
+
+static inline void dump_best(tmp_stack_t *stack, samfile_t *out)
+{
+ int i;
+ for (i = 0; i != stack->n; ++i) {
+ samwrite(out, stack->a[i]);
+ bam_destroy1(stack->a[i]);
+ }
+ stack->n = 0;
+}
+
+static void clear_del_set(khash_t(name) *del_set)
+{
+ khint_t k;
+ for (k = kh_begin(del_set); k < kh_end(del_set); ++k)
+ if (kh_exist(del_set, k))
+ free((char*)kh_key(del_set, k));
+ kh_clear(name, del_set);
+}
+
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+ khint_t k = kh_get(lib, aux, lib);
+ if (k == kh_end(aux)) {
+ int ret;
+ char *p = strdup(lib);
+ lib_aux_t *q;
+ k = kh_put(lib, aux, p, &ret);
+ q = &kh_val(aux, k);
+ q->n_checked = q->n_removed = 0;
+ q->best_hash = kh_init(pos);
+ return q;
+ } else return &kh_val(aux, k);
+}
+
+static void clear_best(khash_t(lib) *aux, int max)
+{
+ khint_t k;
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ if (kh_size(q->best_hash) >= max)
+ kh_clear(pos, q->best_hash);
+ }
+ }
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+ int i, q;
+ uint8_t *qual = bam1_qual(b);
+ for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+ return q;
+}
+
+void bam_rmdup_core(samfile_t *in, samfile_t *out)
+{
+ bam1_t *b;
+ int last_tid = -1, last_pos = -1;
+ tmp_stack_t stack;
+ khint_t k;
+ khash_t(lib) *aux;
+ khash_t(name) *del_set;
+
+ aux = kh_init(lib);
+ del_set = kh_init(name);
+ b = bam_init1();
+ memset(&stack, 0, sizeof(tmp_stack_t));
+
+ kh_resize(name, del_set, 4 * BUFFER_SIZE);
+ while (samread(in, b) >= 0) {
+ bam1_core_t *c = &b->core;
+ if (c->tid != last_tid || last_pos != c->pos) {
+ dump_best(&stack, out); // write the result
+ clear_best(aux, BUFFER_SIZE);
+ if (c->tid != last_tid) {
+ clear_best(aux, 0);
+ if (kh_size(del_set)) { // check
+ fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
+ clear_del_set(del_set);
+ }
+ if ((int)c->tid == -1) { // append unmapped reads
+ samwrite(out, b);
+ while (samread(in, b) >= 0) samwrite(out, b);
+ break;
+ }
+ last_tid = c->tid;
+ fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]);
+ }
+ }
+ if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
+ samwrite(out, b);
+ } else if (c->isize > 0) { // paired, head
+ uint64_t key = (uint64_t)c->pos<<32 | c->isize;
+ const char *lib;
+ lib_aux_t *q;
+ int ret;
+ lib = bam_get_library(in->header, b);
+ q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+ ++q->n_checked;
+ k = kh_put(pos, q->best_hash, key, &ret);
+ if (ret == 0) { // found in best_hash
+ bam1_t *p = kh_val(q->best_hash, k);
+ ++q->n_removed;
+ if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle
+ kh_put(name, del_set, strdup(bam1_qname(p)), &ret); // p will be removed
+ bam_copy1(p, b); // replaced as b
+ } else kh_put(name, del_set, strdup(bam1_qname(b)), &ret); // b will be removed
+ if (ret == 0)
+ fprintf(stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam1_qname(b));
+ } else { // not found in best_hash
+ kh_val(q->best_hash, k) = bam_dup1(b);
+ stack_insert(&stack, kh_val(q->best_hash, k));
+ }
+ } else { // paired, tail
+ k = kh_get(name, del_set, bam1_qname(b));
+ if (k != kh_end(del_set)) {
+ free((char*)kh_key(del_set, k));
+ kh_del(name, del_set, k);
+ } else samwrite(out, b);
+ }
+ last_pos = c->pos;
+ }
+
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ dump_best(&stack, out);
+ fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+ (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+ kh_destroy(pos, q->best_hash);
+ free((char*)kh_key(aux, k));
+ }
+ }
+ kh_destroy(lib, aux);
+
+ clear_del_set(del_set);
+ kh_destroy(name, del_set);
+ free(stack.a);
+ bam_destroy1(b);
+}
+
+void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se);
+
+int bam_rmdup(int argc, char *argv[])
+{
+ int c, is_se = 0, force_se = 0;
+ samfile_t *in, *out;
+ while ((c = getopt(argc, argv, "sS")) >= 0) {
+ switch (c) {
+ case 's': is_se = 1; break;
+ case 'S': force_se = is_se = 1; break;
+ }
+ }
+ if (optind + 2 > argc) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
+ fprintf(stderr, "Option: -s rmdup for SE reads\n");
+ fprintf(stderr, " -S treat PE reads as SE in rmdup (force -s)\n\n");
+ return 1;
+ }
+ in = samopen(argv[optind], "rb", 0);
+ out = samopen(argv[optind+1], "wb", in->header);
+ if (in == 0 || out == 0) {
+ fprintf(stderr, "[bam_rmdup] fail to read/write input files\n");
+ return 1;
+ }
+ if (is_se) bam_rmdupse_core(in, out, force_se);
+ else bam_rmdup_core(in, out);
+ samclose(in); samclose(out);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam_rmdupse.c b/src/samtools-0.1.18/bam_rmdupse.c
new file mode 100644
index 0000000..e7dbdc7
--- /dev/null
+++ b/src/samtools-0.1.18/bam_rmdupse.c
@@ -0,0 +1,159 @@
+#include <math.h>
+#include "sam.h"
+#include "khash.h"
+#include "klist.h"
+
+#define QUEUE_CLEAR_SIZE 0x100000
+#define MAX_POS 0x7fffffff
+
+typedef struct {
+ int endpos;
+ uint32_t score:31, discarded:1;
+ bam1_t *b;
+} elem_t, *elem_p;
+#define __free_elem(p) bam_destroy1((p)->data.b)
+KLIST_INIT(q, elem_t, __free_elem)
+typedef klist_t(q) queue_t;
+
+KHASH_MAP_INIT_INT(best, elem_p)
+typedef khash_t(best) besthash_t;
+
+typedef struct {
+ uint64_t n_checked, n_removed;
+ besthash_t *left, *rght;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+ khint_t k = kh_get(lib, aux, lib);
+ if (k == kh_end(aux)) {
+ int ret;
+ char *p = strdup(lib);
+ lib_aux_t *q;
+ k = kh_put(lib, aux, p, &ret);
+ q = &kh_val(aux, k);
+ q->left = kh_init(best);
+ q->rght = kh_init(best);
+ q->n_checked = q->n_removed = 0;
+ return q;
+ } else return &kh_val(aux, k);
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+ int i, q;
+ uint8_t *qual = bam1_qual(b);
+ for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+ return q;
+}
+
+static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
+{
+ elem_t *p = kl_pushp(q, queue);
+ p->discarded = 0;
+ p->endpos = endpos; p->score = score;
+ if (p->b == 0) p->b = bam_init1();
+ bam_copy1(p->b, b);
+ return p;
+}
+
+static void clear_besthash(besthash_t *h, int32_t pos)
+{
+ khint_t k;
+ for (k = kh_begin(h); k != kh_end(h); ++k)
+ if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
+ kh_del(best, h, k);
+}
+
+static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
+{
+ if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
+ khint_t k;
+ while (1) {
+ elem_t *q;
+ if (queue->head == queue->tail) break;
+ q = &kl_val(queue->head);
+ if (q->discarded) {
+ q->b->data_len = 0;
+ kl_shift(q, queue, 0);
+ continue;
+ }
+ if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
+ samwrite(out, q->b);
+ q->b->data_len = 0;
+ kl_shift(q, queue, 0);
+ }
+ for (k = kh_begin(h); k != kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ clear_besthash(kh_val(h, k).left, pos);
+ clear_besthash(kh_val(h, k).rght, pos);
+ }
+ }
+ }
+}
+
+void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
+{
+ bam1_t *b;
+ queue_t *queue;
+ khint_t k;
+ int last_tid = -2;
+ khash_t(lib) *aux;
+
+ aux = kh_init(lib);
+ b = bam_init1();
+ queue = kl_init(q);
+ while (samread(in, b) >= 0) {
+ bam1_core_t *c = &b->core;
+ int endpos = bam_calend(c, bam1_cigar(b));
+ int score = sum_qual(b);
+
+ if (last_tid != c->tid) {
+ if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
+ last_tid = c->tid;
+ } else dump_alignment(out, queue, c->pos, aux);
+ if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
+ push_queue(queue, b, endpos, score);
+ } else {
+ const char *lib;
+ lib_aux_t *q;
+ besthash_t *h;
+ uint32_t key;
+ int ret;
+ lib = bam_get_library(in->header, b);
+ q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+ ++q->n_checked;
+ h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
+ key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
+ k = kh_put(best, h, key, &ret);
+ if (ret == 0) { // in the hash table
+ elem_t *p = kh_val(h, k);
+ ++q->n_removed;
+ if (p->score < score) {
+ if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
+ p->discarded = 1;
+ kh_val(h, k) = push_queue(queue, b, endpos, score);
+ } else { // replace
+ p->score = score; p->endpos = endpos;
+ bam_copy1(p->b, b);
+ }
+ } // otherwise, discard the alignment
+ } else kh_val(h, k) = push_queue(queue, b, endpos, score);
+ }
+ }
+ dump_alignment(out, queue, MAX_POS, aux);
+
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+ (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+ kh_destroy(best, q->left); kh_destroy(best, q->rght);
+ free((char*)kh_key(aux, k));
+ }
+ }
+ kh_destroy(lib, aux);
+ bam_destroy1(b);
+ kl_destroy(q, queue);
+}
diff --git a/src/samtools-0.1.18/bam_sort.c b/src/samtools-0.1.18/bam_sort.c
new file mode 100644
index 0000000..abf8d4f
--- /dev/null
+++ b/src/samtools-0.1.18/bam_sort.c
@@ -0,0 +1,438 @@
+#include <stdlib.h>
+#include <ctype.h>
+#include <assert.h>
+#include <errno.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include "bam.h"
+#include "ksort.h"
+
+static int g_is_by_qname = 0;
+
+static inline int strnum_cmp(const char *a, const char *b)
+{
+ char *pa, *pb;
+ pa = (char*)a; pb = (char*)b;
+ while (*pa && *pb) {
+ if (isdigit(*pa) && isdigit(*pb)) {
+ long ai, bi;
+ ai = strtol(pa, &pa, 10);
+ bi = strtol(pb, &pb, 10);
+ if (ai != bi) return ai<bi? -1 : ai>bi? 1 : 0;
+ } else {
+ if (*pa != *pb) break;
+ ++pa; ++pb;
+ }
+ }
+ if (*pa == *pb)
+ return (pa-a) < (pb-b)? -1 : (pa-a) > (pb-b)? 1 : 0;
+ return *pa<*pb? -1 : *pa>*pb? 1 : 0;
+}
+
+#define HEAP_EMPTY 0xffffffffffffffffull
+
+typedef struct {
+ int i;
+ uint64_t pos, idx;
+ bam1_t *b;
+} heap1_t;
+
+#define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx))))
+
+static inline int heap_lt(const heap1_t a, const heap1_t b)
+{
+ if (g_is_by_qname) {
+ int t;
+ if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
+ t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
+ return (t > 0 || (t == 0 && __pos_cmp(a, b)));
+ } else return __pos_cmp(a, b);
+}
+
+KSORT_INIT(heap, heap1_t, heap_lt)
+
+static void swap_header_targets(bam_header_t *h1, bam_header_t *h2)
+{
+ bam_header_t t;
+ t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;
+ t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;
+ t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;
+}
+
+static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
+{
+ int tempi;
+ char *temps;
+ tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
+ temps = h1->text, h1->text = h2->text, h2->text = temps;
+}
+
+#define MERGE_RG 1
+#define MERGE_UNCOMP 2
+#define MERGE_LEVEL1 4
+#define MERGE_FORCE 8
+
+/*!
+ @abstract Merge multiple sorted BAM.
+ @param is_by_qname whether to sort by query name
+ @param out output BAM file name
+ @param headers name of SAM file from which to copy '@' header lines,
+ or NULL to copy them from the first file to be merged
+ @param n number of files to be merged
+ @param fn names of files to be merged
+
+ @discussion Padding information may NOT correctly maintained. This
+ function is NOT thread safe.
+ */
+int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn,
+ int flag, const char *reg)
+{
+ bamFile fpout, *fp;
+ heap1_t *heap;
+ bam_header_t *hout = 0;
+ bam_header_t *hheaders = NULL;
+ int i, j, *RG_len = 0;
+ uint64_t idx = 0;
+ char **RG = 0;
+ bam_iter_t *iter = 0;
+
+ if (headers) {
+ tamFile fpheaders = sam_open(headers);
+ if (fpheaders == 0) {
+ const char *message = strerror(errno);
+ fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
+ return -1;
+ }
+ hheaders = sam_header_read(fpheaders);
+ sam_close(fpheaders);
+ }
+
+ g_is_by_qname = by_qname;
+ fp = (bamFile*)calloc(n, sizeof(bamFile));
+ heap = (heap1_t*)calloc(n, sizeof(heap1_t));
+ iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));
+ // prepare RG tag
+ if (flag & MERGE_RG) {
+ RG = (char**)calloc(n, sizeof(void*));
+ RG_len = (int*)calloc(n, sizeof(int));
+ for (i = 0; i != n; ++i) {
+ int l = strlen(fn[i]);
+ const char *s = fn[i];
+ if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
+ for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
+ ++j; l -= j;
+ RG[i] = calloc(l + 1, 1);
+ RG_len[i] = l;
+ strncpy(RG[i], s + j, l);
+ }
+ }
+ // read the first
+ for (i = 0; i != n; ++i) {
+ bam_header_t *hin;
+ fp[i] = bam_open(fn[i], "r");
+ if (fp[i] == 0) {
+ int j;
+ fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
+ for (j = 0; j < i; ++j) bam_close(fp[j]);
+ free(fp); free(heap);
+ // FIXME: possible memory leak
+ return -1;
+ }
+ hin = bam_header_read(fp[i]);
+ if (i == 0) { // the first BAM
+ hout = hin;
+ } else { // validate multiple baf
+ int min_n_targets = hout->n_targets;
+ if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;
+
+ for (j = 0; j < min_n_targets; ++j)
+ if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {
+ fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",
+ hout->target_name[j], hin->target_name[j], fn[i]);
+ return -1;
+ }
+
+ // If this input file has additional target reference sequences,
+ // add them to the headers to be output
+ if (hin->n_targets > hout->n_targets) {
+ swap_header_targets(hout, hin);
+ // FIXME Possibly we should also create @SQ text headers
+ // for the newly added reference sequences
+ }
+
+ bam_header_destroy(hin);
+ }
+ }
+
+ if (hheaders) {
+ // If the text headers to be swapped in include any @SQ headers,
+ // check that they are consistent with the existing binary list
+ // of reference information.
+ if (hheaders->n_targets > 0) {
+ if (hout->n_targets != hheaders->n_targets) {
+ fprintf(stderr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers);
+ if (!reg) return -1;
+ }
+ for (j = 0; j < hout->n_targets; ++j)
+ if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {
+ fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence\n", hheaders->target_name[j], headers);
+ if (!reg) return -1;
+ }
+ }
+
+ swap_header_text(hout, hheaders);
+ bam_header_destroy(hheaders);
+ }
+
+ if (reg) {
+ int tid, beg, end;
+ if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {
+ fprintf(stderr, "[%s] Malformated region string or undefined reference name\n", __func__);
+ return -1;
+ }
+ for (i = 0; i < n; ++i) {
+ bam_index_t *idx;
+ idx = bam_index_load(fn[i]);
+ iter[i] = bam_iter_query(idx, tid, beg, end);
+ bam_index_destroy(idx);
+ }
+ }
+
+ for (i = 0; i < n; ++i) {
+ heap1_t *h = heap + i;
+ h->i = i;
+ h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {
+ h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);
+ h->idx = idx++;
+ }
+ else h->pos = HEAP_EMPTY;
+ }
+ if (flag & MERGE_UNCOMP) fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
+ else if (flag & MERGE_LEVEL1) fpout = strcmp(out, "-")? bam_open(out, "w1") : bam_dopen(fileno(stdout), "w1");
+ else fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
+ if (fpout == 0) {
+ fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
+ return -1;
+ }
+ bam_header_write(fpout, hout);
+ bam_header_destroy(hout);
+
+ ks_heapmake(heap, n, heap);
+ while (heap->pos != HEAP_EMPTY) {
+ bam1_t *b = heap->b;
+ if (flag & MERGE_RG) {
+ uint8_t *rg = bam_aux_get(b, "RG");
+ if (rg) bam_aux_del(b, rg);
+ bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
+ }
+ bam_write1_core(fpout, &b->core, b->data_len, b->data);
+ if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
+ heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);
+ heap->idx = idx++;
+ } else if (j == -1) {
+ heap->pos = HEAP_EMPTY;
+ free(heap->b->data); free(heap->b);
+ heap->b = 0;
+ } else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
+ ks_heapadjust(heap, 0, n, heap);
+ }
+
+ if (flag & MERGE_RG) {
+ for (i = 0; i != n; ++i) free(RG[i]);
+ free(RG); free(RG_len);
+ }
+ for (i = 0; i != n; ++i) {
+ bam_iter_destroy(iter[i]);
+ bam_close(fp[i]);
+ }
+ bam_close(fpout);
+ free(fp); free(heap); free(iter);
+ return 0;
+}
+
+int bam_merge(int argc, char *argv[])
+{
+ int c, is_by_qname = 0, flag = 0, ret = 0;
+ char *fn_headers = NULL, *reg = 0;
+
+ while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
+ switch (c) {
+ case 'r': flag |= MERGE_RG; break;
+ case 'f': flag |= MERGE_FORCE; break;
+ case 'h': fn_headers = strdup(optarg); break;
+ case 'n': is_by_qname = 1; break;
+ case '1': flag |= MERGE_LEVEL1; break;
+ case 'u': flag |= MERGE_UNCOMP; break;
+ case 'R': reg = strdup(optarg); break;
+ }
+ }
+ if (optind + 2 >= argc) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
+ fprintf(stderr, "Options: -n sort by read names\n");
+ fprintf(stderr, " -r attach RG tag (inferred from file names)\n");
+ fprintf(stderr, " -u uncompressed BAM output\n");
+ fprintf(stderr, " -f overwrite the output BAM if exist\n");
+ fprintf(stderr, " -1 compress level 1\n");
+ fprintf(stderr, " -R STR merge file in the specified region STR [all]\n");
+ fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
+ fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
+ fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");
+ fprintf(stderr, " the header dictionary in merging.\n\n");
+ return 1;
+ }
+ if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
+ FILE *fp = fopen(argv[optind], "rb");
+ if (fp != NULL) {
+ fclose(fp);
+ fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);
+ return 1;
+ }
+ }
+ if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
+ free(reg);
+ free(fn_headers);
+ return ret;
+}
+
+typedef bam1_t *bam1_p;
+
+static inline int bam1_lt(const bam1_p a, const bam1_p b)
+{
+ if (g_is_by_qname) {
+ int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
+ return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)))));
+ } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
+}
+KSORT_INIT(sort, bam1_p, bam1_lt)
+
+static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
+{
+ char *name, mode[3];
+ int i;
+ bamFile fp;
+ ks_mergesort(sort, k, buf, 0);
+ name = (char*)calloc(strlen(prefix) + 20, 1);
+ if (n >= 0) {
+ sprintf(name, "%s.%.4d.bam", prefix, n);
+ strcpy(mode, "w1");
+ } else {
+ sprintf(name, "%s.bam", prefix);
+ strcpy(mode, "w");
+ }
+ fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode);
+ if (fp == 0) {
+ fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
+ free(name);
+ // FIXME: possible memory leak
+ return;
+ }
+ free(name);
+ bam_header_write(fp, h);
+ for (i = 0; i < k; ++i)
+ bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data);
+ bam_close(fp);
+}
+
+/*!
+ @abstract Sort an unsorted BAM file based on the chromosome order
+ and the leftmost position of an alignment
+
+ @param is_by_qname whether to sort by query name
+ @param fn name of the file to be sorted
+ @param prefix prefix of the output and the temporary files; upon
+ sucessess, prefix.bam will be written.
+ @param max_mem approxiate maximum memory (very inaccurate)
+
+ @discussion It may create multiple temporary subalignment files
+ and then merge them by calling bam_merge_core(). This function is
+ NOT thread safe.
+ */
+void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t max_mem, int is_stdout)
+{
+ int n, ret, k, i;
+ size_t mem;
+ bam_header_t *header;
+ bamFile fp;
+ bam1_t *b, **buf;
+
+ g_is_by_qname = is_by_qname;
+ n = k = 0; mem = 0;
+ fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
+ if (fp == 0) {
+ fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);
+ return;
+ }
+ header = bam_header_read(fp);
+ buf = (bam1_t**)calloc(max_mem / BAM_CORE_SIZE, sizeof(bam1_t*));
+ // write sub files
+ for (;;) {
+ if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
+ b = buf[k];
+ if ((ret = bam_read1(fp, b)) < 0) break;
+ mem += ret;
+ ++k;
+ if (mem >= max_mem) {
+ sort_blocks(n++, k, buf, prefix, header, 0);
+ mem = 0; k = 0;
+ }
+ }
+ if (ret != -1)
+ fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n");
+ if (n == 0) sort_blocks(-1, k, buf, prefix, header, is_stdout);
+ else { // then merge
+ char **fns, *fnout;
+ fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n+1);
+ sort_blocks(n++, k, buf, prefix, header, 0);
+ fnout = (char*)calloc(strlen(prefix) + 20, 1);
+ if (is_stdout) sprintf(fnout, "-");
+ else sprintf(fnout, "%s.bam", prefix);
+ fns = (char**)calloc(n, sizeof(char*));
+ for (i = 0; i < n; ++i) {
+ fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
+ sprintf(fns[i], "%s.%.4d.bam", prefix, i);
+ }
+ bam_merge_core(is_by_qname, fnout, 0, n, fns, 0, 0);
+ free(fnout);
+ for (i = 0; i < n; ++i) {
+ unlink(fns[i]);
+ free(fns[i]);
+ }
+ free(fns);
+ }
+ for (k = 0; k < max_mem / BAM_CORE_SIZE; ++k) {
+ if (buf[k]) {
+ free(buf[k]->data);
+ free(buf[k]);
+ }
+ }
+ free(buf);
+ bam_header_destroy(header);
+ bam_close(fp);
+}
+
+void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
+{
+ bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0);
+}
+
+int bam_sort(int argc, char *argv[])
+{
+ size_t max_mem = 500000000;
+ int c, is_by_qname = 0, is_stdout = 0;
+ while ((c = getopt(argc, argv, "nom:")) >= 0) {
+ switch (c) {
+ case 'o': is_stdout = 1; break;
+ case 'n': is_by_qname = 1; break;
+ case 'm': max_mem = atol(optarg); break;
+ }
+ }
+ if (optind + 2 > argc) {
+ fprintf(stderr, "Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>\n");
+ return 1;
+ }
+ bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam_stat.c b/src/samtools-0.1.18/bam_stat.c
new file mode 100644
index 0000000..f2de0f1
--- /dev/null
+++ b/src/samtools-0.1.18/bam_stat.c
@@ -0,0 +1,77 @@
+#include <unistd.h>
+#include <assert.h>
+#include "bam.h"
+
+typedef struct {
+ long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
+ long long n_sgltn[2], n_read1[2], n_read2[2];
+ long long n_dup[2];
+ long long n_diffchr[2], n_diffhigh[2];
+} bam_flagstat_t;
+
+#define flagstat_loop(s, c) do { \
+ int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0; \
+ ++(s)->n_reads[w]; \
+ if ((c)->flag & BAM_FPAIRED) { \
+ ++(s)->n_pair_all[w]; \
+ if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good[w]; \
+ if ((c)->flag & BAM_FREAD1) ++(s)->n_read1[w]; \
+ if ((c)->flag & BAM_FREAD2) ++(s)->n_read2[w]; \
+ if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn[w]; \
+ if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
+ ++(s)->n_pair_map[w]; \
+ if ((c)->mtid != (c)->tid) { \
+ ++(s)->n_diffchr[w]; \
+ if ((c)->qual >= 5) ++(s)->n_diffhigh[w]; \
+ } \
+ } \
+ } \
+ if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped[w]; \
+ if ((c)->flag & BAM_FDUP) ++(s)->n_dup[w]; \
+ } while (0)
+
+bam_flagstat_t *bam_flagstat_core(bamFile fp)
+{
+ bam_flagstat_t *s;
+ bam1_t *b;
+ bam1_core_t *c;
+ int ret;
+ s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
+ b = bam_init1();
+ c = &b->core;
+ while ((ret = bam_read1(fp, b)) >= 0)
+ flagstat_loop(s, c);
+ bam_destroy1(b);
+ if (ret != -1)
+ fprintf(stderr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
+ return s;
+}
+int bam_flagstat(int argc, char *argv[])
+{
+ bamFile fp;
+ bam_header_t *header;
+ bam_flagstat_t *s;
+ if (argc == optind) {
+ fprintf(stderr, "Usage: samtools flagstat <in.bam>\n");
+ return 1;
+ }
+ fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
+ assert(fp);
+ header = bam_header_read(fp);
+ s = bam_flagstat_core(fp);
+ printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
+ printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
+ printf("%lld + %lld mapped (%.2f%%:%.2f%%)\n", s->n_mapped[0], s->n_mapped[1], (float)s->n_mapped[0] / s->n_reads[0] * 100.0, (float)s->n_mapped[1] / s->n_reads[1] * 100.0);
+ printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
+ printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
+ printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
+ printf("%lld + %lld properly paired (%.2f%%:%.2f%%)\n", s->n_pair_good[0], s->n_pair_good[1], (float)s->n_pair_good[0] / s->n_pair_all[0] * 100.0, (float)s->n_pair_good[1] / s->n_pair_all[1] * 100.0);
+ printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
+ printf("%lld + %lld singletons (%.2f%%:%.2f%%)\n", s->n_sgltn[0], s->n_sgltn[1], (float)s->n_sgltn[0] / s->n_pair_all[0] * 100.0, (float)s->n_sgltn[1] / s->n_pair_all[1] * 100.0);
+ printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
+ printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
+ free(s);
+ bam_header_destroy(header);
+ bam_close(fp);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bam_tview.c b/src/samtools-0.1.18/bam_tview.c
new file mode 100644
index 0000000..4eea955
--- /dev/null
+++ b/src/samtools-0.1.18/bam_tview.c
@@ -0,0 +1,440 @@
+#undef _HAVE_CURSES
+
+#if _CURSES_LIB == 0
+#elif _CURSES_LIB == 1
+#include <curses.h>
+#ifndef NCURSES_VERSION
+#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
+#else
+#define _HAVE_CURSES
+#endif
+#elif _CURSES_LIB == 2
+#include <xcurses.h>
+#define _HAVE_CURSES
+#else
+#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
+#endif
+
+#ifdef _HAVE_CURSES
+#include <ctype.h>
+#include <assert.h>
+#include <string.h>
+#include <math.h>
+#include "bam.h"
+#include "faidx.h"
+#include "bam2bcf.h"
+
+char bam_aux_getCEi(bam1_t *b, int i);
+char bam_aux_getCSi(bam1_t *b, int i);
+char bam_aux_getCQi(bam1_t *b, int i);
+
+#define TV_MIN_ALNROW 2
+#define TV_MAX_GOTO 40
+#define TV_LOW_MAPQ 10
+
+#define TV_COLOR_MAPQ 0
+#define TV_COLOR_BASEQ 1
+#define TV_COLOR_NUCL 2
+#define TV_COLOR_COL 3
+#define TV_COLOR_COLQ 4
+
+#define TV_BASE_NUCL 0
+#define TV_BASE_COLOR_SPACE 1
+
+typedef struct {
+ int mrow, mcol;
+ WINDOW *wgoto, *whelp;
+
+ bam_index_t *idx;
+ bam_lplbuf_t *lplbuf;
+ bam_header_t *header;
+ bamFile fp;
+ int curr_tid, left_pos;
+ faidx_t *fai;
+ bcf_callaux_t *bca;
+
+ int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
+ char *ref;
+} tview_t;
+
+int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
+{
+ extern unsigned char bam_nt16_table[256];
+ tview_t *tv = (tview_t*)data;
+ int i, j, c, rb, attr, max_ins = 0;
+ uint32_t call = 0;
+ if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
+ // print referece
+ rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
+ for (i = tv->last_pos + 1; i < pos; ++i) {
+ if (i%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", i+1);
+ c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
+ mvaddch(1, tv->ccol++, c);
+ }
+ if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
+ { // call consensus
+ bcf_callret1_t bcr;
+ int qsum[4], a1, a2, tmp;
+ double p[3], prior = 30;
+ bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr);
+ for (i = 0; i < 4; ++i) qsum[i] = bcr.qsum[i]<<2 | i;
+ for (i = 1; i < 4; ++i) // insertion sort
+ for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j)
+ tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
+ a1 = qsum[0]&3; a2 = qsum[1]&3;
+ p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2];
+ if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3;
+ if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3;
+ if (p[0] < p[1] && p[0] < p[2]) call = (1<<a1)<<16 | (int)((p[1]<p[2]?p[1]:p[2]) - p[0] + .499);
+ else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
+ else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
+ }
+ attr = A_UNDERLINE;
+ c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
+ i = (call&0xffff)/10+1;
+ if (i > 4) i = 4;
+ attr |= COLOR_PAIR(i);
+ if (c == toupper(rb)) c = '.';
+ attron(attr);
+ mvaddch(2, tv->ccol, c);
+ attroff(attr);
+ if(tv->ins) {
+ // calculate maximum insert
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
+ }
+ }
+ // core loop
+ for (j = 0; j <= max_ins; ++j) {
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ int row = TV_MIN_ALNROW + p->level - tv->row_shift;
+ if (j == 0) {
+ if (!p->is_del) {
+ if (tv->base_for == TV_BASE_COLOR_SPACE &&
+ (c = bam_aux_getCSi(p->b, p->qpos))) {
+ c = bam_aux_getCSi(p->b, p->qpos);
+ // assume that if we found one color, we will be able to get the color error
+ if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
+ } else {
+ if (tv->show_name) {
+ char *name = bam1_qname(p->b);
+ c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos];
+ } else {
+ c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+ if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+ }
+ }
+ } else c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
+ } else { // padding
+ if (j > p->indel) c = '*';
+ else { // insertion
+ if (tv->base_for == TV_BASE_NUCL) {
+ if (tv->show_name) {
+ char *name = bam1_qname(p->b);
+ c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j];
+ } else {
+ c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
+ if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+ }
+ } else {
+ c = bam_aux_getCSi(p->b, p->qpos + j);
+ if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam1_strand(p->b)? ',' : '.';
+ }
+ }
+ }
+ if (row > TV_MIN_ALNROW && row < tv->mrow) {
+ int x;
+ attr = 0;
+ if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
+ || (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
+ if (tv->color_for == TV_COLOR_BASEQ) {
+ x = bam1_qual(p->b)[p->qpos]/10 + 1;
+ if (x > 4) x = 4;
+ attr |= COLOR_PAIR(x);
+ } else if (tv->color_for == TV_COLOR_MAPQ) {
+ x = p->b->core.qual/10 + 1;
+ if (x > 4) x = 4;
+ attr |= COLOR_PAIR(x);
+ } else if (tv->color_for == TV_COLOR_NUCL) {
+ x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
+ attr |= COLOR_PAIR(x);
+ } else if(tv->color_for == TV_COLOR_COL) {
+ x = 0;
+ switch(bam_aux_getCSi(p->b, p->qpos)) {
+ case '0': x = 0; break;
+ case '1': x = 1; break;
+ case '2': x = 2; break;
+ case '3': x = 3; break;
+ case '4': x = 4; break;
+ default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
+ }
+ x+=5;
+ attr |= COLOR_PAIR(x);
+ } else if(tv->color_for == TV_COLOR_COLQ) {
+ x = bam_aux_getCQi(p->b, p->qpos);
+ if(0 == x) x = bam1_qual(p->b)[p->qpos];
+ x = x/10 + 1;
+ if (x > 4) x = 4;
+ attr |= COLOR_PAIR(x);
+ }
+ attron(attr);
+ mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
+ attroff(attr);
+ }
+ }
+ c = j? '*' : rb;
+ if (c == '*') {
+ attr = COLOR_PAIR(8);
+ attron(attr);
+ mvaddch(1, tv->ccol++, c);
+ attroff(attr);
+ } else mvaddch(1, tv->ccol++, c);
+ }
+ tv->last_pos = pos;
+ return 0;
+}
+
+tview_t *tv_init(const char *fn, const char *fn_fa)
+{
+ tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
+ tv->is_dot = 1;
+ tv->fp = bam_open(fn, "r");
+ bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
+ assert(tv->fp);
+ tv->header = bam_header_read(tv->fp);
+ tv->idx = bam_index_load(fn);
+ if (tv->idx == 0) exit(1);
+ tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
+ if (fn_fa) tv->fai = fai_load(fn_fa);
+ tv->bca = bcf_call_init(0.83, 13);
+ tv->ins = 1;
+
+ initscr();
+ keypad(stdscr, TRUE);
+ clear();
+ noecho();
+ cbreak();
+ tv->mrow = 24; tv->mcol = 80;
+ getmaxyx(stdscr, tv->mrow, tv->mcol);
+ tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
+ tv->whelp = newwin(29, 40, 5, 5);
+ tv->color_for = TV_COLOR_MAPQ;
+ start_color();
+ init_pair(1, COLOR_BLUE, COLOR_BLACK);
+ init_pair(2, COLOR_GREEN, COLOR_BLACK);
+ init_pair(3, COLOR_YELLOW, COLOR_BLACK);
+ init_pair(4, COLOR_WHITE, COLOR_BLACK);
+ init_pair(5, COLOR_GREEN, COLOR_BLACK);
+ init_pair(6, COLOR_CYAN, COLOR_BLACK);
+ init_pair(7, COLOR_YELLOW, COLOR_BLACK);
+ init_pair(8, COLOR_RED, COLOR_BLACK);
+ init_pair(9, COLOR_BLUE, COLOR_BLACK);
+ return tv;
+}
+
+void tv_destroy(tview_t *tv)
+{
+ delwin(tv->wgoto); delwin(tv->whelp);
+ endwin();
+
+ bam_lplbuf_destroy(tv->lplbuf);
+ bcf_call_destroy(tv->bca);
+ bam_index_destroy(tv->idx);
+ if (tv->fai) fai_destroy(tv->fai);
+ free(tv->ref);
+ bam_header_destroy(tv->header);
+ bam_close(tv->fp);
+ free(tv);
+}
+
+int tv_fetch_func(const bam1_t *b, void *data)
+{
+ tview_t *tv = (tview_t*)data;
+ if (tv->no_skip) {
+ uint32_t *cigar = bam1_cigar(b); // this is cheating...
+ int i;
+ for (i = 0; i <b->core.n_cigar; ++i) {
+ if ((cigar[i]&0xf) == BAM_CREF_SKIP)
+ cigar[i] = cigar[i]>>4<<4 | BAM_CDEL;
+ }
+ }
+ bam_lplbuf_push(b, tv->lplbuf);
+ return 0;
+}
+
+int tv_draw_aln(tview_t *tv, int tid, int pos)
+{
+ // reset
+ clear();
+ tv->curr_tid = tid; tv->left_pos = pos;
+ tv->last_pos = tv->left_pos - 1;
+ tv->ccol = 0;
+ // print ref and consensus
+ if (tv->fai) {
+ char *str;
+ if (tv->ref) free(tv->ref);
+ str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
+ sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol);
+ tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
+ free(str);
+ }
+ // draw aln
+ bam_lplbuf_reset(tv->lplbuf);
+ bam_fetch(tv->fp, tv->idx, tv->curr_tid, tv->left_pos, tv->left_pos + tv->mcol, tv, tv_fetch_func);
+ bam_lplbuf_push(0, tv->lplbuf);
+
+ while (tv->ccol < tv->mcol) {
+ int pos = tv->last_pos + 1;
+ if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
+ mvaddch(1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
+ ++tv->last_pos;
+ }
+ return 0;
+}
+
+static void tv_win_goto(tview_t *tv, int *tid, int *pos)
+{
+ char str[256], *p;
+ int i, l = 0;
+ wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
+ mvwprintw(tv->wgoto, 1, 2, "Goto: ");
+ for (;;) {
+ int c = wgetch(tv->wgoto);
+ wrefresh(tv->wgoto);
+ if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
+ --l;
+ } else if (c == KEY_ENTER || c == '\012' || c == '\015') {
+ int _tid = -1, _beg, _end;
+ if (str[0] == '=') {
+ _beg = strtol(str+1, &p, 10) - 1;
+ if (_beg > 0) {
+ *pos = _beg;
+ return;
+ }
+ } else {
+ bam_parse_region(tv->header, str, &_tid, &_beg, &_end);
+ if (_tid >= 0) {
+ *tid = _tid; *pos = _beg;
+ return;
+ }
+ }
+ } else if (isgraph(c)) {
+ if (l < TV_MAX_GOTO) str[l++] = c;
+ } else if (c == '\027') l = 0;
+ else if (c == '\033') return;
+ str[l] = '\0';
+ for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
+ mvwprintw(tv->wgoto, 1, 8, "%s", str);
+ }
+}
+
+static void tv_win_help(tview_t *tv) {
+ int r = 1;
+ WINDOW *win = tv->whelp;
+ wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
+ mvwprintw(win, r++, 2, " -=- Help -=- ");
+ r++;
+ mvwprintw(win, r++, 2, "? This window");
+ mvwprintw(win, r++, 2, "Arrows Small scroll movement");
+ mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
+ mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
+ mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
+ mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
+ mvwprintw(win, r++, 2, "space Scroll one screen");
+ mvwprintw(win, r++, 2, "backspace Scroll back one screen");
+ mvwprintw(win, r++, 2, "g Go to specific location");
+ mvwprintw(win, r++, 2, "m Color for mapping qual");
+ mvwprintw(win, r++, 2, "n Color for nucleotide");
+ mvwprintw(win, r++, 2, "b Color for base quality");
+ mvwprintw(win, r++, 2, "c Color for cs color");
+ mvwprintw(win, r++, 2, "z Color for cs qual");
+ mvwprintw(win, r++, 2, ". Toggle on/off dot view");
+ mvwprintw(win, r++, 2, "s Toggle on/off ref skip");
+ mvwprintw(win, r++, 2, "r Toggle on/off rd name");
+ mvwprintw(win, r++, 2, "N Turn on nt view");
+ mvwprintw(win, r++, 2, "C Turn on cs view");
+ mvwprintw(win, r++, 2, "i Toggle on/off ins");
+ mvwprintw(win, r++, 2, "q Exit");
+ r++;
+ mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
+ mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
+ mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
+ wrefresh(win);
+ wgetch(win);
+}
+
+void tv_loop(tview_t *tv)
+{
+ int tid, pos;
+ tid = tv->curr_tid; pos = tv->left_pos;
+ while (1) {
+ int c = getch();
+ switch (c) {
+ case '?': tv_win_help(tv); break;
+ case '\033':
+ case 'q': goto end_loop;
+ case '/':
+ case 'g': tv_win_goto(tv, &tid, &pos); break;
+ case 'm': tv->color_for = TV_COLOR_MAPQ; break;
+ case 'b': tv->color_for = TV_COLOR_BASEQ; break;
+ case 'n': tv->color_for = TV_COLOR_NUCL; break;
+ case 'c': tv->color_for = TV_COLOR_COL; break;
+ case 'z': tv->color_for = TV_COLOR_COLQ; break;
+ case 's': tv->no_skip = !tv->no_skip; break;
+ case 'r': tv->show_name = !tv->show_name; break;
+ case KEY_LEFT:
+ case 'h': --pos; break;
+ case KEY_RIGHT:
+ case 'l': ++pos; break;
+ case KEY_SLEFT:
+ case 'H': pos -= 20; break;
+ case KEY_SRIGHT:
+ case 'L': pos += 20; break;
+ case '.': tv->is_dot = !tv->is_dot; break;
+ case 'N': tv->base_for = TV_BASE_NUCL; break;
+ case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
+ case 'i': tv->ins = !tv->ins; break;
+ case '\010': pos -= 1000; break;
+ case '\014': pos += 1000; break;
+ case ' ': pos += tv->mcol; break;
+ case KEY_UP:
+ case 'j': --tv->row_shift; break;
+ case KEY_DOWN:
+ case 'k': ++tv->row_shift; break;
+ case KEY_BACKSPACE:
+ case '\177': pos -= tv->mcol; break;
+ case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+ default: continue;
+ }
+ if (pos < 0) pos = 0;
+ if (tv->row_shift < 0) tv->row_shift = 0;
+ tv_draw_aln(tv, tid, pos);
+ }
+end_loop:
+ return;
+}
+
+int bam_tview_main(int argc, char *argv[])
+{
+ tview_t *tv;
+ if (argc == 1) {
+ fprintf(stderr, "Usage: bamtk tview <aln.bam> [ref.fasta]\n");
+ return 1;
+ }
+ tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
+ tv_draw_aln(tv, 0, 0);
+ tv_loop(tv);
+ tv_destroy(tv);
+ return 0;
+}
+#else // #ifdef _HAVE_CURSES
+#include <stdio.h>
+#warning "No curses library is available; tview is disabled."
+int bam_tview_main(int argc, char *argv[])
+{
+ fprintf(stderr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");
+ return 1;
+}
+#endif // #ifdef _HAVE_CURSES
diff --git a/src/samtools-0.1.18/bamtk.c b/src/samtools-0.1.18/bamtk.c
new file mode 100644
index 0000000..8ba2581
--- /dev/null
+++ b/src/samtools-0.1.18/bamtk.c
@@ -0,0 +1,109 @@
+#include <stdio.h>
+#include <unistd.h>
+#include <assert.h>
+#include <fcntl.h>
+#include "bam.h"
+
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+int bam_taf2baf(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
+int bam_merge(int argc, char *argv[]);
+int bam_index(int argc, char *argv[]);
+int bam_sort(int argc, char *argv[]);
+int bam_tview_main(int argc, char *argv[]);
+int bam_mating(int argc, char *argv[]);
+int bam_rmdup(int argc, char *argv[]);
+int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
+int bam_idxstats(int argc, char *argv[]);
+int main_samview(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_cut_target(int argc, char *argv[]);
+int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
+int main_depth(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
+
+int faidx_main(int argc, char *argv[]);
+
+static int usage()
+{
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
+ fprintf(stderr, "Version: %s\n\n", BAM_VERSION);
+ fprintf(stderr, "Usage: samtools <command> [options]\n\n");
+ fprintf(stderr, "Command: view SAM<->BAM conversion\n");
+ fprintf(stderr, " sort sort alignment file\n");
+ fprintf(stderr, " mpileup multi-way pileup\n");
+ fprintf(stderr, " depth compute the depth\n");
+ fprintf(stderr, " faidx index/extract FASTA\n");
+#if _CURSES_LIB != 0
+ fprintf(stderr, " tview text alignment viewer\n");
+#endif
+ fprintf(stderr, " index index alignment\n");
+ fprintf(stderr, " idxstats BAM index stats (r595 or later)\n");
+ fprintf(stderr, " fixmate fix mate information\n");
+ fprintf(stderr, " flagstat simple stats\n");
+ fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
+ fprintf(stderr, " merge merge sorted alignments\n");
+ fprintf(stderr, " rmdup remove PCR duplicates\n");
+ fprintf(stderr, " reheader replace BAM header\n");
+ fprintf(stderr, " cat concatenate BAMs\n");
+ fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
+ fprintf(stderr, " phase phase heterozygotes\n");
+ fprintf(stderr, "\n");
+#ifdef _WIN32
+ fprintf(stderr, "\
+Note: The Windows version of SAMtools is mainly designed for read-only\n\
+ operations, such as viewing the alignments and generating the pileup.\n\
+ Binary files generated by the Windows version may be buggy.\n\n");
+#endif
+ return 1;
+}
+
+int main(int argc, char *argv[])
+{
+#ifdef _WIN32
+ setmode(fileno(stdout), O_BINARY);
+ setmode(fileno(stdin), O_BINARY);
+#ifdef _USE_KNETFILE
+ knet_win32_init();
+#endif
+#endif
+ if (argc < 2) return usage();
+ if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
+ else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
+ else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
+ else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
+ else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
+ else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
+ else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
+ else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
+ else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
+ else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
+ else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
+ else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
+ else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
+ else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
+ else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
+ else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
+ else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
+ else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
+ else if (strcmp(argv[1], "pileup") == 0) {
+ fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
+ return 1;
+ }
+#if _CURSES_LIB != 0
+ else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
+#endif
+ else {
+ fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+ return 1;
+ }
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bcftools/Makefile b/src/samtools-0.1.18/bcftools/Makefile
new file mode 100644
index 0000000..9b6f863
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/Makefile
@@ -0,0 +1,51 @@
+CC= gcc
+CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
+DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+OMISC= ..
+AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
+PROG= bcftools
+INCLUDES=
+SUBDIRS= .
+
+.SUFFIXES:.c .o
+
+.c.o:
+ $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+ @target=`echo $@ | sed s/-recur//`; \
+ wdir=`pwd`; \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ cd $$subdir; \
+ $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+ cd $$wdir; \
+ done;
+
+all:$(PROG)
+
+lib:libbcf.a
+
+libbcf.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
+
+bcftools:lib $(AOBJS)
+ $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz
+
+bcf.o:bcf.h
+vcf.o:bcf.h
+index.o:bcf.h
+bcfutils.o:bcf.h
+prob1.o:prob1.h bcf.h
+call1.o:prob1.h bcf.h
+bcf2qcall.o:bcf.h
+main.o:bcf.h
+
+bcf.pdf:bcf.tex
+ pdflatex bcf
+
+cleanlocal:
+ rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
+
+clean:cleanlocal-recur
diff --git a/src/samtools-0.1.18/bcftools/README b/src/samtools-0.1.18/bcftools/README
new file mode 100644
index 0000000..1d7159d
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/README
@@ -0,0 +1,36 @@
+The view command of bcftools calls variants, tests Hardy-Weinberg
+equilibrium (HWE), tests allele balances and estimates allele frequency.
+
+This command calls a site as a potential variant if P(ref|D,F) is below
+0.9 (controlled by the -p option), where D is data and F is the prior
+allele frequency spectrum (AFS).
+
+The view command performs two types of allele balance tests, both based
+on Fisher's exact test for 2x2 contingency tables with the row variable
+being reference allele or not. In the first table, the column variable
+is strand. Two-tail P-value is taken. We test if variant bases tend to
+come from one strand. In the second table, the column variable is
+whether a base appears in the first or the last 11bp of the read.
+One-tail P-value is taken. We test if variant bases tend to occur
+towards the end of reads, which is usually an indication of
+misalignment.
+
+Site allele frequency is estimated in two ways. In the first way, the
+frequency is esimated as \argmax_f P(D|f) under the assumption of
+HWE. Prior AFS is not used. In the second way, the frequency is
+estimated as the posterior expectation of allele counts \sum_k
+kP(k|D,F), dividied by the total number of haplotypes. HWE is not
+assumed, but the estimate depends on the prior AFS. The two estimates
+largely agree when the signal is strong, but may differ greatly on weak
+sites as in this case, the prior plays an important role.
+
+To test HWE, we calculate the posterior distribution of genotypes
+(ref-hom, het and alt-hom). Chi-square test is performed. It is worth
+noting that the model used here is prior dependent and assumes HWE,
+which is different from both models for allele frequency estimate. The
+new model actually yields a third estimate of site allele frequency.
+
+The estimate allele frequency spectrum is printed to stderr per 64k
+sites. The estimate is in fact only the first round of a EM
+procedure. The second model (not the model for HWE testing) is used to
+estimate the AFS.
\ No newline at end of file
diff --git a/src/samtools-0.1.18/bcftools/bcf.c b/src/samtools-0.1.18/bcftools/bcf.c
new file mode 100644
index 0000000..84a8e76
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/bcf.c
@@ -0,0 +1,328 @@
+#include <string.h>
+#include <ctype.h>
+#include <stdio.h>
+#include "kstring.h"
+#include "bcf.h"
+
+bcf_t *bcf_open(const char *fn, const char *mode)
+{
+ bcf_t *b;
+ b = calloc(1, sizeof(bcf_t));
+ if (strchr(mode, 'w')) {
+ b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdout), mode);
+ } else {
+ b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
+ }
+#ifndef BCF_LITE
+ b->fp->owned_file = 1;
+#endif
+ return b;
+}
+
+int bcf_close(bcf_t *b)
+{
+ int ret;
+ if (b == 0) return 0;
+ ret = bgzf_close(b->fp);
+ free(b);
+ return ret;
+}
+
+int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
+{
+ if (b == 0 || h == 0) return -1;
+ bgzf_write(b->fp, "BCF\4", 4);
+ bgzf_write(b->fp, &h->l_nm, 4);
+ bgzf_write(b->fp, h->name, h->l_nm);
+ bgzf_write(b->fp, &h->l_smpl, 4);
+ bgzf_write(b->fp, h->sname, h->l_smpl);
+ bgzf_write(b->fp, &h->l_txt, 4);
+ bgzf_write(b->fp, h->txt, h->l_txt);
+ bgzf_flush(b->fp);
+ return 16 + h->l_nm + h->l_smpl + h->l_txt;
+}
+
+bcf_hdr_t *bcf_hdr_read(bcf_t *b)
+{
+ uint8_t magic[4];
+ bcf_hdr_t *h;
+ if (b == 0) return 0;
+ h = calloc(1, sizeof(bcf_hdr_t));
+ bgzf_read(b->fp, magic, 4);
+ bgzf_read(b->fp, &h->l_nm, 4);
+ h->name = malloc(h->l_nm);
+ bgzf_read(b->fp, h->name, h->l_nm);
+ bgzf_read(b->fp, &h->l_smpl, 4);
+ h->sname = malloc(h->l_smpl);
+ bgzf_read(b->fp, h->sname, h->l_smpl);
+ bgzf_read(b->fp, &h->l_txt, 4);
+ h->txt = malloc(h->l_txt);
+ bgzf_read(b->fp, h->txt, h->l_txt);
+ bcf_hdr_sync(h);
+ return h;
+}
+
+void bcf_hdr_destroy(bcf_hdr_t *h)
+{
+ if (h == 0) return;
+ free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
+ free(h);
+}
+
+static inline char **cnt_null(int l, char *str, int *_n)
+{
+ int n = 0;
+ char *p, **list;
+ *_n = 0;
+ if (l == 0 || str == 0) return 0;
+ for (p = str; p != str + l; ++p)
+ if (*p == 0) ++n;
+ *_n = n;
+ list = calloc(n, sizeof(void*));
+ list[0] = str;
+ for (p = str, n = 1; p < str + l - 1; ++p)
+ if (*p == 0) list[n++] = p + 1;
+ return list;
+}
+
+int bcf_hdr_sync(bcf_hdr_t *b)
+{
+ if (b == 0) return -1;
+ if (b->ns) free(b->ns);
+ if (b->sns) free(b->sns);
+ if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
+ else b->ns = 0, b->n_ref = 0;
+ b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
+ return 0;
+}
+
+int bcf_sync(bcf1_t *b)
+{
+ char *p, *tmp[5];
+ int i, n, n_smpl = b->n_smpl;
+ ks_tokaux_t aux;
+ // set ref, alt, flt, info, fmt
+ b->ref = b->alt = b->flt = b->info = b->fmt = 0;
+ for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
+ if (*p == 0 && p+1 != b->str + b->l_str) {
+ if (n == 5) {
+ ++n;
+ break;
+ } else tmp[n++] = p + 1;
+ }
+ }
+ if (n != 5) {
+ fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
+ return -1;
+ }
+ b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
+ // set n_alleles
+ if (*b->alt == 0) b->n_alleles = 1;
+ else {
+ for (p = b->alt, n = 1; *p; ++p)
+ if (*p == ',') ++n;
+ b->n_alleles = n + 1;
+ }
+ // set n_gi and gi[i].fmt
+ for (p = b->fmt, n = 1; *p; ++p)
+ if (*p == ':') ++n;
+ if (n > b->m_gi) {
+ int old_m = b->m_gi;
+ b->m_gi = n;
+ kroundup32(b->m_gi);
+ b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
+ memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
+ }
+ b->n_gi = n;
+ for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
+ b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
+ // set gi[i].len
+ for (i = 0; i < b->n_gi; ++i) {
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
+ b->gi[i].len = 2;
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
+ b->gi[i].len = 1;
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ b->gi[i].len = 4;
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
+ }
+ b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
+ }
+ return 0;
+}
+
+int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
+{
+ int i, l = 0;
+ if (b == 0) return -1;
+ bgzf_write(bp->fp, &b->tid, 4);
+ bgzf_write(bp->fp, &b->pos, 4);
+ bgzf_write(bp->fp, &b->qual, 4);
+ bgzf_write(bp->fp, &b->l_str, 4);
+ bgzf_write(bp->fp, b->str, b->l_str);
+ l = 12 + b->l_str;
+ for (i = 0; i < b->n_gi; ++i) {
+ bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
+ l += b->gi[i].len * h->n_smpl;
+ }
+ return l;
+}
+
+int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
+{
+ int i, l = 0;
+ if (b == 0) return -1;
+ if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
+ b->n_smpl = h->n_smpl;
+ bgzf_read(bp->fp, &b->pos, 4);
+ bgzf_read(bp->fp, &b->qual, 4);
+ bgzf_read(bp->fp, &b->l_str, 4);
+ if (b->l_str > b->m_str) {
+ b->m_str = b->l_str;
+ kroundup32(b->m_str);
+ b->str = realloc(b->str, b->m_str);
+ }
+ bgzf_read(bp->fp, b->str, b->l_str);
+ l = 12 + b->l_str;
+ if (bcf_sync(b) < 0) return -2;
+ for (i = 0; i < b->n_gi; ++i) {
+ bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
+ l += b->gi[i].len * h->n_smpl;
+ }
+ return l;
+}
+
+int bcf_destroy(bcf1_t *b)
+{
+ int i;
+ if (b == 0) return -1;
+ free(b->str);
+ for (i = 0; i < b->m_gi; ++i)
+ free(b->gi[i].data);
+ free(b->gi);
+ free(b);
+ return 0;
+}
+
+static inline void fmt_str(const char *p, kstring_t *s)
+{
+ if (*p == 0) kputc('.', s);
+ else kputs(p, s);
+}
+
+void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
+{
+ int i, j, x;
+ s->l = 0;
+ if (h->n_ref) kputs(h->ns[b->tid], s);
+ else kputw(b->tid, s);
+ kputc('\t', s);
+ kputw(b->pos + 1, s); kputc('\t', s);
+ fmt_str(b->str, s); kputc('\t', s);
+ fmt_str(b->ref, s); kputc('\t', s);
+ fmt_str(b->alt, s); kputc('\t', s);
+ ksprintf(s, "%.3g", b->qual); kputc('\t', s);
+ fmt_str(b->flt, s); kputc('\t', s);
+ fmt_str(b->info, s);
+ if (b->fmt[0]) {
+ kputc('\t', s);
+ fmt_str(b->fmt, s);
+ }
+ x = b->n_alleles * (b->n_alleles + 1) / 2;
+ if (b->n_gi == 0) return;
+ for (j = 0; j < h->n_smpl; ++j) {
+ kputc('\t', s);
+ for (i = 0; i < b->n_gi; ++i) {
+ if (i) kputc(':', s);
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
+ int k;
+ for (k = 0; k < x; ++k) {
+ if (k > 0) kputc(',', s);
+ kputw(d[k], s);
+ }
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ kputw(((uint16_t*)b->gi[i].data)[j], s);
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
+ kputw(((uint8_t*)b->gi[i].data)[j], s);
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ kputw(((int32_t*)b->gi[i].data)[j], s);
+ } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
+ int y = ((uint8_t*)b->gi[i].data)[j];
+ if (y>>7&1) {
+ kputsn("./.", 3, s);
+ } else {
+ kputc('0' + (y>>3&7), s);
+ kputc("/|"[y>>6&1], s);
+ kputc('0' + (y&7), s);
+ }
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ float *d = (float*)b->gi[i].data + j * x;
+ int k;
+ //printf("- %lx\n", d);
+ for (k = 0; k < x; ++k) {
+ if (k > 0) kputc(',', s);
+ ksprintf(s, "%.2f", d[k]);
+ }
+ } else kputc('.', s); // custom fields
+ }
+ }
+}
+
+char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
+{
+ kstring_t s;
+ s.l = s.m = 0; s.s = 0;
+ bcf_fmt_core(h, b, &s);
+ return s.s;
+}
+
+int bcf_append_info(bcf1_t *b, const char *info, int l)
+{
+ int shift = b->fmt - b->str;
+ int l_fmt = b->l_str - shift;
+ char *ori = b->str;
+ if (b->l_str + l > b->m_str) { // enlarge if necessary
+ b->m_str = b->l_str + l;
+ kroundup32(b->m_str);
+ b->str = realloc(b->str, b->m_str);
+ }
+ memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
+ memcpy(b->str + shift - 1, info, l); // append to the INFO field
+ b->str[shift + l - 1] = '\0';
+ b->fmt = b->str + shift + l;
+ b->l_str += l;
+ if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
+ return 0;
+}
+
+int bcf_cpy(bcf1_t *r, const bcf1_t *b)
+{
+ char *t1 = r->str;
+ bcf_ginfo_t *t2 = r->gi;
+ int i, t3 = r->m_str, t4 = r->m_gi;
+ *r = *b;
+ r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
+ if (r->m_str < b->m_str) {
+ r->m_str = b->m_str;
+ r->str = realloc(r->str, r->m_str);
+ }
+ memcpy(r->str, b->str, r->m_str);
+ bcf_sync(r); // calling bcf_sync() is simple but inefficient
+ for (i = 0; i < r->n_gi; ++i)
+ memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
+ return 0;
+}
+
+int bcf_is_indel(const bcf1_t *b)
+{
+ char *p;
+ if (strlen(b->ref) > 1) return 1;
+ for (p = b->alt; *p; ++p)
+ if (*p != ',' && p[1] != ',' && p[1] != '\0')
+ return 1;
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bcftools/bcf.h b/src/samtools-0.1.18/bcftools/bcf.h
new file mode 100644
index 0000000..822ae5c
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/bcf.h
@@ -0,0 +1,190 @@
+/* The MIT License
+
+ Copyright (c) 2010 Broad Institute
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3 at live.co.uk> */
+
+#ifndef BCF_H
+#define BCF_H
+
+#define BCF_VERSION "0.1.17-dev (r973:277)"
+
+#include <stdint.h>
+#include <zlib.h>
+
+#ifndef BCF_LITE
+#include "bgzf.h"
+typedef BGZF *bcfFile;
+#else
+typedef gzFile bcfFile;
+#define bgzf_open(fn, mode) gzopen(fn, mode)
+#define bgzf_fdopen(fd, mode) gzdopen(fd, mode)
+#define bgzf_close(fp) gzclose(fp)
+#define bgzf_read(fp, buf, len) gzread(fp, buf, len)
+#define bgzf_write(fp, buf, len)
+#define bgzf_flush(fp)
+#endif
+
+/*
+ A member in the structs below is said to "primary" if its content
+ cannot be inferred from other members in any of structs below; a
+ member is said to be "derived" if its content can be derived from
+ other members. For example, bcf1_t::str is primary as this comes from
+ the input data, while bcf1_t::info is derived as it can always be
+ correctly set if we know bcf1_t::str. Derived members are for quick
+ access to the content and must be synchronized with the primary data.
+ */
+
+typedef struct {
+ uint32_t fmt; // format of the block, set by bcf_str2int().
+ int len; // length of data for each individual
+ void *data; // concatenated data
+ // derived info: fmt, len (<-bcf1_t::fmt)
+} bcf_ginfo_t;
+
+typedef struct {
+ int32_t tid, pos; // refID and 0-based position
+ int32_t l_str, m_str; // length and the allocated size of ->str
+ float qual; // SNP quality
+ char *str; // concatenated string of variable length strings in VCF (from col.2 to col.7)
+ char *ref, *alt, *flt, *info, *fmt; // they all point to ->str; no memory allocation
+ int n_gi, m_gi; // number and the allocated size of geno fields
+ bcf_ginfo_t *gi; // array of geno fields
+ int n_alleles, n_smpl; // number of alleles and samples
+ // derived info: ref, alt, flt, info, fmt (<-str), n_gi (<-fmt), n_alleles (<-alt), n_smpl (<-bcf_hdr_t::n_smpl)
+} bcf1_t;
+
+typedef struct {
+ int32_t n_ref, n_smpl; // number of reference sequences and samples
+ int32_t l_nm; // length of concatenated sequence names; 0 padded
+ int32_t l_smpl; // length of concatenated sample names; 0 padded
+ int32_t l_txt; // length of header text (lines started with ##)
+ char *name, *sname, *txt; // concatenated sequence names, sample names and header text
+ char **ns, **sns; // array of sequence and sample names; point to name and sname, respectively
+ // derived info: n_ref (<-name), n_smpl (<-sname), ns (<-name), sns (<-sname)
+} bcf_hdr_t;
+
+typedef struct {
+ int is_vcf; // if the file in operation is a VCF
+ void *v; // auxillary data structure for VCF
+ bcfFile fp; // file handler for BCF
+} bcf_t;
+
+struct __bcf_idx_t;
+typedef struct __bcf_idx_t bcf_idx_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ // open a BCF file; for BCF file only
+ bcf_t *bcf_open(const char *fn, const char *mode);
+ // close file
+ int bcf_close(bcf_t *b);
+ // read one record from BCF; return -1 on end-of-file, and <-1 for errors
+ int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b);
+ // call this function if b->str is changed
+ int bcf_sync(bcf1_t *b);
+ // write a BCF record
+ int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b);
+ // read the BCF header; BCF only
+ bcf_hdr_t *bcf_hdr_read(bcf_t *b);
+ // write the BCF header
+ int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h);
+ // set bcf_hdr_t::ns and bcf_hdr_t::sns
+ int bcf_hdr_sync(bcf_hdr_t *b);
+ // destroy the header
+ void bcf_hdr_destroy(bcf_hdr_t *h);
+ // destroy a record
+ int bcf_destroy(bcf1_t *b);
+ // BCF->VCF conversion
+ char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b);
+ // append more info
+ int bcf_append_info(bcf1_t *b, const char *info, int l);
+ // copy
+ int bcf_cpy(bcf1_t *r, const bcf1_t *b);
+
+ // open a VCF or BCF file if "b" is set in "mode"
+ bcf_t *vcf_open(const char *fn, const char *mode);
+ // close a VCF/BCF file
+ int vcf_close(bcf_t *bp);
+ // read the VCF/BCF header
+ bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
+ // read the sequence dictionary from a separate file; required for VCF->BCF conversion
+ int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn);
+ // read a VCF/BCF record; return -1 on end-of-file and <-1 for errors
+ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
+ // write the VCF header
+ int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h);
+ // write a VCF record
+ int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
+
+ // keep the first n alleles and discard the rest
+ int bcf_shrink_alt(bcf1_t *b, int n);
+ // convert GL to PL
+ int bcf_gl2pl(bcf1_t *b);
+ // if the site is an indel
+ int bcf_is_indel(const bcf1_t *b);
+ bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list);
+ int bcf_subsam(int n_smpl, int *list, bcf1_t *b);
+ // move GT to the first FORMAT field
+ int bcf_fix_gt(bcf1_t *b);
+ // update PL generated by old samtools
+ int bcf_fix_pl(bcf1_t *b);
+ // convert PL to GLF-like 10-likelihood GL
+ int bcf_gl10(const bcf1_t *b, uint8_t *gl);
+ // convert up to 4 INDEL alleles to GLF-like 10-likelihood GL
+ int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl);
+
+ // string hash table
+ void *bcf_build_refhash(bcf_hdr_t *h);
+ void bcf_str2id_destroy(void *_hash);
+ void bcf_str2id_thorough_destroy(void *_hash);
+ int bcf_str2id_add(void *_hash, const char *str);
+ int bcf_str2id(void *_hash, const char *str);
+ void *bcf_str2id_init();
+
+ // indexing related functions
+ int bcf_idx_build(const char *fn);
+ uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg);
+ int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end);
+ bcf_idx_t *bcf_idx_load(const char *fn);
+ void bcf_idx_destroy(bcf_idx_t *idx);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline uint32_t bcf_str2int(const char *str, int l)
+{
+ int i;
+ uint32_t x = 0;
+ for (i = 0; i < l && i < 4; ++i) {
+ if (str[i] == 0) return x;
+ x = x<<8 | str[i];
+ }
+ return x;
+}
+
+#endif
diff --git a/src/samtools-0.1.18/bcftools/bcf.tex b/src/samtools-0.1.18/bcftools/bcf.tex
new file mode 100644
index 0000000..442fc2a
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/bcf.tex
@@ -0,0 +1,77 @@
+\documentclass[10pt,pdftex]{article}
+\usepackage{color}
+\definecolor{gray}{rgb}{0.7,0.7,0.7}
+
+\setlength{\topmargin}{0.0cm}
+\setlength{\textheight}{21.5cm}
+\setlength{\oddsidemargin}{0cm}
+\setlength{\textwidth}{16.5cm}
+\setlength{\columnsep}{0.6cm}
+
+\begin{document}
+
+\begin{center}
+\begin{tabular}{|l|l|l|l|l|}
+\hline
+\multicolumn{2}{|c|}{\bf Field} & \multicolumn{1}{c|}{\bf Descrption} & \multicolumn{1}{c|}{\bf Type} & \multicolumn{1}{c|}{\bf Value} \\\hline\hline
+\multicolumn{2}{|l|}{\sf magic} & Magic string & {\tt char[4]} & {\tt BCF\char92 4} \\\hline
+\multicolumn{2}{|l|}{\sf l\_seqnm} & Length of concatenated sequence names & {\tt int32\_t} & \\\hline
+\multicolumn{2}{|l|}{\sf seqnm} & Concatenated names, {\tt NULL} padded & {\tt char[{\sf l\_seqnm}]} & \\\hline
+\multicolumn{2}{|l|}{\sf l\_smpl} & Length of concatenated sample names & {\tt int32\_t} & \\\hline
+\multicolumn{2}{|l|}{\sf smpl} & Concatenated sample names & {\tt char[{\sf l\_smpl}]} & \\\hline
+\multicolumn{2}{|l|}{\sf l\_meta} & Length of the meta text (double-hash lines)& {\tt int32\_t} & \\\hline
+\multicolumn{2}{|l|}{\sf meta} & Meta text, {\tt NULL} terminated & {\tt char[{\sf l\_meta}]} & \\\hline
+\multicolumn{5}{|c|}{\it \color{gray}{List of records until the end of the file}}\\\cline{2-5}
+& {\sf seq\_id} & Reference sequence ID & {\tt int32\_t} & \\\cline{2-5}
+& {\sf pos} & Position & {\tt int32\_t} & \\\cline{2-5}
+& {\sf qual} & Variant quality & {\tt float} & \\\cline{2-5}
+& {\sf l\_str} & Length of {\sf str} & {\tt int32\_t} & \\\cline{2-5}
+& {\sf str} & {\tt ID+REF+ALT+FILTER+INFO+FORMAT}, {\tt NULL} padded & {\tt char[{\sf l\_str}]} &\\\cline{2-5}
+& \multicolumn{4}{c|}{Blocks of data; \#blocks and formats defined by {\tt FORMAT} (table below)}\\
+\hline
+\end{tabular}
+\end{center}
+
+\begin{center}
+\begin{tabular}{clp{9cm}}
+\hline
+\multicolumn{1}{l}{\bf Field} & \multicolumn{1}{l}{\bf Type} & \multicolumn{1}{l}{\bf Description} \\\hline
+{\tt DP} & {\tt uint16\_t[n]} & Read depth \\
+{\tt GL} & {\tt float[n*G]} & Log10 likelihood of data; $G=\frac{A(A+1)}{2}$, $A=\#\{alleles\}$\\
+{\tt GT} & {\tt uint8\_t[n]} & {\tt missing\char60\char60 7 | phased\char60\char60 6 | allele1\char60\char60 3 | allele2} \\
+{\tt \_GT} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic GT; the first int equals the max ploidy $P$. If the highest bit is set,
+ the allele is not present (e.g. due to different ploidy between samples).} \\
+{\tt GQ} & {\tt uint8\_t[n]} & {Genotype quality}\\
+{\tt HQ} & {\tt uint8\_t[n*2]} & {Haplotype quality}\\
+{\tt \_HQ} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic HQ}\\
+{\tt IBD} & {\tt uint32\_t[n*2]} & {IBD}\\
+{\tt \_IBD} & {\tt uint8\_t+uint32\_t[n*P]} & {Generic IBD}\\
+{\tt PL} & {\tt uint8\_t[n*G]} & {Phred-scaled likelihood of data}\\
+{\tt PS} & {\tt uint32\_t[n]} & {Phase set}\\
+%{\tt SP} & {\tt uint8\_t[n]} & {Strand bias P-value (bcftools only)}\\
+\emph{Integer} & {\tt int32\_t[n*X]} & {Fix-sized custom Integer; $X$ defined in the header}\\
+\emph{Numeric} & {\tt double[n*X]} & {Fix-sized custom Numeric}\\
+\emph{String} & {\tt uint32\_t+char*} & {\tt NULL} padded concat. strings (int equals to the length) \\
+\hline
+\end{tabular}
+\end{center}
+
+\begin{itemize}
+\item A BCF file is in the {\tt BGZF} format.
+\item All multi-byte numbers are little-endian.
+\item In a string, a missing value `.' is an empty C string ``{\tt
+ \char92 0}'' (not ``{\tt .\char92 0}'')
+\item For {\tt GL} and {\tt PL}, likelihoods of genotypes appear in the
+ order of alleles in {\tt REF} and then {\tt ALT}. For example, if {\tt
+ REF=C}, {\tt ALT=T,A}, likelihoods appear in the order of {\tt
+ CC,CT,TT,CA,TA,AA} (NB: the ordering is different from the one in the original
+ BCF proposal).
+\item Predefined {\tt FORMAT} fields can be missing from VCF headers, but custom {\tt FORMAT} fields
+ are required to be explicitly defined in the headers.
+\item A {\tt FORMAT} field with its name starting with `{\tt \_}' is specific to BCF only.
+ It gives an alternative binary representation of the corresponding VCF field, in case
+ the default representation is unable to keep the genotype information,
+ for example, when the ploidy is not 2 or there are more than 8 alleles.
+\end{itemize}
+
+\end{document}
diff --git a/src/samtools-0.1.18/bcftools/bcf2qcall.c b/src/samtools-0.1.18/bcftools/bcf2qcall.c
new file mode 100644
index 0000000..a86bac2
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/bcf2qcall.c
@@ -0,0 +1,91 @@
+#include <errno.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include "bcf.h"
+
+static int8_t nt4_table[256] = {
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
+};
+
+static int read_I16(bcf1_t *b, int anno[16])
+{
+ char *p;
+ int i;
+ if ((p = strstr(b->info, "I16=")) == 0) return -1;
+ p += 4;
+ for (i = 0; i < 16; ++i) {
+ anno[i] = strtol(p, &p, 10);
+ if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
+ ++p;
+ }
+ return 0;
+}
+
+int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b)
+{
+ int a[4], k, g[10], l, map[4], k1, j, i, i0, anno[16], dp, mq, d_rest;
+ char *s;
+ if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ if (read_I16(b, anno) != 0) return -1; // no I16; FIXME: can be improved
+ d_rest = dp = anno[0] + anno[1] + anno[2] + anno[3];
+ if (dp == 0) return -1; // depth is zero
+ mq = (int)(sqrt((double)(anno[9] + anno[11]) / dp) + .499);
+ i0 = i;
+ a[0] = nt4_table[(int)b->ref[0]];
+ if (a[0] > 3) return -1; // ref is not A/C/G/T
+ a[1] = a[2] = a[3] = -2; // -1 has a special meaning
+ if (b->alt[0] == 0) return -1; // no alternate allele
+ map[0] = map[1] = map[2] = map[3] = -2;
+ map[a[0]] = 0;
+ for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) {
+ if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base
+ a[k+1] = nt4_table[(int)*s];
+ if (a[k+1] >= 0) map[a[k+1]] = k+1;
+ else k1 = k+1;
+ if (s[1] == 0) break;
+ }
+ for (k = 0; k < 4; ++k)
+ if (map[k] < 0) map[k] = k1;
+ for (i = 0; i < h->n_smpl; ++i) {
+ int d;
+ uint8_t *p = b->gi[i0].data + i * b->gi[i0].len;
+ for (j = 0; j < b->gi[i0].len; ++j)
+ if (p[j]) break;
+ d = (int)((double)d_rest / (h->n_smpl - i) + .499);
+ if (d == 0) d = 1;
+ if (j == b->gi[i0].len) d = 0;
+ d_rest -= d;
+ for (k = j = 0; k < 4; ++k) {
+ for (l = k; l < 4; ++l) {
+ int t, x = map[k], y = map[l];
+ if (x > y) t = x, x = y, y = t; // swap
+ g[j++] = p[y * (y+1) / 2 + x];
+ }
+ }
+ printf("%s\t%d\t%c", h->ns[b->tid], b->pos+1, *b->ref);
+ printf("\t%d\t%d\t0", d, mq);
+ for (j = 0; j < 10; ++j)
+ printf("\t%d", g[j]);
+ printf("\t%s\n", h->sns[i]);
+ }
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bcftools/bcfutils.c b/src/samtools-0.1.18/bcftools/bcfutils.c
new file mode 100644
index 0000000..0eab4c1
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/bcfutils.c
@@ -0,0 +1,390 @@
+#include <string.h>
+#include <math.h>
+#include "bcf.h"
+#include "kstring.h"
+#include "khash.h"
+KHASH_MAP_INIT_STR(str2id, int)
+
+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
+// FIXME: valgrind report a memory leak in this function. Probably it does not get deallocated...
+void *bcf_build_refhash(bcf_hdr_t *h)
+{
+ khash_t(str2id) *hash;
+ int i, ret;
+ hash = kh_init(str2id);
+ for (i = 0; i < h->n_ref; ++i) {
+ khint_t k;
+ k = kh_put(str2id, hash, h->ns[i], &ret); // FIXME: check ret
+ kh_val(hash, k) = i;
+ }
+ return hash;
+}
+
+void *bcf_str2id_init()
+{
+ return kh_init(str2id);
+}
+
+void bcf_str2id_destroy(void *_hash)
+{
+ khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+ if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
+}
+
+void bcf_str2id_thorough_destroy(void *_hash)
+{
+ khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+ khint_t k;
+ if (hash == 0) return;
+ for (k = 0; k < kh_end(hash); ++k)
+ if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+ kh_destroy(str2id, hash);
+}
+
+int bcf_str2id(void *_hash, const char *str)
+{
+ khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+ khint_t k;
+ if (!hash) return -1;
+ k = kh_get(str2id, hash, str);
+ return k == kh_end(hash)? -1 : kh_val(hash, k);
+}
+
+int bcf_str2id_add(void *_hash, const char *str)
+{
+ khint_t k;
+ int ret;
+ khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+ if (!hash) return -1;
+ k = kh_put(str2id, hash, str, &ret);
+ if (ret == 0) return kh_val(hash, k);
+ kh_val(hash, k) = kh_size(hash) - 1;
+ return kh_val(hash, k);
+}
+
+int bcf_shrink_alt(bcf1_t *b, int n)
+{
+ char *p;
+ int i, j, k, n_smpl = b->n_smpl;
+ if (b->n_alleles <= n) return -1;
+ // update ALT
+ if (n > 1) {
+ for (p = b->alt, k = 1; *p; ++p)
+ if (*p == ',' && ++k == n) break;
+ *p = '\0';
+ } else p = b->alt, *p = '\0';
+ ++p;
+ memmove(p, b->flt, b->str + b->l_str - b->flt);
+ b->l_str -= b->flt - p;
+ // update PL
+ for (i = 0; i < b->n_gi; ++i) {
+ bcf_ginfo_t *g = b->gi + i;
+ if (g->fmt == bcf_str2int("PL", 2)) {
+ int l, x = b->n_alleles * (b->n_alleles + 1) / 2;
+ uint8_t *d = (uint8_t*)g->data;
+ g->len = n * (n + 1) / 2;
+ for (l = k = 0; l < n_smpl; ++l) {
+ uint8_t *dl = d + l * x;
+ for (j = 0; j < g->len; ++j) d[k++] = dl[j];
+ }
+ } // FIXME: to add GL
+ }
+ b->n_alleles = n;
+ bcf_sync(b);
+ return 0;
+}
+
+int bcf_gl2pl(bcf1_t *b)
+{
+ char *p;
+ int i, n_smpl = b->n_smpl;
+ bcf_ginfo_t *g;
+ float *d0;
+ uint8_t *d1;
+ if (strstr(b->fmt, "PL")) return -1;
+ if ((p = strstr(b->fmt, "GL")) == 0) return -1;
+ *p = 'P';
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("GL", 2))
+ break;
+ g = b->gi + i;
+ g->fmt = bcf_str2int("PL", 2);
+ g->len /= 4; // 4 == sizeof(float)
+ d0 = (float*)g->data; d1 = (uint8_t*)g->data;
+ for (i = 0; i < n_smpl * g->len; ++i) {
+ int x = (int)(-10. * d0[i] + .499);
+ if (x > 255) x = 255;
+ if (x < 0) x = 0;
+ d1[i] = x;
+ }
+ return 0;
+}
+/* FIXME: this function will fail given AB:GTX:GT. BCFtools never
+ * produces such FMT, but others may do. */
+int bcf_fix_gt(bcf1_t *b)
+{
+ char *s;
+ int i;
+ uint32_t tmp;
+ bcf_ginfo_t gt;
+ // check the presence of the GT FMT
+ if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
+ if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
+ tmp = bcf_str2int("GT", 2);
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == tmp) break;
+ if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug...
+ gt = b->gi[i];
+ // move GT to the first
+ for (; i > 0; --i) b->gi[i] = b->gi[i-1];
+ b->gi[0] = gt;
+ memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
+ b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
+ return 0;
+}
+
+int bcf_fix_pl(bcf1_t *b)
+{
+ int i;
+ uint32_t tmp;
+ uint8_t *PL, *swap;
+ bcf_ginfo_t *gi;
+ // pinpoint PL
+ tmp = bcf_str2int("PL", 2);
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == tmp) break;
+ if (i == b->n_gi) return 0;
+ // prepare
+ gi = b->gi + i;
+ PL = (uint8_t*)gi->data;
+ swap = alloca(gi->len);
+ // loop through individuals
+ for (i = 0; i < b->n_smpl; ++i) {
+ int k, l, x;
+ uint8_t *PLi = PL + i * gi->len;
+ memcpy(swap, PLi, gi->len);
+ for (k = x = 0; k < b->n_alleles; ++k)
+ for (l = k; l < b->n_alleles; ++l)
+ PLi[l*(l+1)/2 + k] = swap[x++];
+ }
+ return 0;
+}
+
+int bcf_smpl_covered(const bcf1_t *b)
+{
+ int i, j, n = 0;
+ uint32_t tmp;
+ bcf_ginfo_t *gi;
+ // pinpoint PL
+ tmp = bcf_str2int("PL", 2);
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == tmp) break;
+ if (i == b->n_gi) return 0;
+ // count how many samples having PL!=[0..0]
+ gi = b->gi + i;
+ for (i = 0; i < b->n_smpl; ++i) {
+ uint8_t *PLi = ((uint8_t*)gi->data) + i * gi->len;
+ for (j = 0; j < gi->len; ++j)
+ if (PLi[j]) break;
+ if (j < gi->len) ++n;
+ }
+ return n;
+}
+
+static void *locate_field(const bcf1_t *b, const char *fmt, int l)
+{
+ int i;
+ uint32_t tmp;
+ tmp = bcf_str2int(fmt, l);
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == tmp) break;
+ return i == b->n_gi? 0 : b->gi[i].data;
+}
+
+int bcf_anno_max(bcf1_t *b)
+{
+ int k, max_gq, max_sp, n_het;
+ kstring_t str;
+ uint8_t *gt, *gq;
+ int32_t *sp;
+ max_gq = max_sp = n_het = 0;
+ gt = locate_field(b, "GT", 2);
+ if (gt == 0) return -1;
+ gq = locate_field(b, "GQ", 2);
+ sp = locate_field(b, "SP", 2);
+ if (sp)
+ for (k = 0; k < b->n_smpl; ++k)
+ if (gt[k]&0x3f)
+ max_sp = max_sp > (int)sp[k]? max_sp : sp[k];
+ if (gq)
+ for (k = 0; k < b->n_smpl; ++k)
+ if (gt[k]&0x3f)
+ max_gq = max_gq > (int)gq[k]? max_gq : gq[k];
+ for (k = 0; k < b->n_smpl; ++k) {
+ int a1, a2;
+ a1 = gt[k]&7; a2 = gt[k]>>3&7;
+ if ((!a1 && a2) || (!a2 && a1)) { // a het
+ if (gq == 0) ++n_het;
+ else if (gq[k] >= 20) ++n_het;
+ }
+ }
+ if (n_het) max_sp -= (int)(4.343 * log(n_het) + .499);
+ if (max_sp < 0) max_sp = 0;
+ memset(&str, 0, sizeof(kstring_t));
+ if (*b->info) kputc(';', &str);
+ ksprintf(&str, "MXSP=%d;MXGQ=%d", max_sp, max_gq);
+ bcf_append_info(b, str.s, str.l);
+ free(str.s);
+ return 0;
+}
+
+// FIXME: only data are shuffled; the header is NOT
+int bcf_shuffle(bcf1_t *b, int seed)
+{
+ int i, j, *a;
+ if (seed > 0) srand48(seed);
+ a = malloc(b->n_smpl * sizeof(int));
+ for (i = 0; i < b->n_smpl; ++i) a[i] = i;
+ for (i = b->n_smpl; i > 1; --i) {
+ int tmp;
+ j = (int)(drand48() * i);
+ tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;
+ }
+ for (j = 0; j < b->n_gi; ++j) {
+ bcf_ginfo_t *gi = b->gi + j;
+ uint8_t *swap, *data = (uint8_t*)gi->data;
+ swap = malloc(gi->len * b->n_smpl);
+ for (i = 0; i < b->n_smpl; ++i)
+ memcpy(swap + gi->len * a[i], data + gi->len * i, gi->len);
+ free(gi->data);
+ gi->data = swap;
+ }
+ free(a);
+ return 0;
+}
+
+bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list)
+{
+ int i, ret, j;
+ khint_t k;
+ bcf_hdr_t *h;
+ khash_t(str2id) *hash;
+ kstring_t s;
+ s.l = s.m = 0; s.s = 0;
+ hash = kh_init(str2id);
+ for (i = 0; i < h0->n_smpl; ++i) {
+ k = kh_put(str2id, hash, h0->sns[i], &ret);
+ kh_val(hash, k) = i;
+ }
+ for (i = j = 0; i < n; ++i) {
+ k = kh_get(str2id, hash, samples[i]);
+ if (k != kh_end(hash)) {
+ list[j++] = kh_val(hash, k);
+ kputs(samples[i], &s); kputc('\0', &s);
+ }
+ }
+ if (j < n) fprintf(stderr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
+ kh_destroy(str2id, hash);
+ h = calloc(1, sizeof(bcf_hdr_t));
+ *h = *h0;
+ h->ns = 0; h->sns = 0;
+ h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm);
+ h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt);
+ h->l_smpl = s.l; h->sname = s.s;
+ bcf_hdr_sync(h);
+ return h;
+}
+
+int bcf_subsam(int n_smpl, int *list, bcf1_t *b)
+{
+ int i, j;
+ for (j = 0; j < b->n_gi; ++j) {
+ bcf_ginfo_t *gi = b->gi + j;
+ uint8_t *swap;
+ swap = malloc(gi->len * b->n_smpl);
+ for (i = 0; i < n_smpl; ++i)
+ memcpy(swap + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len);
+ free(gi->data);
+ gi->data = swap;
+ }
+ b->n_smpl = n_smpl;
+ return 0;
+}
+
+static int8_t nt4_table[128] = {
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4
+};
+
+int bcf_gl10(const bcf1_t *b, uint8_t *gl)
+{
+ int a[4], k, l, map[4], k1, j, i;
+ const bcf_ginfo_t *PL;
+ char *s;
+ if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base or >4 alleles
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ PL = b->gi + i;
+ a[0] = nt4_table[(int)b->ref[0]];
+ if (a[0] > 3 || a[0] < 0) return -1; // ref is not A/C/G/T
+ a[1] = a[2] = a[3] = -2; // -1 has a special meaning
+ if (b->alt[0] == 0) return -1; // no alternate allele
+ map[0] = map[1] = map[2] = map[3] = -2;
+ map[a[0]] = 0;
+ for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) {
+ if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base
+ a[k+1] = nt4_table[(int)*s];
+ if (a[k+1] >= 0) map[a[k+1]] = k+1;
+ else k1 = k + 1;
+ if (s[1] == 0) break; // the end of the ALT string
+ }
+ for (k = 0; k < 4; ++k)
+ if (map[k] < 0) map[k] = k1;
+ for (i = 0; i < b->n_smpl; ++i) {
+ const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+ uint8_t *g = gl + 10 * i;
+ for (k = j = 0; k < 4; ++k) {
+ for (l = k; l < 4; ++l) {
+ int t, x = map[k], y = map[l];
+ if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+ g[j++] = p[y * (y+1) / 2 + x];
+ }
+ }
+ }
+ return 0;
+}
+
+int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl)
+{
+ int k, l, j, i;
+ const bcf_ginfo_t *PL;
+ if (b->alt[0] == 0) return -1; // no alternate allele
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ PL = b->gi + i;
+ for (i = 0; i < b->n_smpl; ++i) {
+ const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+ uint8_t *g = gl + 10 * i;
+ for (k = j = 0; k < 4; ++k) {
+ for (l = k; l < 4; ++l) {
+ int t, x = k, y = l;
+ if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+ x = y * (y+1) / 2 + x;
+ g[j++] = x < PL->len? p[x] : 255;
+ }
+ }
+ }
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bcftools/call1.c b/src/samtools-0.1.18/bcftools/call1.c
new file mode 100644
index 0000000..3cc4649
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/call1.c
@@ -0,0 +1,586 @@
+#include <unistd.h>
+#include <stdlib.h>
+#include <math.h>
+#include <zlib.h>
+#include <errno.h>
+#include "bcf.h"
+#include "prob1.h"
+#include "kstring.h"
+#include "time.h"
+
+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define lrand48() rand()
+#endif
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define VC_NO_GENO 2
+#define VC_BCFOUT 4
+#define VC_CALL 8
+#define VC_VARONLY 16
+#define VC_VCFIN 32
+#define VC_UNCOMP 64
+#define VC_KEEPALT 256
+#define VC_ACGT_ONLY 512
+#define VC_QCALL 1024
+#define VC_CALL_GT 2048
+#define VC_ADJLD 4096
+#define VC_NO_INDEL 8192
+#define VC_ANNO_MAX 16384
+#define VC_FIX_PL 32768
+#define VC_EM 0x10000
+#define VC_PAIRCALL 0x20000
+#define VC_QCNT 0x40000
+
+typedef struct {
+ int flag, prior_type, n1, n_sub, *sublist, n_perm;
+ uint32_t *trio_aux;
+ char *prior_file, **subsam, *fn_dict;
+ uint8_t *ploidy;
+ double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
+ void *bed;
+} viewconf_t;
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
+
+typedef struct {
+ double p[4];
+ int mq, depth, is_tested, d[4];
+} anno16_t;
+
+static double ttest(int n1, int n2, int a[4])
+{
+ extern double kf_betai(double a, double b, double x);
+ double t, v, u1, u2;
+ if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
+ u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
+ if (u1 <= u2) return 1.;
+ t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2));
+ v = n1 + n2 - 2;
+// printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2);
+ return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
+}
+
+static int test16_core(int anno[16], anno16_t *a)
+{
+ extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+ double left, right;
+ int i;
+ a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+ memcpy(a->d, anno, 4 * sizeof(int));
+ a->depth = anno[0] + anno[1] + anno[2] + anno[3];
+ a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
+ if (a->depth == 0) return -1;
+ a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
+ kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
+ for (i = 1; i < 4; ++i)
+ a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
+ return 0;
+}
+
+static int test16(bcf1_t *b, anno16_t *a)
+{
+ char *p;
+ int i, anno[16];
+ a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+ a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
+ a->mq = a->depth = a->is_tested = 0;
+ if ((p = strstr(b->info, "I16=")) == 0) return -1;
+ p += 4;
+ for (i = 0; i < 16; ++i) {
+ errno = 0; anno[i] = strtol(p, &p, 10);
+ if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
+ ++p;
+ }
+ return test16_core(anno, a);
+}
+
+static void rm_info(bcf1_t *b, const char *key)
+{
+ char *p, *q;
+ if ((p = strstr(b->info, key)) == 0) return;
+ for (q = p; *q && *q != ';'; ++q);
+ if (p > b->info && *(p-1) == ';') --p;
+ memmove(p, q, b->l_str - (q - b->str));
+ b->l_str -= q - p;
+ bcf_sync(b);
+}
+
+static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[10], int cons_llr, int64_t cons_gt)
+{
+ kstring_t s;
+ int has_I16, is_var;
+ double fq, r;
+ anno16_t a;
+
+ has_I16 = test16(b, &a) >= 0? 1 : 0;
+ rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
+
+ memset(&s, 0, sizeof(kstring_t));
+ kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
+ kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
+ kputs(b->info, &s);
+ if (b->info[0]) kputc(';', &s);
+ { // print EM
+ if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]);
+ if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]);
+ if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
+ if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
+ if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
+ }
+ if (cons_llr > 0) {
+ ksprintf(&s, ";CLR=%d", cons_llr);
+ if (cons_gt > 0)
+ ksprintf(&s, ";UGT=%c%c%c;CGT=%c%c%c", cons_gt&0xff, cons_gt>>8&0xff, cons_gt>>16&0xff,
+ cons_gt>>32&0xff, cons_gt>>40&0xff, cons_gt>>48&0xff);
+ }
+ if (pr == 0) { // if pr is unset, return
+ kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s);
+ free(b->str);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+ return 1;
+ }
+
+ is_var = (pr->p_ref < pref);
+ r = is_var? pr->p_ref : pr->p_var;
+
+// ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
+ ksprintf(&s, ";AC1=%d", pr->ac);
+ if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+ fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
+ if (fq < -999) fq = -999;
+ if (fq > 999) fq = 999;
+ ksprintf(&s, ";FQ=%.3g", fq);
+ if (pr->cmp[0] >= 0.) { // two sample groups
+ int i, q[3];
+ for (i = 1; i < 3; ++i) {
+ double x = pr->cmp[i] + pr->cmp[0]/2.;
+ q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
+ if (q[i] > 255) q[i] = 255;
+ }
+ if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
+ // ksprintf(&s, ";LRT3=%.3g", pr->lrt);
+ ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
+ }
+ if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
+ kputc('\0', &s);
+ kputs(b->fmt, &s); kputc('\0', &s);
+ free(b->str);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ b->qual = r < 1e-100? 999 : -4.343 * log(r);
+ if (b->qual > 999) b->qual = 999;
+ bcf_sync(b);
+ if (!is_var) bcf_shrink_alt(b, 1);
+ else if (!(flag&VC_KEEPALT))
+ bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1);
+ if (is_var && (flag&VC_CALL_GT)) { // call individual genotype
+ int i, x, old_n_gi = b->n_gi;
+ s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
+ kputs(":GT:GQ", &s); kputc('\0', &s);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+ for (i = 0; i < b->n_smpl; ++i) {
+ x = bcf_p1_call_gt(pa, pr->f_exp, i);
+ ((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0;
+ ((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2;
+ }
+ }
+ return is_var;
+}
+
+static char **read_samples(const char *fn, int *_n)
+{
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t s;
+ int dret, n = 0, max = 0;
+ char **sam = 0;
+ *_n = 0;
+ s.l = s.m = 0; s.s = 0;
+ fp = gzopen(fn, "r");
+ if (fp == 0) return 0; // fail to open file
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ int l;
+ if (max == n) {
+ max = max? max<<1 : 4;
+ sam = realloc(sam, sizeof(void*)*max);
+ }
+ l = s.l;
+ sam[n] = malloc(s.l + 2);
+ strcpy(sam[n], s.s);
+ sam[n][l+1] = 2; // by default, diploid
+ if (dret != '\n') {
+ if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2
+ int x = (int)s.s[0] - '0';
+ if (x == 1 || x == 2) sam[n][l+1] = x;
+ else fprintf(stderr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__);
+ }
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ++n;
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(s.s);
+ *_n = n;
+ return sam;
+}
+
+static void write_header(bcf_hdr_t *h)
+{
+ kstring_t str;
+ str.l = h->l_txt? h->l_txt - 1 : 0;
+ str.m = str.l + 1; str.s = h->txt;
+ if (!strstr(str.s, "##INFO=<ID=DP,"))
+ kputs("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=DP4,"))
+ kputs("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=MQ,"))
+ kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=FQ,"))
+ kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AF1,"))
+ kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele frequency (assuming HWE)\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AC1,"))
+ kputs("##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=G3,"))
+ kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=HWE,"))
+ kputs("##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=CLR,"))
+ kputs("##INFO=<ID=CLR,Number=1,Type=Integer,Description=\"Log ratio of genotype likelihoods with and without the constraint\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=UGT,"))
+ kputs("##INFO=<ID=UGT,Number=1,Type=String,Description=\"The most probable unconstrained genotype configuration in the trio\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=CGT,"))
+ kputs("##INFO=<ID=CGT,Number=1,Type=String,Description=\"The most probable constrained genotype configuration in the trio\">\n", &str);
+// if (!strstr(str.s, "##INFO=<ID=CI95,"))
+// kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=PV4,"))
+ kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=INDEL,"))
+ kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=PC2,"))
+ kputs("##INFO=<ID=PC2,Number=2,Type=Integer,Description=\"Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=PCHI2,"))
+ kputs("##INFO=<ID=PCHI2,Number=1,Type=Float,Description=\"Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=QCHI2,"))
+ kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=RP,"))
+ kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=VDB,"))
+ kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GT,"))
+ kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
+ kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GL,"))
+ kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=DP,"))
+ kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=SP,"))
+ kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=PL,"))
+ kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
+ h->l_txt = str.l + 1; h->txt = str.s;
+}
+
+double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
+
+int bcfview(int argc, char *argv[])
+{
+ extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
+ extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
+ extern int bcf_fix_gt(bcf1_t *b);
+ extern int bcf_anno_max(bcf1_t *b);
+ extern int bcf_shuffle(bcf1_t *b, int seed);
+ extern uint32_t *bcf_trio_prep(int is_x, int is_son);
+ extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
+ extern int bcf_pair_call(const bcf1_t *b);
+ extern int bcf_min_diff(const bcf1_t *b);
+
+ bcf_t *bp, *bout = 0;
+ bcf1_t *b, *blast;
+ int c, *seeds = 0;
+ uint64_t n_processed = 0, qcnt[256];
+ viewconf_t vc;
+ bcf_p1aux_t *p1 = 0;
+ bcf_hdr_t *hin, *hout;
+ int tid, begin, end;
+ char moder[4], modew[4];
+
+ tid = begin = end = -1;
+ memset(&vc, 0, sizeof(viewconf_t));
+ vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
+ memset(qcnt, 0, 8 * 256);
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Y")) >= 0) {
+ switch (c) {
+ case '1': vc.n1 = atoi(optarg); break;
+ case 'l': vc.bed = bed_read(optarg); break;
+ case 'D': vc.fn_dict = strdup(optarg); break;
+ case 'F': vc.flag |= VC_FIX_PL; break;
+ case 'N': vc.flag |= VC_ACGT_ONLY; break;
+ case 'G': vc.flag |= VC_NO_GENO; break;
+ case 'A': vc.flag |= VC_KEEPALT; break;
+ case 'b': vc.flag |= VC_BCFOUT; break;
+ case 'S': vc.flag |= VC_VCFIN; break;
+ case 'c': vc.flag |= VC_CALL; break;
+ case 'e': vc.flag |= VC_EM; break;
+ case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
+ case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
+ case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
+ case 'I': vc.flag |= VC_NO_INDEL; break;
+ case 'M': vc.flag |= VC_ANNO_MAX; break;
+ case 'Y': vc.flag |= VC_QCNT; break;
+ case 't': vc.theta = atof(optarg); break;
+ case 'p': vc.pref = atof(optarg); break;
+ case 'i': vc.indel_frac = atof(optarg); break;
+ case 'Q': vc.flag |= VC_QCALL; break;
+ case 'L': vc.flag |= VC_ADJLD; break;
+ case 'U': vc.n_perm = atoi(optarg); break;
+ case 'C': vc.min_lrt = atof(optarg); break;
+ case 'X': vc.min_perm_p = atof(optarg); break;
+ case 'd': vc.min_smpl_frac = atof(optarg); break;
+ case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
+ vc.ploidy = calloc(vc.n_sub + 1, 1);
+ for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
+ tid = -1;
+ break;
+ case 'T':
+ if (strcmp(optarg, "trioauto") == 0) vc.trio_aux = bcf_trio_prep(0, 0);
+ else if (strcmp(optarg, "trioxd") == 0) vc.trio_aux = bcf_trio_prep(1, 0);
+ else if (strcmp(optarg, "trioxs") == 0) vc.trio_aux = bcf_trio_prep(1, 1);
+ else if (strcmp(optarg, "pair") == 0) vc.flag |= VC_PAIRCALL;
+ else {
+ fprintf(stderr, "[%s] Option '-T' can only take value trioauto, trioxd or trioxs.\n", __func__);
+ return 1;
+ }
+ break;
+ case 'P':
+ if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
+ else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
+ else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
+ else vc.prior_file = strdup(optarg);
+ break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
+ fprintf(stderr, "Input/output options:\n\n");
+ fprintf(stderr, " -A keep all possible alternate alleles at variant sites\n");
+ fprintf(stderr, " -b output BCF instead of VCF\n");
+ fprintf(stderr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n");
+ fprintf(stderr, " -F PL generated by r921 or before (which generate old ordering)\n");
+ fprintf(stderr, " -G suppress all individual genotype information\n");
+ fprintf(stderr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n");
+ fprintf(stderr, " -L calculate LD for adjacent sites\n");
+ fprintf(stderr, " -N skip sites where REF is not A/C/G/T\n");
+ fprintf(stderr, " -Q output the QCALL likelihood format\n");
+ fprintf(stderr, " -s FILE list of samples to use [all samples]\n");
+ fprintf(stderr, " -S input is VCF\n");
+ fprintf(stderr, " -u uncompressed BCF output (force -b)\n");
+ fprintf(stderr, "\nConsensus/variant calling options:\n\n");
+ fprintf(stderr, " -c SNP calling (force -e)\n");
+ fprintf(stderr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n");
+ fprintf(stderr, " -e likelihood based analyses\n");
+ fprintf(stderr, " -g call genotypes at variant sites (force -c)\n");
+ fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
+ fprintf(stderr, " -I skip indels\n");
+ fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
+ fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
+ fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
+ fprintf(stderr, " -T STR constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]\n");
+ fprintf(stderr, " -v output potential variant sites only (force -c)\n");
+ fprintf(stderr, "\nContrast calling and association test options:\n\n");
+ fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
+ fprintf(stderr, " -C FLOAT posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt);
+ fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
+ fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
+ fprintf(stderr, "\n");
+ return 1;
+ }
+
+ if (vc.flag & VC_CALL) vc.flag |= VC_EM;
+ if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) {
+ fprintf(stderr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
+ return 1;
+ }
+ if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here!
+ if (vc.n_perm > 0) {
+ seeds = malloc(vc.n_perm * sizeof(int));
+ srand48(time(0));
+ for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48();
+ }
+ b = calloc(1, sizeof(bcf1_t));
+ blast = calloc(1, sizeof(bcf1_t));
+ strcpy(moder, "r");
+ if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
+ strcpy(modew, "w");
+ if (vc.flag & VC_BCFOUT) strcat(modew, "b");
+ if (vc.flag & VC_UNCOMP) strcat(modew, "u");
+ bp = vcf_open(argv[optind], moder);
+ hin = hout = vcf_hdr_read(bp);
+ if (vc.fn_dict && (vc.flag & VC_VCFIN))
+ vcf_dictread(bp, hin, vc.fn_dict);
+ bout = vcf_open("-", modew);
+ if (!(vc.flag & VC_QCALL)) {
+ if (vc.n_sub) {
+ vc.sublist = calloc(vc.n_sub, sizeof(int));
+ hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
+ }
+ if (vc.flag & VC_CALL) write_header(hout);
+ vcf_hdr_write(bout, hout);
+ }
+ if (vc.flag & VC_CALL) {
+ p1 = bcf_p1_init(hout->n_smpl, vc.ploidy);
+ if (vc.prior_file) {
+ if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
+ fprintf(stderr, "[%s] fail to read the prior AFS.\n", __func__);
+ return 1;
+ }
+ } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
+ if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1
+ bcf_p1_set_n1(p1, vc.n1);
+ bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
+ }
+ if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
+ }
+ if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
+ void *str2id = bcf_build_refhash(hout);
+ if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
+ bcf_idx_t *idx;
+ idx = bcf_idx_load(argv[optind]);
+ if (idx) {
+ uint64_t off;
+ off = bcf_idx_query(idx, tid, begin);
+ if (off == 0) {
+ fprintf(stderr, "[%s] no records in the query region.\n", __func__);
+ return 1; // FIXME: a lot of memory leaks...
+ }
+ bgzf_seek(bp->fp, off, SEEK_SET);
+ bcf_idx_destroy(idx);
+ }
+ }
+ }
+ while (vcf_read(bp, hin, b) > 0) {
+ int is_indel, cons_llr = -1;
+ int64_t cons_gt = -1;
+ double em[10];
+ if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
+ if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
+ extern int bcf_smpl_covered(const bcf1_t *b);
+ int n = bcf_smpl_covered(b);
+ if ((double)n / b->n_smpl < vc.min_smpl_frac) continue;
+ }
+ if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b);
+ if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
+ is_indel = bcf_is_indel(b);
+ if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
+ if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
+ int x;
+ if (b->ref[0] == 0 || b->ref[1] != 0) continue;
+ x = toupper(b->ref[0]);
+ if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue;
+ }
+ if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue;
+ if (tid >= 0) {
+ int l = strlen(b->ref);
+ l = b->pos + (l > 0? l : 1);
+ if (b->tid != tid || b->pos >= end) break;
+ if (!(l > begin && end > b->pos)) continue;
+ }
+ ++n_processed;
+ if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference
+ int x = bcf_min_diff(b);
+ if (x > 255) x = 255;
+ if (x >= 0) ++qcnt[x];
+ }
+ if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
+ bcf_2qcall(hout, b);
+ continue;
+ }
+ if (vc.trio_aux) // do trio calling
+ bcf_trio_call(vc.trio_aux, b, &cons_llr, &cons_gt);
+ else if (vc.flag & VC_PAIRCALL)
+ cons_llr = bcf_pair_call(b);
+ if (vc.flag & (VC_CALL|VC_ADJLD|VC_EM)) bcf_gl2pl(b);
+ if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0x1ff, em);
+ else {
+ int i;
+ for (i = 0; i < 9; ++i) em[i] = -1.;
+ }
+ if (vc.flag & VC_CALL) { // call variants
+ bcf_p1rst_t pr;
+ int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
+ if (n_processed % 100000 == 0) {
+ fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
+ bcf_p1_dump_afs(p1);
+ }
+ if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
+ if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test
+ bcf_p1rst_t r;
+ int i, n = 0;
+ for (i = 0; i < vc.n_perm; ++i) {
+#ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
+ double x[10];
+ bcf_shuffle(b, seeds[i]);
+ bcf_em1(b, vc.n1, 1<<7, x);
+ if (x[7] < em[7]) ++n;
+#else
+ bcf_shuffle(b, seeds[i]);
+ bcf_p1_cal(b, 1, p1, &r);
+ if (pr.p_chi2 >= r.p_chi2) ++n;
+#endif
+ }
+ pr.perm_rank = n;
+ }
+ if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em, cons_llr, cons_gt);
+ } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em, cons_llr, cons_gt);
+ if (vc.flag & VC_ADJLD) { // compute LD
+ double f[4], r2;
+ if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
+ kstring_t s;
+ s.m = s.l = 0; s.s = 0;
+ if (*b->info) kputc(';', &s);
+ ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]);
+ bcf_append_info(b, s.s, s.l);
+ free(s.s);
+ }
+ bcf_cpy(blast, b);
+ }
+ if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b);
+ if (vc.flag & VC_NO_GENO) { // do not output GENO fields
+ b->n_gi = 0;
+ b->fmt[0] = '\0';
+ b->l_str = b->fmt - b->str + 1;
+ } else bcf_fix_gt(b);
+ vcf_write(bout, hout, b);
+ }
+ if (vc.prior_file) free(vc.prior_file);
+ if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
+ if (hin != hout) bcf_hdr_destroy(hout);
+ bcf_hdr_destroy(hin);
+ bcf_destroy(b); bcf_destroy(blast);
+ vcf_close(bp); vcf_close(bout);
+ if (vc.fn_dict) free(vc.fn_dict);
+ if (vc.ploidy) free(vc.ploidy);
+ if (vc.trio_aux) free(vc.trio_aux);
+ if (vc.n_sub) {
+ int i;
+ for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
+ free(vc.subsam); free(vc.sublist);
+ }
+ if (vc.bed) bed_destroy(vc.bed);
+ if (vc.flag & VC_QCNT)
+ for (c = 0; c < 256; ++c)
+ fprintf(stderr, "QT\t%d\t%lld\n", c, (long long)qcnt[c]);
+ if (seeds) free(seeds);
+ if (p1) bcf_p1_destroy(p1);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bcftools/em.c b/src/samtools-0.1.18/bcftools/em.c
new file mode 100644
index 0000000..b7dfe1a
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/em.c
@@ -0,0 +1,310 @@
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "bcf.h"
+#include "kmin.h"
+
+static double g_q2p[256];
+
+#define ITER_MAX 50
+#define ITER_TRY 10
+#define EPS 1e-5
+
+extern double kf_gammaq(double, double);
+
+/*
+ Generic routines
+ */
+// get the 3 genotype likelihoods
+static double *get_pdg3(const bcf1_t *b)
+{
+ double *pdg;
+ const uint8_t *PL = 0;
+ int i, PL_len = 0;
+ // initialize g_q2p if necessary
+ if (g_q2p[0] == 0.)
+ for (i = 0; i < 256; ++i)
+ g_q2p[i] = pow(10., -i / 10.);
+ // set PL and PL_len
+ for (i = 0; i < b->n_gi; ++i) {
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ PL = (const uint8_t*)b->gi[i].data;
+ PL_len = b->gi[i].len;
+ break;
+ }
+ }
+ if (i == b->n_gi) return 0; // no PL
+ // fill pdg
+ pdg = malloc(3 * b->n_smpl * sizeof(double));
+ for (i = 0; i < b->n_smpl; ++i) {
+ const uint8_t *pi = PL + i * PL_len;
+ double *p = pdg + i * 3;
+ p[0] = g_q2p[pi[2]]; p[1] = g_q2p[pi[1]]; p[2] = g_q2p[pi[0]];
+ }
+ return pdg;
+}
+
+// estimate site allele frequency in a very naive and inaccurate way
+static double est_freq(int n, const double *pdg)
+{
+ int i, gcnt[3], tmp1;
+ // get a rough estimate of the genotype frequency
+ gcnt[0] = gcnt[1] = gcnt[2] = 0;
+ for (i = 0; i < n; ++i) {
+ const double *p = pdg + i * 3;
+ if (p[0] != 1. || p[1] != 1. || p[2] != 1.) {
+ int which = p[0] > p[1]? 0 : 1;
+ which = p[which] > p[2]? which : 2;
+ ++gcnt[which];
+ }
+ }
+ tmp1 = gcnt[0] + gcnt[1] + gcnt[2];
+ return (tmp1 == 0)? -1.0 : (.5 * gcnt[1] + gcnt[2]) / tmp1;
+}
+
+/*
+ Single-locus EM
+ */
+
+typedef struct {
+ int beg, end;
+ const double *pdg;
+} minaux1_t;
+
+static double prob1(double f, void *data)
+{
+ minaux1_t *a = (minaux1_t*)data;
+ double p = 1., l = 0., f3[3];
+ int i;
+// printf("brent %lg\n", f);
+ if (f < 0 || f > 1) return 1e300;
+ f3[0] = (1.-f)*(1.-f); f3[1] = 2.*f*(1.-f); f3[2] = f*f;
+ for (i = a->beg; i < a->end; ++i) {
+ const double *pdg = a->pdg + i * 3;
+ p *= pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2];
+ if (p < 1e-200) l -= log(p), p = 1.;
+ }
+ return l - log(p);
+}
+
+// one EM iteration for allele frequency estimate
+static double freq_iter(double *f, const double *_pdg, int beg, int end)
+{
+ double f0 = *f, f3[3], err;
+ int i;
+// printf("em %lg\n", *f);
+ f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+ for (i = beg, f0 = 0.; i < end; ++i) {
+ const double *pdg = _pdg + i * 3;
+ f0 += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
+ / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
+ }
+ f0 /= (end - beg) * 2;
+ err = fabs(f0 - *f);
+ *f = f0;
+ return err;
+}
+
+/* The following function combines EM and Brent's method. When the signal from
+ * the data is strong, EM is faster but sometimes, EM may converge very slowly.
+ * When this happens, we switch to Brent's method. The idea is learned from
+ * Rasmus Nielsen.
+ */
+static double freqml(double f0, int beg, int end, const double *pdg)
+{
+ int i;
+ double f;
+ for (i = 0, f = f0; i < ITER_TRY; ++i)
+ if (freq_iter(&f, pdg, beg, end) < EPS) break;
+ if (i == ITER_TRY) { // haven't converged yet; try Brent's method
+ minaux1_t a;
+ a.beg = beg; a.end = end; a.pdg = pdg;
+ kmin_brent(prob1, f0 == f? .5*f0 : f0, f, (void*)&a, EPS, &f);
+ }
+ return f;
+}
+
+// one EM iteration for genotype frequency estimate
+static double g3_iter(double g[3], const double *_pdg, int beg, int end)
+{
+ double err, gg[3];
+ int i;
+ gg[0] = gg[1] = gg[2] = 0.;
+// printf("%lg,%lg,%lg\n", g[0], g[1], g[2]);
+ for (i = beg; i < end; ++i) {
+ double sum, tmp[3];
+ const double *pdg = _pdg + i * 3;
+ tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2];
+ sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg);
+ gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum;
+ }
+ err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]);
+ err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]);
+ g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2];
+ return err;
+}
+
+// perform likelihood ratio test
+static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3])
+{
+ double r;
+ int i;
+ for (i = 0, r = 1.; i < n1; ++i) {
+ const double *p = pdg + i * 3;
+ r *= (p[0] * f3[1][0] + p[1] * f3[1][1] + p[2] * f3[1][2])
+ / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
+ }
+ for (; i < n; ++i) {
+ const double *p = pdg + i * 3;
+ r *= (p[0] * f3[2][0] + p[1] * f3[2][1] + p[2] * f3[2][2])
+ / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
+ }
+ return r;
+}
+
+// x[0]: ref frequency
+// x[1..3]: alt-alt, alt-ref, ref-ref frequenc
+// x[4]: HWE P-value
+// x[5..6]: group1 freq, group2 freq
+// x[7]: 1-degree P-value
+// x[8]: 2-degree P-value
+int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10])
+{
+ double *pdg;
+ int i, n, n2;
+ if (b->n_alleles < 2) return -1; // one allele only
+ // initialization
+ if (n1 < 0 || n1 > b->n_smpl) n1 = 0;
+ if (flag & 1<<7) flag |= 7<<5; // compute group freq if LRT is required
+ if (flag & 0xf<<1) flag |= 0xf<<1;
+ n = b->n_smpl; n2 = n - n1;
+ pdg = get_pdg3(b);
+ if (pdg == 0) return -1;
+ for (i = 0; i < 10; ++i) x[i] = -1.; // set to negative
+ {
+ if ((x[0] = est_freq(n, pdg)) < 0.) {
+ free(pdg);
+ return -1; // no data
+ }
+ x[0] = freqml(x[0], 0, n, pdg);
+ }
+ if (flag & (0xf<<1|3<<8)) { // estimate the genotype frequency and test HWE
+ double *g = x + 1, f3[3], r;
+ f3[0] = g[0] = (1 - x[0]) * (1 - x[0]);
+ f3[1] = g[1] = 2 * x[0] * (1 - x[0]);
+ f3[2] = g[2] = x[0] * x[0];
+ for (i = 0; i < ITER_MAX; ++i)
+ if (g3_iter(g, pdg, 0, n) < EPS) break;
+ // Hardy-Weinberg equilibrium (HWE)
+ for (i = 0, r = 1.; i < n; ++i) {
+ double *p = pdg + i * 3;
+ r *= (p[0] * g[0] + p[1] * g[1] + p[2] * g[2]) / (p[0] * f3[0] + p[1] * f3[1] + p[2] * f3[2]);
+ }
+ x[4] = kf_gammaq(.5, log(r));
+ }
+ if ((flag & 7<<5) && n1 > 0 && n1 < n) { // group frequency
+ x[5] = freqml(x[0], 0, n1, pdg);
+ x[6] = freqml(x[0], n1, n, pdg);
+ }
+ if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value
+ double f[3], f3[3][3], tmp;
+ f[0] = x[0]; f[1] = x[5]; f[2] = x[6];
+ for (i = 0; i < 3; ++i)
+ f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i];
+ tmp = log(lk_ratio_test(n, n1, pdg, f3));
+ if (tmp < 0) tmp = 0;
+ x[7] = kf_gammaq(.5, tmp);
+ }
+ if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value
+ double g[3][3], tmp;
+ for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double));
+ for (i = 0; i < ITER_MAX; ++i)
+ if (g3_iter(g[1], pdg, 0, n1) < EPS) break;
+ for (i = 0; i < ITER_MAX; ++i)
+ if (g3_iter(g[2], pdg, n1, n) < EPS) break;
+ tmp = log(lk_ratio_test(n, n1, pdg, g));
+ if (tmp < 0) tmp = 0;
+ x[8] = kf_gammaq(1., tmp);
+ }
+ // free
+ free(pdg);
+ return 0;
+}
+
+/*
+ Two-locus EM (LD)
+ */
+
+#define _G1(h, k) ((h>>1&1) + (k>>1&1))
+#define _G2(h, k) ((h&1) + (k&1))
+
+// 0: the previous site; 1: the current site
+static int pair_freq_iter(int n, double *pdg[2], double f[4])
+{
+ double ff[4];
+ int i, k, h;
+// printf("%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]);
+ memset(ff, 0, 4 * sizeof(double));
+ for (i = 0; i < n; ++i) {
+ double *p[2], sum, tmp;
+ p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3;
+ for (k = 0, sum = 0.; k < 4; ++k)
+ for (h = 0; h < 4; ++h)
+ sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
+ for (k = 0; k < 4; ++k) {
+ tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)])
+ + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)])
+ + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)])
+ + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]);
+ ff[k] += f[k] * tmp / sum;
+ }
+ }
+ for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n);
+ return 0;
+}
+
+double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
+{
+ const bcf1_t *b[2];
+ int i, j, n_smpl;
+ double *pdg[2], flast[4], r, f0[2];
+ // initialize others
+ if (b0->n_smpl != b1->n_smpl) return -1; // different number of samples
+ n_smpl = b0->n_smpl;
+ b[0] = b0; b[1] = b1;
+ f[0] = f[1] = f[2] = f[3] = -1.;
+ if (b[0]->n_alleles < 2 || b[1]->n_alleles < 2) return -1; // one allele only
+ pdg[0] = get_pdg3(b0); pdg[1] = get_pdg3(b1);
+ if (pdg[0] == 0 || pdg[1] == 0) {
+ free(pdg[0]); free(pdg[1]);
+ return -1;
+ }
+ // set the initial value
+ f0[0] = est_freq(n_smpl, pdg[0]);
+ f0[1] = est_freq(n_smpl, pdg[1]);
+ f[0] = (1 - f0[0]) * (1 - f0[1]); f[3] = f0[0] * f0[1];
+ f[1] = (1 - f0[0]) * f0[1]; f[2] = f0[0] * (1 - f0[1]);
+ // iteration
+ for (j = 0; j < ITER_MAX; ++j) {
+ double eps = 0;
+ memcpy(flast, f, 4 * sizeof(double));
+ pair_freq_iter(n_smpl, pdg, f);
+ for (i = 0; i < 4; ++i) {
+ double x = fabs(f[i] - flast[i]);
+ if (x > eps) eps = x;
+ }
+ if (eps < EPS) break;
+ }
+ // free
+ free(pdg[0]); free(pdg[1]);
+ { // calculate r^2
+ double p[2], q[2], D;
+ p[0] = f[0] + f[1]; q[0] = 1 - p[0];
+ p[1] = f[0] + f[2]; q[1] = 1 - p[1];
+ D = f[0] * f[3] - f[1] * f[2];
+ r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1]));
+// printf("R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r);
+ if (isnan(r)) r = -1.;
+ }
+ return r;
+}
diff --git a/src/samtools-0.1.18/bcftools/fet.c b/src/samtools-0.1.18/bcftools/fet.c
new file mode 100644
index 0000000..5812517
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/fet.c
@@ -0,0 +1,112 @@
+#include <math.h>
+#include <stdlib.h>
+
+/* This program is implemented with ideas from this web page:
+ *
+ * http://www.langsrud.com/fisher.htm
+ */
+
+// log\binom{n}{k}
+static double lbinom(int n, int k)
+{
+ if (k == 0 || n == k) return 0;
+ return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
+}
+
+// n11 n12 | n1_
+// n21 n22 | n2_
+//-----------+----
+// n_1 n_2 | n
+
+// hypergeometric distribution
+static double hypergeo(int n11, int n1_, int n_1, int n)
+{
+ return exp(lbinom(n1_, n11) + lbinom(n-n1_, n_1-n11) - lbinom(n, n_1));
+}
+
+typedef struct {
+ int n11, n1_, n_1, n;
+ double p;
+} hgacc_t;
+
+// incremental version of hypergenometric distribution
+static double hypergeo_acc(int n11, int n1_, int n_1, int n, hgacc_t *aux)
+{
+ if (n1_ || n_1 || n) {
+ aux->n11 = n11; aux->n1_ = n1_; aux->n_1 = n_1; aux->n = n;
+ } else { // then only n11 changed; the rest fixed
+ if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
+ if (n11 == aux->n11 + 1) { // incremental
+ aux->p *= (double)(aux->n1_ - aux->n11) / n11
+ * (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1);
+ aux->n11 = n11;
+ return aux->p;
+ }
+ if (n11 == aux->n11 - 1) { // incremental
+ aux->p *= (double)aux->n11 / (aux->n1_ - n11)
+ * (aux->n11 + aux->n - aux->n1_ - aux->n_1) / (aux->n_1 - n11);
+ aux->n11 = n11;
+ return aux->p;
+ }
+ }
+ aux->n11 = n11;
+ }
+ aux->p = hypergeo(aux->n11, aux->n1_, aux->n_1, aux->n);
+ return aux->p;
+}
+
+double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two)
+{
+ int i, j, max, min;
+ double p, q, left, right;
+ hgacc_t aux;
+ int n1_, n_1, n;
+
+ n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n
+ max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail
+ min = n1_ + n_1 - n;
+ if (min < 0) min = 0; // min n11, for left tail
+ *two = *_left = *_right = 1.;
+ if (min == max) return 1.; // no need to do test
+ q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table
+ // left tail
+ p = hypergeo_acc(min, 0, 0, 0, &aux);
+ for (left = 0., i = min + 1; p < 0.99999999 * q; ++i) // loop until underflow
+ left += p, p = hypergeo_acc(i, 0, 0, 0, &aux);
+ --i;
+ if (p < 1.00000001 * q) left += p;
+ else --i;
+ // right tail
+ p = hypergeo_acc(max, 0, 0, 0, &aux);
+ for (right = 0., j = max - 1; p < 0.99999999 * q; --j) // loop until underflow
+ right += p, p = hypergeo_acc(j, 0, 0, 0, &aux);
+ ++j;
+ if (p < 1.00000001 * q) right += p;
+ else ++j;
+ // two-tail
+ *two = left + right;
+ if (*two > 1.) *two = 1.;
+ // adjust left and right
+ if (abs(i - n11) < abs(j - n11)) right = 1. - left + q;
+ else left = 1.0 - right + q;
+ *_left = left; *_right = right;
+ return q;
+}
+
+#ifdef FET_MAIN
+#include <stdio.h>
+
+int main(int argc, char *argv[])
+{
+ char id[1024];
+ int n11, n12, n21, n22;
+ double left, right, twotail, prob;
+
+ while (scanf("%s%d%d%d%d", id, &n11, &n12, &n21, &n22) == 5) {
+ prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &twotail);
+ printf("%s\t%d\t%d\t%d\t%d\t%.6g\t%.6g\t%.6g\t%.6g\n", id, n11, n12, n21, n22,
+ prob, left, right, twotail);
+ }
+ return 0;
+}
+#endif
diff --git a/src/samtools-0.1.18/bcftools/index.c b/src/samtools-0.1.18/bcftools/index.c
new file mode 100644
index 0000000..014856d
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/index.c
@@ -0,0 +1,335 @@
+#include <assert.h>
+#include <ctype.h>
+#include <sys/stat.h>
+#include "bam_endian.h"
+#include "kstring.h"
+#include "bcf.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+#define TAD_LIDX_SHIFT 13
+
+typedef struct {
+ int32_t n, m;
+ uint64_t *offset;
+} bcf_lidx_t;
+
+struct __bcf_idx_t {
+ int32_t n;
+ bcf_lidx_t *index2;
+};
+
+/************
+ * indexing *
+ ************/
+
+static inline void insert_offset2(bcf_lidx_t *index2, int _beg, int _end, uint64_t offset)
+{
+ int i, beg, end;
+ beg = _beg >> TAD_LIDX_SHIFT;
+ end = (_end - 1) >> TAD_LIDX_SHIFT;
+ if (index2->m < end + 1) {
+ int old_m = index2->m;
+ index2->m = end + 1;
+ kroundup32(index2->m);
+ index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
+ memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
+ }
+ if (beg == end) {
+ if (index2->offset[beg] == 0) index2->offset[beg] = offset;
+ } else {
+ for (i = beg; i <= end; ++i)
+ if (index2->offset[i] == 0) index2->offset[i] = offset;
+ }
+ if (index2->n < end + 1) index2->n = end + 1;
+}
+
+bcf_idx_t *bcf_idx_core(bcf_t *bp, bcf_hdr_t *h)
+{
+ bcf_idx_t *idx;
+ int32_t last_coor, last_tid;
+ uint64_t last_off;
+ kstring_t *str;
+ BGZF *fp = bp->fp;
+ bcf1_t *b;
+ int ret;
+
+ b = calloc(1, sizeof(bcf1_t));
+ str = calloc(1, sizeof(kstring_t));
+ idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t));
+ idx->n = h->n_ref;
+ idx->index2 = calloc(h->n_ref, sizeof(bcf_lidx_t));
+
+ last_tid = 0xffffffffu;
+ last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
+ while ((ret = bcf_read(bp, h, b)) > 0) {
+ int end, tmp;
+ if (last_tid != b->tid) { // change of chromosomes
+ last_tid = b->tid;
+ } else if (last_coor > b->pos) {
+ fprintf(stderr, "[bcf_idx_core] the input is out of order\n");
+ free(str->s); free(str); free(idx); bcf_destroy(b);
+ return 0;
+ }
+ tmp = strlen(b->ref);
+ end = b->pos + (tmp > 0? tmp : 1);
+ insert_offset2(&idx->index2[b->tid], b->pos, end, last_off);
+ last_off = bgzf_tell(fp);
+ last_coor = b->pos;
+ }
+ free(str->s); free(str); bcf_destroy(b);
+ return idx;
+}
+
+void bcf_idx_destroy(bcf_idx_t *idx)
+{
+ int i;
+ if (idx == 0) return;
+ for (i = 0; i < idx->n; ++i) free(idx->index2[i].offset);
+ free(idx->index2);
+ free(idx);
+}
+
+/******************
+ * index file I/O *
+ ******************/
+
+void bcf_idx_save(const bcf_idx_t *idx, BGZF *fp)
+{
+ int32_t i, ti_is_be;
+ ti_is_be = bam_is_big_endian();
+ bgzf_write(fp, "BCI\4", 4);
+ if (ti_is_be) {
+ uint32_t x = idx->n;
+ bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ } else bgzf_write(fp, &idx->n, 4);
+ for (i = 0; i < idx->n; ++i) {
+ bcf_lidx_t *index2 = idx->index2 + i;
+ // write linear index (index2)
+ if (ti_is_be) {
+ int x = index2->n;
+ bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ } else bgzf_write(fp, &index2->n, 4);
+ if (ti_is_be) { // big endian
+ int x;
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ bgzf_write(fp, index2->offset, 8 * index2->n);
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ } else bgzf_write(fp, index2->offset, 8 * index2->n);
+ }
+}
+
+static bcf_idx_t *bcf_idx_load_core(BGZF *fp)
+{
+ int i, ti_is_be;
+ char magic[4];
+ bcf_idx_t *idx;
+ ti_is_be = bam_is_big_endian();
+ if (fp == 0) {
+ fprintf(stderr, "[%s] fail to load index.\n", __func__);
+ return 0;
+ }
+ bgzf_read(fp, magic, 4);
+ if (strncmp(magic, "BCI\4", 4)) {
+ fprintf(stderr, "[%s] wrong magic number.\n", __func__);
+ return 0;
+ }
+ idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t));
+ bgzf_read(fp, &idx->n, 4);
+ if (ti_is_be) bam_swap_endian_4p(&idx->n);
+ idx->index2 = (bcf_lidx_t*)calloc(idx->n, sizeof(bcf_lidx_t));
+ for (i = 0; i < idx->n; ++i) {
+ bcf_lidx_t *index2 = idx->index2 + i;
+ int j;
+ bgzf_read(fp, &index2->n, 4);
+ if (ti_is_be) bam_swap_endian_4p(&index2->n);
+ index2->m = index2->n;
+ index2->offset = (uint64_t*)calloc(index2->m, 8);
+ bgzf_read(fp, index2->offset, index2->n * 8);
+ if (ti_is_be)
+ for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
+ }
+ return idx;
+}
+
+bcf_idx_t *bcf_idx_load_local(const char *fnidx)
+{
+ BGZF *fp;
+ fp = bgzf_open(fnidx, "r");
+ if (fp) {
+ bcf_idx_t *idx = bcf_idx_load_core(fp);
+ bgzf_close(fp);
+ return idx;
+ } else return 0;
+}
+
+#ifdef _USE_KNETFILE
+static void download_from_remote(const char *url)
+{
+ const int buf_size = 1 * 1024 * 1024;
+ char *fn;
+ FILE *fp;
+ uint8_t *buf;
+ knetFile *fp_remote;
+ int l;
+ if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
+ l = strlen(url);
+ for (fn = (char*)url + l - 1; fn >= url; --fn)
+ if (*fn == '/') break;
+ ++fn; // fn now points to the file name
+ fp_remote = knet_open(url, "r");
+ if (fp_remote == 0) {
+ fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
+ return;
+ }
+ if ((fp = fopen(fn, "w")) == 0) {
+ fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
+ knet_close(fp_remote);
+ return;
+ }
+ buf = (uint8_t*)calloc(buf_size, 1);
+ while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+ fwrite(buf, 1, l, fp);
+ free(buf);
+ fclose(fp);
+ knet_close(fp_remote);
+}
+#else
+static void download_from_remote(const char *url)
+{
+ return;
+}
+#endif
+
+static char *get_local_version(const char *fn)
+{
+ struct stat sbuf;
+ char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcat(strcpy(fnidx, fn), ".bci");
+ if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
+ char *p, *url;
+ int l = strlen(fnidx);
+ for (p = fnidx + l - 1; p >= fnidx; --p)
+ if (*p == '/') break;
+ url = fnidx; fnidx = strdup(p + 1);
+ if (stat(fnidx, &sbuf) == 0) {
+ free(url);
+ return fnidx;
+ }
+ fprintf(stderr, "[%s] downloading the index file...\n", __func__);
+ download_from_remote(url);
+ free(url);
+ }
+ if (stat(fnidx, &sbuf) == 0) return fnidx;
+ free(fnidx); return 0;
+}
+
+bcf_idx_t *bcf_idx_load(const char *fn)
+{
+ bcf_idx_t *idx;
+ char *fname = get_local_version(fn);
+ if (fname == 0) return 0;
+ idx = bcf_idx_load_local(fname);
+ free(fname);
+ return idx;
+}
+
+int bcf_idx_build2(const char *fn, const char *_fnidx)
+{
+ char *fnidx;
+ BGZF *fpidx;
+ bcf_t *bp;
+ bcf_idx_t *idx;
+ bcf_hdr_t *h;
+ if ((bp = bcf_open(fn, "r")) == 0) {
+ fprintf(stderr, "[bcf_idx_build2] fail to open the BAM file.\n");
+ return -1;
+ }
+ h = bcf_hdr_read(bp);
+ idx = bcf_idx_core(bp, h);
+ bcf_close(bp);
+ if (_fnidx == 0) {
+ fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcpy(fnidx, fn); strcat(fnidx, ".bci");
+ } else fnidx = strdup(_fnidx);
+ fpidx = bgzf_open(fnidx, "w");
+ if (fpidx == 0) {
+ fprintf(stderr, "[bcf_idx_build2] fail to create the index file.\n");
+ free(fnidx);
+ return -1;
+ }
+ bcf_idx_save(idx, fpidx);
+ bcf_idx_destroy(idx);
+ bgzf_close(fpidx);
+ free(fnidx);
+ return 0;
+}
+
+int bcf_idx_build(const char *fn)
+{
+ return bcf_idx_build2(fn, 0);
+}
+
+/********************************************
+ * parse a region in the format chr:beg-end *
+ ********************************************/
+
+int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end)
+{
+ char *s, *p;
+ int i, l, k;
+ l = strlen(str);
+ p = s = (char*)malloc(l+1);
+ /* squeeze out "," */
+ for (i = k = 0; i != l; ++i)
+ if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
+ s[k] = 0;
+ for (i = 0; i != k; ++i) if (s[i] == ':') break;
+ s[i] = 0;
+ if ((*tid = bcf_str2id(str2id, s)) < 0) {
+ free(s);
+ return -1;
+ }
+ if (i == k) { /* dump the whole sequence */
+ *begin = 0; *end = 1<<29; free(s);
+ return 0;
+ }
+ for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
+ *begin = atoi(p);
+ if (i < k) {
+ p = s + i + 1;
+ *end = atoi(p);
+ } else *end = 1<<29;
+ if (*begin > 0) --*begin;
+ free(s);
+ if (*begin > *end) return -1;
+ return 0;
+}
+
+/*******************************
+ * retrieve a specified region *
+ *******************************/
+
+uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg)
+{
+ uint64_t min_off, *offset;
+ int i;
+ if (beg < 0) beg = 0;
+ offset = idx->index2[tid].offset;
+ for (i = beg>>TAD_LIDX_SHIFT; i < idx->index2[tid].n && offset[i] == 0; ++i);
+ min_off = (i == idx->index2[tid].n)? offset[idx->index2[tid].n-1] : offset[i];
+ return min_off;
+}
+
+int bcf_main_index(int argc, char *argv[])
+{
+ if (argc == 1) {
+ fprintf(stderr, "Usage: bcftools index <in.bcf>\n");
+ return 1;
+ }
+ bcf_idx_build(argv[1]);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bcftools/kfunc.c b/src/samtools-0.1.18/bcftools/kfunc.c
new file mode 100644
index 0000000..a637b6c
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/kfunc.c
@@ -0,0 +1,162 @@
+#include <math.h>
+
+
+/* Log gamma function
+ * \log{\Gamma(z)}
+ * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
+ */
+double kf_lgamma(double z)
+{
+ double x = 0;
+ x += 0.1659470187408462e-06 / (z+7);
+ x += 0.9934937113930748e-05 / (z+6);
+ x -= 0.1385710331296526 / (z+5);
+ x += 12.50734324009056 / (z+4);
+ x -= 176.6150291498386 / (z+3);
+ x += 771.3234287757674 / (z+2);
+ x -= 1259.139216722289 / (z+1);
+ x += 676.5203681218835 / z;
+ x += 0.9999999999995183;
+ return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);
+}
+
+/* complementary error function
+ * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt
+ * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66
+ */
+double kf_erfc(double x)
+{
+ const double p0 = 220.2068679123761;
+ const double p1 = 221.2135961699311;
+ const double p2 = 112.0792914978709;
+ const double p3 = 33.912866078383;
+ const double p4 = 6.37396220353165;
+ const double p5 = .7003830644436881;
+ const double p6 = .03526249659989109;
+ const double q0 = 440.4137358247522;
+ const double q1 = 793.8265125199484;
+ const double q2 = 637.3336333788311;
+ const double q3 = 296.5642487796737;
+ const double q4 = 86.78073220294608;
+ const double q5 = 16.06417757920695;
+ const double q6 = 1.755667163182642;
+ const double q7 = .08838834764831844;
+ double expntl, z, p;
+ z = fabs(x) * M_SQRT2;
+ if (z > 37.) return x > 0.? 0. : 2.;
+ expntl = exp(z * z * - .5);
+ if (z < 10. / M_SQRT2) // for small z
+ p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0)
+ / (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0);
+ else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65)))));
+ return x > 0.? 2. * p : 2. * (1. - p);
+}
+
+/* The following computes regularized incomplete gamma functions.
+ * Formulas are taken from Wiki, with additional input from Numerical
+ * Recipes in C (for modified Lentz's algorithm) and AS245
+ * (http://lib.stat.cmu.edu/apstat/245).
+ *
+ * A good online calculator is available at:
+ *
+ * http://www.danielsoper.com/statcalc/calc23.aspx
+ *
+ * It calculates upper incomplete gamma function, which equals
+ * kf_gammaq(s,z)*tgamma(s).
+ */
+
+#define KF_GAMMA_EPS 1e-14
+#define KF_TINY 1e-290
+
+// regularized lower incomplete gamma function, by series expansion
+static double _kf_gammap(double s, double z)
+{
+ double sum, x;
+ int k;
+ for (k = 1, sum = x = 1.; k < 100; ++k) {
+ sum += (x *= z / (s + k));
+ if (x / sum < KF_GAMMA_EPS) break;
+ }
+ return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum));
+}
+// regularized upper incomplete gamma function, by continued fraction
+static double _kf_gammaq(double s, double z)
+{
+ int j;
+ double C, D, f;
+ f = 1. + z - s; C = f; D = 0.;
+ // Modified Lentz's algorithm for computing continued fraction
+ // See Numerical Recipes in C, 2nd edition, section 5.2
+ for (j = 1; j < 100; ++j) {
+ double a = j * (s - j), b = (j<<1) + 1 + z - s, d;
+ D = b + a * D;
+ if (D < KF_TINY) D = KF_TINY;
+ C = b + a / C;
+ if (C < KF_TINY) C = KF_TINY;
+ D = 1. / D;
+ d = C * D;
+ f *= d;
+ if (fabs(d - 1.) < KF_GAMMA_EPS) break;
+ }
+ return exp(s * log(z) - z - kf_lgamma(s) - log(f));
+}
+
+double kf_gammap(double s, double z)
+{
+ return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z);
+}
+
+double kf_gammaq(double s, double z)
+{
+ return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z);
+}
+
+/* Regularized incomplete beta function. The method is taken from
+ * Numerical Recipe in C, 2nd edition, section 6.4. The following web
+ * page calculates the incomplete beta function, which equals
+ * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b):
+ *
+ * http://www.danielsoper.com/statcalc/calc36.aspx
+ */
+static double kf_betai_aux(double a, double b, double x)
+{
+ double C, D, f;
+ int j;
+ if (x == 0.) return 0.;
+ if (x == 1.) return 1.;
+ f = 1.; C = f; D = 0.;
+ // Modified Lentz's algorithm for computing continued fraction
+ for (j = 1; j < 200; ++j) {
+ double aa, d;
+ int m = j>>1;
+ aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1))
+ : m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m));
+ D = 1. + aa * D;
+ if (D < KF_TINY) D = KF_TINY;
+ C = 1. + aa / C;
+ if (C < KF_TINY) C = KF_TINY;
+ D = 1. / D;
+ d = C * D;
+ f *= d;
+ if (fabs(d - 1.) < KF_GAMMA_EPS) break;
+ }
+ return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f;
+}
+double kf_betai(double a, double b, double x)
+{
+ return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x);
+}
+
+#ifdef KF_MAIN
+#include <stdio.h>
+int main(int argc, char *argv[])
+{
+ double x = 5.5, y = 3;
+ double a, b;
+ printf("erfc(%lg): %lg, %lg\n", x, erfc(x), kf_erfc(x));
+ printf("upper-gamma(%lg,%lg): %lg\n", x, y, kf_gammaq(y, x)*tgamma(y));
+ a = 2; b = 2; x = 0.5;
+ printf("incomplete-beta(%lg,%lg,%lg): %lg\n", a, b, x, kf_betai(a, b, x) / exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b)));
+ return 0;
+}
+#endif
diff --git a/src/samtools-0.1.18/bcftools/kmin.c b/src/samtools-0.1.18/bcftools/kmin.c
new file mode 100644
index 0000000..5b8193b
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/kmin.c
@@ -0,0 +1,209 @@
+/* The MIT License
+
+ Copyright (c) 2008, 2010 by Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* Hooke-Jeeves algorithm for nonlinear minimization
+
+ Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and
+ the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the
+ papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM
+ 6(6):313-314). The original algorithm was designed by Hooke and
+ Jeeves (ACM 8:212-229). This program is further revised according to
+ Johnson's implementation at Netlib (opt/hooke.c).
+
+ Hooke-Jeeves algorithm is very simple and it works quite well on a
+ few examples. However, it might fail to converge due to its heuristic
+ nature. A possible improvement, as is suggested by Johnson, may be to
+ choose a small r at the beginning to quickly approach to the minimum
+ and a large r at later step to hit the minimum.
+ */
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "kmin.h"
+
+static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls)
+{
+ int k, j = *n_calls;
+ double ftmp;
+ for (k = 0; k != n; ++k) {
+ x1[k] += dx[k];
+ ftmp = func(n, x1, data); ++j;
+ if (ftmp < fx1) fx1 = ftmp;
+ else { /* search the opposite direction */
+ dx[k] = 0.0 - dx[k];
+ x1[k] += dx[k] + dx[k];
+ ftmp = func(n, x1, data); ++j;
+ if (ftmp < fx1) fx1 = ftmp;
+ else x1[k] -= dx[k]; /* back to the original x[k] */
+ }
+ }
+ *n_calls = j;
+ return fx1; /* here: fx1=f(n,x1) */
+}
+
+double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls)
+{
+ double fx, fx1, *x1, *dx, radius;
+ int k, n_calls = 0;
+ x1 = (double*)calloc(n, sizeof(double));
+ dx = (double*)calloc(n, sizeof(double));
+ for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */
+ dx[k] = fabs(x[k]) * r;
+ if (dx[k] == 0) dx[k] = r;
+ }
+ radius = r;
+ fx1 = fx = func(n, x, data); ++n_calls;
+ for (;;) {
+ memcpy(x1, x, n * sizeof(double)); /* x1 = x */
+ fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls);
+ while (fx1 < fx) {
+ for (k = 0; k != n; ++k) {
+ double t = x[k];
+ dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]);
+ x[k] = x1[k];
+ x1[k] = x1[k] + x1[k] - t;
+ }
+ fx = fx1;
+ if (n_calls >= max_calls) break;
+ fx1 = func(n, x1, data); ++n_calls;
+ fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls);
+ if (fx1 >= fx) break;
+ for (k = 0; k != n; ++k)
+ if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break;
+ if (k == n) break;
+ }
+ if (radius >= eps) {
+ if (n_calls >= max_calls) break;
+ radius *= r;
+ for (k = 0; k != n; ++k) dx[k] *= r;
+ } else break; /* converge */
+ }
+ free(x1); free(dx);
+ return fx1;
+}
+
+// I copied this function somewhere several years ago with some of my modifications, but I forgot the source.
+double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin)
+{
+ double bound, u, r, q, fu, tmp, fa, fb, fc, c;
+ const double gold1 = 1.6180339887;
+ const double gold2 = 0.3819660113;
+ const double tiny = 1e-20;
+ const int max_iter = 100;
+
+ double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw;
+ int iter;
+
+ fa = func(a, data); fb = func(b, data);
+ if (fb > fa) { // swap, such that f(a) > f(b)
+ tmp = a; a = b; b = tmp;
+ tmp = fa; fa = fb; fb = tmp;
+ }
+ c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation
+ while (fb > fc) {
+ bound = b + 100.0 * (c - b); // the farthest point where we want to go
+ r = (b - a) * (fb - fc);
+ q = (b - c) * (fb - fa);
+ if (fabs(q - r) < tiny) { // avoid 0 denominator
+ tmp = q > r? tiny : 0.0 - tiny;
+ } else tmp = q - r;
+ u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point
+ if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c
+ fu = func(u, data);
+ if (fu < fc) { // (b,u,c) bracket the minimum
+ a = b; b = u; fa = fb; fb = fu;
+ break;
+ } else if (fu > fb) { // (a,b,u) bracket the minimum
+ c = u; fc = fu;
+ break;
+ }
+ u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation
+ } else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound
+ fu = func(u, data);
+ if (fu < fc) { // fb > fc > fu
+ b = c; c = u; u = c + gold1 * (c - b);
+ fb = fc; fc = fu; fu = func(u, data);
+ } else { // (b,c,u) bracket the minimum
+ a = b; b = c; c = u;
+ fa = fb; fb = fc; fc = fu;
+ break;
+ }
+ } else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound
+ u = bound; fu = func(u, data);
+ } else { // u goes the other way around, use golden section extrapolation
+ u = c + gold1 * (c - b); fu = func(u, data);
+ }
+ a = b; b = c; c = u;
+ fa = fb; fb = fc; fc = fu;
+ }
+ if (a > c) u = a, a = c, c = u; // swap
+
+ // now, a<b<c, fa>fb and fb<fc, move on to Brent's algorithm
+ e = d = 0.0;
+ w = v = b; fv = fw = fb;
+ for (iter = 0; iter != max_iter; ++iter) {
+ mid = 0.5 * (a + c);
+ tol2 = 2.0 * (tol1 = tol * fabs(b) + tiny);
+ if (fabs(b - mid) <= (tol2 - 0.5 * (c - a))) {
+ *xmin = b; return fb; // found
+ }
+ if (fabs(e) > tol1) {
+ // related to parabolic interpolation
+ r = (b - w) * (fb - fv);
+ q = (b - v) * (fb - fw);
+ p = (b - v) * q - (b - w) * r;
+ q = 2.0 * (q - r);
+ if (q > 0.0) p = 0.0 - p;
+ else q = 0.0 - q;
+ eold = e; e = d;
+ if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) {
+ d = gold2 * (e = (b >= mid ? a - b : c - b));
+ } else {
+ d = p / q; u = b + d; // actual parabolic interpolation happens here
+ if (u - a < tol2 || c - u < tol2)
+ d = (mid > b)? tol1 : 0.0 - tol1;
+ }
+ } else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation
+ u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1);
+ fu = func(u, data);
+ if (fu <= fb) { // u is the minimum point so far
+ if (u >= b) a = b;
+ else c = b;
+ v = w; w = b; b = u; fv = fw; fw = fb; fb = fu;
+ } else { // adjust (a,c) and (u,v,w)
+ if (u < b) a = u;
+ else c = u;
+ if (fu <= fw || w == b) {
+ v = w; w = u;
+ fv = fw; fw = fu;
+ } else if (fu <= fv || v == b || v == w) {
+ v = u; fv = fu;
+ }
+ }
+ }
+ *xmin = b;
+ return fb;
+}
diff --git a/src/samtools-0.1.18/bcftools/kmin.h b/src/samtools-0.1.18/bcftools/kmin.h
new file mode 100644
index 0000000..6feba45
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/kmin.h
@@ -0,0 +1,46 @@
+/*
+ Copyright (c) 2008, 2010 by Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#ifndef KMIN_H
+#define KMIN_H
+
+#define KMIN_RADIUS 0.5
+#define KMIN_EPS 1e-7
+#define KMIN_MAXCALL 50000
+
+typedef double (*kmin_f)(int, double*, void*);
+typedef double (*kmin1_f)(double, void*);
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls);
+ double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/samtools-0.1.18/bcftools/main.c b/src/samtools-0.1.18/bcftools/main.c
new file mode 100644
index 0000000..fcd94b8
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/main.c
@@ -0,0 +1,190 @@
+#include <string.h>
+#include <stdlib.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#include "bcf.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 0x10000)
+
+int bcfview(int argc, char *argv[]);
+int bcf_main_index(int argc, char *argv[]);
+
+#define BUF_SIZE 0x10000
+
+int bcf_cat(int n, char * const *fn)
+{
+ int i;
+ bcf_t *out;
+ uint8_t *buf;
+ buf = malloc(BUF_SIZE);
+ out = bcf_open("-", "w");
+ for (i = 0; i < n; ++i) {
+ bcf_t *in;
+ bcf_hdr_t *h;
+ off_t end;
+ struct stat s;
+ in = bcf_open(fn[i], "r");
+ h = bcf_hdr_read(in);
+ if (i == 0) bcf_hdr_write(out, h);
+ bcf_hdr_destroy(h);
+#ifdef _USE_KNETFILE
+ fstat(knet_fileno(in->fp->x.fpr), &s);
+ end = s.st_size - 28;
+ while (knet_tell(in->fp->x.fpr) < end) {
+ int size = knet_tell(in->fp->x.fpr) + BUF_SIZE < end? BUF_SIZE : end - knet_tell(in->fp->x.fpr);
+ knet_read(in->fp->x.fpr, buf, size);
+ fwrite(buf, 1, size, out->fp->x.fpw);
+ }
+#else
+ abort(); // FIXME: not implemented
+#endif
+ bcf_close(in);
+ }
+ bcf_close(out);
+ free(buf);
+ return 0;
+}
+
+extern double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
+
+int bcf_main_ldpair(int argc, char *argv[])
+{
+ bcf_t *fp;
+ bcf_hdr_t *h;
+ bcf1_t *b0, *b1;
+ bcf_idx_t *idx;
+ kstring_t str;
+ void *str2id;
+ gzFile fplist;
+ kstream_t *ks;
+ int dret, lineno = 0;
+ if (argc < 3) {
+ fprintf(stderr, "Usage: bcftools ldpair <in.bcf> <in.list>\n");
+ return 1;
+ }
+ fplist = gzopen(argv[2], "rb");
+ ks = ks_init(fplist);
+ memset(&str, 0, sizeof(kstring_t));
+ fp = bcf_open(argv[1], "rb");
+ h = bcf_hdr_read(fp);
+ str2id = bcf_build_refhash(h);
+ idx = bcf_idx_load(argv[1]);
+ if (idx == 0) {
+ fprintf(stderr, "[%s] No bcf index is found. Abort!\n", __func__);
+ return 1;
+ }
+ b0 = calloc(1, sizeof(bcf1_t));
+ b1 = calloc(1, sizeof(bcf1_t));
+ while (ks_getuntil(ks, '\n', &str, &dret) >= 0) {
+ char *p, *q;
+ int k;
+ int tid0 = -1, tid1 = -1, pos0 = -1, pos1 = -1;
+ ++lineno;
+ for (p = q = str.s, k = 0; *p; ++p) {
+ if (*p == ' ' || *p == '\t') {
+ *p = '\0';
+ if (k == 0) tid0 = bcf_str2id(str2id, q);
+ else if (k == 1) pos0 = atoi(q) - 1;
+ else if (k == 2) tid1 = strcmp(q, "=")? bcf_str2id(str2id, q) : tid0;
+ else if (k == 3) pos1 = atoi(q) - 1;
+ q = p + 1;
+ ++k;
+ }
+ }
+ if (k == 3) pos1 = atoi(q) - 1;
+ if (tid0 >= 0 && tid1 >= 0 && pos0 >= 0 && pos1 >= 0) {
+ uint64_t off;
+ double r, f[4];
+ off = bcf_idx_query(idx, tid0, pos0);
+ bgzf_seek(fp->fp, off, SEEK_SET);
+ while (bcf_read(fp, h, b0) >= 0 && b0->pos != pos0);
+ off = bcf_idx_query(idx, tid1, pos1);
+ bgzf_seek(fp->fp, off, SEEK_SET);
+ while (bcf_read(fp, h, b1) >= 0 && b1->pos != pos1);
+ r = bcf_pair_freq(b0, b1, f);
+ r *= r;
+ printf("%s\t%d\t%s\t%d\t%.4g\t%.4g\t%.4g\t%.4g\t%.4g\n", h->ns[tid0], pos0+1, h->ns[tid1], pos1+1,
+ r, f[0], f[1], f[2], f[3]);
+ } //else fprintf(stderr, "[%s] Parse error at line %d.\n", __func__, lineno);
+ }
+ bcf_destroy(b0); bcf_destroy(b1);
+ bcf_idx_destroy(idx);
+ bcf_str2id_destroy(str2id);
+ bcf_hdr_destroy(h);
+ bcf_close(fp);
+ free(str.s);
+ ks_destroy(ks);
+ gzclose(fplist);
+ return 0;
+}
+
+int bcf_main_ld(int argc, char *argv[])
+{
+ bcf_t *fp;
+ bcf_hdr_t *h;
+ bcf1_t **b, *b0;
+ int i, j, m, n;
+ double f[4];
+ if (argc == 1) {
+ fprintf(stderr, "Usage: bcftools ld <in.bcf>\n");
+ return 1;
+ }
+ fp = bcf_open(argv[1], "rb");
+ h = bcf_hdr_read(fp);
+ // read the entire BCF
+ m = n = 0; b = 0;
+ b0 = calloc(1, sizeof(bcf1_t));
+ while (bcf_read(fp, h, b0) >= 0) {
+ if (m == n) {
+ m = m? m<<1 : 16;
+ b = realloc(b, sizeof(void*) * m);
+ }
+ b[n] = calloc(1, sizeof(bcf1_t));
+ bcf_cpy(b[n++], b0);
+ }
+ bcf_destroy(b0);
+ // compute pair-wise r^2
+ printf("%d\n", n); // the number of loci
+ for (i = 0; i < n; ++i) {
+ printf("%s:%d", h->ns[b[i]->tid], b[i]->pos + 1);
+ for (j = 0; j < i; ++j) {
+ double r = bcf_pair_freq(b[i], b[j], f);
+ printf("\t%.3f", r*r);
+ }
+ printf("\t1.000\n");
+ }
+ // free
+ for (i = 0; i < n; ++i) bcf_destroy(b[i]);
+ free(b);
+ bcf_hdr_destroy(h);
+ bcf_close(fp);
+ return 0;
+}
+
+int main(int argc, char *argv[])
+{
+ if (argc == 1) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Program: bcftools (Tools for data in the VCF/BCF formats)\n");
+ fprintf(stderr, "Version: %s\n\n", BCF_VERSION);
+ fprintf(stderr, "Usage: bcftools <command> <arguments>\n\n");
+ fprintf(stderr, "Command: view print, extract, convert and call SNPs from BCF\n");
+ fprintf(stderr, " index index BCF\n");
+ fprintf(stderr, " cat concatenate BCFs\n");
+ fprintf(stderr, " ld compute all-pair r^2\n");
+ fprintf(stderr, " ldpair compute r^2 between requested pairs\n");
+ fprintf(stderr, "\n");
+ return 1;
+ }
+ if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
+ else if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "ld") == 0) return bcf_main_ld(argc-1, argv+1);
+ else if (strcmp(argv[1], "ldpair") == 0) return bcf_main_ldpair(argc-1, argv+1);
+ else if (strcmp(argv[1], "cat") == 0) return bcf_cat(argc-2, argv+2); // cat is different ...
+ else {
+ fprintf(stderr, "[main] Unrecognized command.\n");
+ return 1;
+ }
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bcftools/mut.c b/src/samtools-0.1.18/bcftools/mut.c
new file mode 100644
index 0000000..15ef265
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/mut.c
@@ -0,0 +1,127 @@
+#include <stdlib.h>
+#include <stdint.h>
+#include "bcf.h"
+
+#define MAX_GENO 359
+
+int8_t seq_bitcnt[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
+char *seq_nt16rev = "XACMGRSVTWYHKDBN";
+
+uint32_t *bcf_trio_prep(int is_x, int is_son)
+{
+ int i, j, k, n, map[10];
+ uint32_t *ret;
+ ret = calloc(MAX_GENO, 4);
+ for (i = 0, k = 0; i < 4; ++i)
+ for (j = i; j < 4; ++j)
+ map[k++] = 1<<i|1<<j;
+ for (i = 0, n = 1; i < 10; ++i) { // father
+ if (is_x && seq_bitcnt[map[i]] != 1) continue;
+ if (is_x && is_son) {
+ for (j = 0; j < 10; ++j) // mother
+ for (k = 0; k < 10; ++k) // child
+ if (seq_bitcnt[map[k]] == 1 && (map[j]&map[k]))
+ ret[n++] = j<<16 | i<<8 | k;
+ } else {
+ for (j = 0; j < 10; ++j) // mother
+ for (k = 0; k < 10; ++k) // child
+ if ((map[i]&map[k]) && (map[j]&map[k]) && ((map[i]|map[j])&map[k]) == map[k])
+ ret[n++] = j<<16 | i<<8 | k;
+ }
+ }
+ ret[0] = n - 1;
+ return ret;
+}
+
+
+int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
+{
+ int i, j, k;
+ const bcf_ginfo_t *PL;
+ uint8_t *gl10;
+ int map[10];
+ if (b->n_smpl != 3) return -1; // not a trio
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ gl10 = alloca(10 * b->n_smpl);
+ if (bcf_gl10(b, gl10) < 0) {
+ if (bcf_gl10_indel(b, gl10) < 0) return -1;
+ }
+ PL = b->gi + i;
+ for (i = 0, k = 0; i < 4; ++i)
+ for (j = i; j < 4; ++j)
+ map[k++] = seq_nt16rev[1<<i|1<<j];
+ for (j = 0; j < 3; ++j) // check if ref hom is the most probable in all members
+ if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
+ if (j < 3) { // we need to go through the complex procedure
+ uint8_t *g[3];
+ int minc = 1<<30, minc_j = -1, minf = 0, gtf = 0, gtc = 0;
+ g[0] = gl10;
+ g[1] = gl10 + 10;
+ g[2] = gl10 + 20;
+ for (j = 1; j <= (int)prep[0]; ++j) { // compute LK with constraint
+ int sum = g[0][prep[j]&0xff] + g[1][prep[j]>>8&0xff] + g[2][prep[j]>>16&0xff];
+ if (sum < minc) minc = sum, minc_j = j;
+ }
+ gtc |= map[prep[minc_j]&0xff]; gtc |= map[prep[minc_j]>>8&0xff]<<8; gtc |= map[prep[minc_j]>>16]<<16;
+ for (j = 0; j < 3; ++j) { // compute LK without constraint
+ int min = 1<<30, min_k = -1;
+ for (k = 0; k < 10; ++k)
+ if (g[j][k] < min) min = g[j][k], min_k = k;
+ gtf |= map[min_k]<<(j*8);
+ minf += min;
+ }
+ *llr = minc - minf; *gt = (int64_t)gtc<<32 | gtf;
+ } else *llr = 0, *gt = -1;
+ return 0;
+}
+
+int bcf_pair_call(const bcf1_t *b)
+{
+ int i, j, k;
+ const bcf_ginfo_t *PL;
+ if (b->n_smpl != 2) return -1; // not a pair
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ PL = b->gi + i;
+ for (j = 0; j < 2; ++j) // check if ref hom is the most probable in all members
+ if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
+ if (j < 2) { // we need to go through the complex procedure
+ uint8_t *g[2];
+ int minc = 1<<30, minf = 0;
+ g[0] = PL->data;
+ g[1] = (uint8_t*)PL->data + PL->len;
+ for (j = 0; j < PL->len; ++j) // compute LK with constraint
+ minc = minc < g[0][j] + g[1][j]? minc : g[0][j] + g[1][j];
+ for (j = 0; j < 2; ++j) { // compute LK without constraint
+ int min = 1<<30;
+ for (k = 0; k < PL->len; ++k)
+ min = min < g[j][k]? min : g[j][k];
+ minf += min;
+ }
+ return minc - minf;
+ } else return 0;
+}
+
+int bcf_min_diff(const bcf1_t *b)
+{
+ int i, min = 1<<30;
+ const bcf_ginfo_t *PL;
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+ if (i == b->n_gi) return -1; // no PL
+ PL = b->gi + i;
+ for (i = 0; i < b->n_smpl; ++i) {
+ int m1, m2, j;
+ const uint8_t *p = (uint8_t*)PL->data;
+ m1 = m2 = 1<<30;
+ for (j = 0; j < PL->len; ++j) {
+ if ((int)p[j] < m1) m2 = m1, m1 = p[j];
+ else if ((int)p[j] < m2) m2 = p[j];
+ }
+ min = min < m2 - m1? min : m2 - m1;
+ }
+ return min;
+}
diff --git a/src/samtools-0.1.18/bcftools/prob1.c b/src/samtools-0.1.18/bcftools/prob1.c
new file mode 100644
index 0000000..a380484
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/prob1.c
@@ -0,0 +1,554 @@
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <errno.h>
+#include <assert.h>
+#include "prob1.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define MC_MAX_EM_ITER 16
+#define MC_EM_EPS 1e-5
+#define MC_DEF_INDEL 0.15
+
+unsigned char seq_nt4_table[256] = {
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
+};
+
+struct __bcf_p1aux_t {
+ int n, M, n1, is_indel;
+ uint8_t *ploidy; // haploid or diploid ONLY
+ double *q2p, *pdg; // pdg -> P(D|g)
+ double *phi, *phi_indel;
+ double *z, *zswap; // aux for afs
+ double *z1, *z2, *phi1, *phi2; // only calculated when n1 is set
+ double **hg; // hypergeometric distribution
+ double *lf; // log factorial
+ double t, t1, t2;
+ double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
+ const uint8_t *PL; // point to PL
+ int PL_len;
+};
+
+void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x)
+{
+ int i;
+ for (i = 0; i < ma->M; ++i)
+ ma->phi_indel[i] = ma->phi[i] * x;
+ ma->phi_indel[ma->M] = 1. - ma->phi[ma->M] * x;
+}
+
+static void init_prior(int type, double theta, int M, double *phi)
+{
+ int i;
+ if (type == MC_PTYPE_COND2) {
+ for (i = 0; i <= M; ++i)
+ phi[i] = 2. * (i + 1) / (M + 1) / (M + 2);
+ } else if (type == MC_PTYPE_FLAT) {
+ for (i = 0; i <= M; ++i)
+ phi[i] = 1. / (M + 1);
+ } else {
+ double sum;
+ for (i = 0, sum = 0.; i < M; ++i)
+ sum += (phi[i] = theta / (M - i));
+ phi[M] = 1. - sum;
+ }
+}
+
+void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta)
+{
+ init_prior(type, theta, ma->M, ma->phi);
+ bcf_p1_indel_prior(ma, MC_DEF_INDEL);
+}
+
+void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta)
+{
+ if (ma->n1 <= 0 || ma->n1 >= ma->M) return;
+ init_prior(type, theta, 2*ma->n1, ma->phi1);
+ init_prior(type, theta, 2*(ma->n - ma->n1), ma->phi2);
+}
+
+int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn)
+{
+ gzFile fp;
+ kstring_t s;
+ kstream_t *ks;
+ long double sum;
+ int dret, k;
+ memset(&s, 0, sizeof(kstring_t));
+ fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+ ks = ks_init(fp);
+ memset(ma->phi, 0, sizeof(double) * (ma->M + 1));
+ while (ks_getuntil(ks, '\n', &s, &dret) >= 0) {
+ if (strstr(s.s, "[afs] ") == s.s) {
+ char *p = s.s + 6;
+ for (k = 0; k <= ma->M; ++k) {
+ int x;
+ double y;
+ x = strtol(p, &p, 10);
+ if (x != k && (errno == EINVAL || errno == ERANGE)) return -1;
+ ++p;
+ y = strtod(p, &p);
+ if (y == 0. && (errno == EINVAL || errno == ERANGE)) return -1;
+ ma->phi[ma->M - k] += y;
+ }
+ }
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(s.s);
+ for (sum = 0., k = 0; k <= ma->M; ++k) sum += ma->phi[k];
+ fprintf(stderr, "[prior]");
+ for (k = 0; k <= ma->M; ++k) ma->phi[k] /= sum;
+ for (k = 0; k <= ma->M; ++k) fprintf(stderr, " %d:%.3lg", k, ma->phi[ma->M - k]);
+ fputc('\n', stderr);
+ for (sum = 0., k = 1; k < ma->M; ++k) sum += ma->phi[ma->M - k] * (2.* k * (ma->M - k) / ma->M / (ma->M - 1));
+ fprintf(stderr, "[%s] heterozygosity=%lf, ", __func__, (double)sum);
+ for (sum = 0., k = 1; k <= ma->M; ++k) sum += k * ma->phi[ma->M - k] / ma->M;
+ fprintf(stderr, "theta=%lf\n", (double)sum);
+ bcf_p1_indel_prior(ma, MC_DEF_INDEL);
+ return 0;
+}
+
+bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy)
+{
+ bcf_p1aux_t *ma;
+ int i;
+ ma = calloc(1, sizeof(bcf_p1aux_t));
+ ma->n1 = -1;
+ ma->n = n; ma->M = 2 * n;
+ if (ploidy) {
+ ma->ploidy = malloc(n);
+ memcpy(ma->ploidy, ploidy, n);
+ for (i = 0, ma->M = 0; i < n; ++i) ma->M += ploidy[i];
+ if (ma->M == 2 * n) {
+ free(ma->ploidy);
+ ma->ploidy = 0;
+ }
+ }
+ ma->q2p = calloc(256, sizeof(double));
+ ma->pdg = calloc(3 * ma->n, sizeof(double));
+ ma->phi = calloc(ma->M + 1, sizeof(double));
+ ma->phi_indel = calloc(ma->M + 1, sizeof(double));
+ ma->phi1 = calloc(ma->M + 1, sizeof(double));
+ ma->phi2 = calloc(ma->M + 1, sizeof(double));
+ ma->z = calloc(ma->M + 1, sizeof(double));
+ ma->zswap = calloc(ma->M + 1, sizeof(double));
+ ma->z1 = calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
+ ma->z2 = calloc(ma->M + 1, sizeof(double));
+ ma->afs = calloc(ma->M + 1, sizeof(double));
+ ma->afs1 = calloc(ma->M + 1, sizeof(double));
+ ma->lf = calloc(ma->M + 1, sizeof(double));
+ for (i = 0; i < 256; ++i)
+ ma->q2p[i] = pow(10., -i / 10.);
+ for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1);
+ bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
+ return ma;
+}
+
+int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
+{
+ if (n1 == 0 || n1 >= b->n) return -1;
+ if (b->M != b->n * 2) {
+ fprintf(stderr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__);
+ return -1;
+ }
+ b->n1 = n1;
+ return 0;
+}
+
+void bcf_p1_destroy(bcf_p1aux_t *ma)
+{
+ if (ma) {
+ int k;
+ free(ma->lf);
+ if (ma->hg && ma->n1 > 0) {
+ for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]);
+ free(ma->hg);
+ }
+ free(ma->ploidy); free(ma->q2p); free(ma->pdg);
+ free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2);
+ free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
+ free(ma->afs); free(ma->afs1);
+ free(ma);
+ }
+}
+
+static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
+{
+ int i, j;
+ long *p, tmp;
+ p = alloca(b->n_alleles * sizeof(long));
+ memset(p, 0, sizeof(long) * b->n_alleles);
+ for (j = 0; j < ma->n; ++j) {
+ const uint8_t *pi = ma->PL + j * ma->PL_len;
+ double *pdg = ma->pdg + j * 3;
+ pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
+ for (i = 0; i < b->n_alleles; ++i)
+ p[i] += (int)pi[(i+1)*(i+2)/2-1];
+ }
+ for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
+ for (i = 1; i < b->n_alleles; ++i) // insertion sort
+ for (j = i; j > 0 && p[j] < p[j-1]; --j)
+ tmp = p[j], p[j] = p[j-1], p[j-1] = tmp;
+ for (i = b->n_alleles - 1; i >= 0; --i)
+ if ((p[i]&0xf) == 0) break;
+ return i;
+}
+
+int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
+{
+ double sum, g[3];
+ double max, f3[3], *pdg = ma->pdg + k * 3;
+ int q, i, max_i, ploidy;
+ ploidy = ma->ploidy? ma->ploidy[k] : 2;
+ if (ploidy == 2) {
+ f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+ } else {
+ f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0;
+ }
+ for (i = 0, sum = 0.; i < 3; ++i)
+ sum += (g[i] = pdg[i] * f3[i]);
+ for (i = 0, max = -1., max_i = 0; i < 3; ++i) {
+ g[i] /= sum;
+ if (g[i] > max) max = g[i], max_i = i;
+ }
+ max = 1. - max;
+ if (max < 1e-308) max = 1e-308;
+ q = (int)(-4.343 * log(max) + .499);
+ if (q > 99) q = 99;
+ return q<<2|max_i;
+}
+
+#define TINY 1e-20
+
+static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
+{
+ double *z[2], *tmp, *pdg;
+ int _j, last_min, last_max;
+ assert(beg == 0 || ma->M == ma->n*2);
+ z[0] = ma->z;
+ z[1] = ma->zswap;
+ pdg = ma->pdg;
+ memset(z[0], 0, sizeof(double) * (ma->M + 1));
+ memset(z[1], 0, sizeof(double) * (ma->M + 1));
+ z[0][0] = 1.;
+ last_min = last_max = 0;
+ ma->t = 0.;
+ if (ma->M == ma->n * 2) {
+ int M = 0;
+ for (_j = beg; _j < ma->n; ++_j) {
+ int k, j = _j - beg, _min = last_min, _max = last_max, M0;
+ double p[3], sum;
+ M0 = M; M += 2;
+ pdg = ma->pdg + _j * 3;
+ p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
+ for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+ for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
+ _max += 2;
+ if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+ if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+ for (k = _min < 2? 2 : _min; k <= _max; ++k)
+ z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
+ for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+ ma->t += log(sum / (M * (M - 1.)));
+ for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+ if (_min >= 1) z[1][_min-1] = 0.;
+ if (_min >= 2) z[1][_min-2] = 0.;
+ if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+ if (_j == ma->n1 - 1) { // set pop1; ma->n1==-1 when unset
+ ma->t1 = ma->t;
+ memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
+ }
+ tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+ last_min = _min; last_max = _max;
+ }
+ //for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary?
+ //for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.;
+ } else { // this block is very similar to the block above; these two might be merged in future
+ int j, M = 0;
+ for (j = 0; j < ma->n; ++j) {
+ int k, M0, _min = last_min, _max = last_max;
+ double p[3], sum;
+ pdg = ma->pdg + j * 3;
+ for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+ for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
+ M0 = M;
+ M += ma->ploidy[j];
+ if (ma->ploidy[j] == 1) {
+ p[0] = pdg[0]; p[1] = pdg[2];
+ _max++;
+ if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k];
+ for (k = _min < 1? 1 : _min; k <= _max; ++k)
+ z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1];
+ for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+ ma->t += log(sum / M);
+ for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+ if (_min >= 1) z[1][_min-1] = 0.;
+ if (j < ma->n - 1) z[1][_max+1] = 0.;
+ } else if (ma->ploidy[j] == 2) {
+ p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2];
+ _max += 2;
+ if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+ if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+ for (k = _min < 2? 2 : _min; k <= _max; ++k)
+ z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
+ for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+ ma->t += log(sum / (M * (M - 1.)));
+ for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+ if (_min >= 1) z[1][_min-1] = 0.;
+ if (_min >= 2) z[1][_min-2] = 0.;
+ if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+ }
+ tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+ last_min = _min; last_max = _max;
+ }
+ }
+ if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
+}
+
+static void mc_cal_y(bcf_p1aux_t *ma)
+{
+ if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples
+ int k;
+ long double x;
+ memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
+ memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+ ma->t1 = ma->t2 = 0.;
+ mc_cal_y_core(ma, ma->n1);
+ ma->t2 = ma->t;
+ memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+ mc_cal_y_core(ma, 0);
+ // rescale z
+ x = expl(ma->t - (ma->t1 + ma->t2));
+ for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
+ } else mc_cal_y_core(ma, 0);
+}
+
+#define CONTRAST_TINY 1e-30
+
+extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test
+
+static inline double chi2_test(int a, int b, int c, int d)
+{
+ double x, z;
+ x = (double)(a+b) * (c+d) * (b+d) * (a+c);
+ if (x == 0.) return 1;
+ z = a * d - b * c;
+ return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x);
+}
+
+// chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)]
+static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3])
+{
+ double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2];
+ int n1 = p1->n1, n2 = p1->n - p1->n1;
+ if (p < CONTRAST_TINY) return -1;
+ if (.5*k1/n1 < .5*k2/n2) x[1] += p;
+ else if (.5*k1/n1 > .5*k2/n2) x[2] += p;
+ else x[0] += p;
+ return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2);
+}
+
+static double contrast2(bcf_p1aux_t *p1, double ret[3])
+{
+ int k, k1, k2, k10, k20, n1, n2;
+ double sum;
+ // get n1 and n2
+ n1 = p1->n1; n2 = p1->n - p1->n1;
+ if (n1 <= 0 || n2 <= 0) return 0.;
+ if (p1->hg == 0) { // initialize the hypergeometric distribution
+ /* NB: the hg matrix may take a lot of memory when there are many samples. There is a way
+ to avoid precomputing this matrix, but it is slower and quite intricate. The following
+ computation in this block can be accelerated with a similar strategy, but perhaps this
+ is not a serious concern for now. */
+ double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1));
+ p1->hg = calloc(2*n1+1, sizeof(void*));
+ for (k1 = 0; k1 <= 2*n1; ++k1) {
+ p1->hg[k1] = calloc(2*n2+1, sizeof(double));
+ for (k2 = 0; k2 <= 2*n2; ++k2)
+ p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp));
+ }
+ }
+ { // compute
+ long double suml = 0;
+ for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k];
+ sum = suml;
+ }
+ { // get the max k1 and k2
+ double max;
+ int max_k;
+ for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) {
+ double x = p1->phi1[k] * p1->z1[k];
+ if (x > max) max = x, max_k = k;
+ }
+ k10 = max_k;
+ for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) {
+ double x = p1->phi2[k] * p1->z2[k];
+ if (x > max) max = x, max_k = k;
+ }
+ k20 = max_k;
+ }
+ { // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N.
+ double x[3], y;
+ long double z = 0., L[2];
+ x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0;
+ for (k1 = k10; k1 >= 0; --k1) {
+ for (k2 = k20; k2 >= 0; --k2) {
+ if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+ else z += y;
+ }
+ for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+ if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+ else z += y;
+ }
+ }
+ ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2];
+ x[0] = x[1] = x[2] = 0;
+ for (k1 = k10 + 1; k1 <= 2*n1; ++k1) {
+ for (k2 = k20; k2 >= 0; --k2) {
+ if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+ else z += y;
+ }
+ for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+ if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+ else z += y;
+ }
+ }
+ ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2];
+ if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened
+ ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0;
+ for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1)
+ for (k2 = 0; k2 <= 2*n2; ++k2)
+ if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y;
+ if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why...
+ z = 1.0, ret[0] = ret[1] = ret[2] = 1./3;
+ }
+ return (double)z;
+ }
+}
+
+static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded)
+{
+ int k;
+ long double sum = 0., sum2;
+ double *phi = ma->is_indel? ma->phi_indel : ma->phi;
+ memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
+ mc_cal_y(ma);
+ // compute AFS
+ for (k = 0, sum = 0.; k <= ma->M; ++k)
+ sum += (long double)phi[k] * ma->z[k];
+ for (k = 0; k <= ma->M; ++k) {
+ ma->afs1[k] = phi[k] * ma->z[k] / sum;
+ if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
+ }
+ // compute folded variant probability
+ for (k = 0, sum = 0.; k <= ma->M; ++k)
+ sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+ for (k = 1, sum2 = 0.; k < ma->M; ++k)
+ sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+ *p_var_folded = sum2 / sum;
+ *p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
+ // the expected frequency
+ for (k = 0, sum = 0.; k <= ma->M; ++k) {
+ ma->afs[k] += ma->afs1[k];
+ sum += k * ma->afs1[k];
+ }
+ return sum / ma->M;
+}
+
+int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
+{
+ int i, k;
+ long double sum = 0.;
+ ma->is_indel = bcf_is_indel(b);
+ rst->perm_rank = -1;
+ // set PL and PL_len
+ for (i = 0; i < b->n_gi; ++i) {
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ ma->PL = (uint8_t*)b->gi[i].data;
+ ma->PL_len = b->gi[i].len;
+ break;
+ }
+ }
+ if (i == b->n_gi) return -1; // no PL
+ if (b->n_alleles < 2) return -1; // FIXME: find a better solution
+ //
+ rst->rank0 = cal_pdg(b, ma);
+ rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded);
+ rst->p_ref = ma->afs1[ma->M];
+ for (k = 0, sum = 0.; k < ma->M; ++k)
+ sum += ma->afs1[k];
+ rst->p_var = (double)sum;
+ { // compute the allele count
+ double max = -1;
+ rst->ac = -1;
+ for (k = 0; k <= ma->M; ++k)
+ if (max < ma->z[k]) max = ma->z[k], rst->ac = k;
+ rst->ac = ma->M - rst->ac;
+ }
+ // calculate f_flat and f_em
+ for (k = 0, sum = 0.; k <= ma->M; ++k)
+ sum += (long double)ma->z[k];
+ rst->f_flat = 0.;
+ for (k = 0; k <= ma->M; ++k) {
+ double p = ma->z[k] / sum;
+ rst->f_flat += k * p;
+ }
+ rst->f_flat /= ma->M;
+ { // estimate equal-tail credible interval (95% level)
+ int l, h;
+ double p;
+ for (i = 0, p = 0.; i <= ma->M; ++i)
+ if (p + ma->afs1[i] > 0.025) break;
+ else p += ma->afs1[i];
+ l = i;
+ for (i = ma->M, p = 0.; i >= 0; --i)
+ if (p + ma->afs1[i] > 0.025) break;
+ else p += ma->afs1[i];
+ h = i;
+ rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M;
+ }
+ if (ma->n1 > 0) { // compute LRT
+ double max0, max1, max2;
+ for (k = 0, max0 = -1; k <= ma->M; ++k)
+ if (max0 < ma->z[k]) max0 = ma->z[k];
+ for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k)
+ if (max1 < ma->z1[k]) max1 = ma->z1[k];
+ for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k)
+ if (max2 < ma->z2[k]) max2 = ma->z2[k];
+ rst->lrt = log(max1 * max2 / max0);
+ rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt);
+ } else rst->lrt = -1.0;
+ rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0;
+ if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant
+ rst->p_chi2 = contrast2(ma, rst->cmp);
+ return 0;
+}
+
+void bcf_p1_dump_afs(bcf_p1aux_t *ma)
+{
+ int k;
+ fprintf(stderr, "[afs]");
+ for (k = 0; k <= ma->M; ++k)
+ fprintf(stderr, " %d:%.3lf", k, ma->afs[ma->M - k]);
+ fprintf(stderr, "\n");
+ memset(ma->afs, 0, sizeof(double) * (ma->M + 1));
+}
diff --git a/src/samtools-0.1.18/bcftools/prob1.h b/src/samtools-0.1.18/bcftools/prob1.h
new file mode 100644
index 0000000..0a51a0a
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/prob1.h
@@ -0,0 +1,42 @@
+#ifndef BCF_PROB1_H
+#define BCF_PROB1_H
+
+#include "bcf.h"
+
+struct __bcf_p1aux_t;
+typedef struct __bcf_p1aux_t bcf_p1aux_t;
+
+typedef struct {
+ int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
+ int ac; // ML alternative allele count
+ double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
+ double cil, cih;
+ double cmp[3], p_chi2, lrt; // used by contrast2()
+} bcf_p1rst_t;
+
+#define MC_PTYPE_FULL 1
+#define MC_PTYPE_COND2 2
+#define MC_PTYPE_FLAT 3
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy);
+ void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
+ void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
+ void bcf_p1_destroy(bcf_p1aux_t *ma);
+ int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+ int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
+ void bcf_p1_dump_afs(bcf_p1aux_t *ma);
+ int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
+ int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
+ void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
+
+ int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/samtools-0.1.18/bcftools/vcf.c b/src/samtools-0.1.18/bcftools/vcf.c
new file mode 100644
index 0000000..9daa845
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/vcf.c
@@ -0,0 +1,244 @@
+#include <zlib.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include "bcf.h"
+#include "kstring.h"
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 4096)
+
+typedef struct {
+ gzFile fp;
+ FILE *fpout;
+ kstream_t *ks;
+ void *refhash;
+ kstring_t line;
+ int max_ref;
+} vcf_t;
+
+bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
+{
+ kstring_t meta, smpl;
+ int dret;
+ vcf_t *v;
+ bcf_hdr_t *h;
+ if (!bp->is_vcf) return bcf_hdr_read(bp);
+ h = calloc(1, sizeof(bcf_hdr_t));
+ v = (vcf_t*)bp->v;
+ v->line.l = 0;
+ memset(&meta, 0, sizeof(kstring_t));
+ memset(&smpl, 0, sizeof(kstring_t));
+ while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
+ if (v->line.l < 2) continue;
+ if (v->line.s[0] != '#') return 0; // no sample line
+ if (v->line.s[0] == '#' && v->line.s[1] == '#') {
+ kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
+ } else if (v->line.s[0] == '#') {
+ int k;
+ ks_tokaux_t aux;
+ char *p;
+ for (p = kstrtok(v->line.s, "\t\n", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
+ if (k >= 9) {
+ kputsn(p, aux.p - p, &smpl);
+ kputc('\0', &smpl);
+ }
+ }
+ break;
+ }
+ }
+ kputc('\0', &meta);
+ h->name = 0;
+ h->sname = smpl.s; h->l_smpl = smpl.l;
+ h->txt = meta.s; h->l_txt = meta.l;
+ bcf_hdr_sync(h);
+ return h;
+}
+
+bcf_t *vcf_open(const char *fn, const char *mode)
+{
+ bcf_t *bp;
+ vcf_t *v;
+ if (strchr(mode, 'b')) return bcf_open(fn, mode);
+ bp = calloc(1, sizeof(bcf_t));
+ v = calloc(1, sizeof(vcf_t));
+ bp->is_vcf = 1;
+ bp->v = v;
+ v->refhash = bcf_str2id_init();
+ if (strchr(mode, 'r')) {
+ v->fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+ v->ks = ks_init(v->fp);
+ } else if (strchr(mode, 'w'))
+ v->fpout = strcmp(fn, "-")? fopen(fn, "w") : stdout;
+ return bp;
+}
+
+int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn)
+{
+ vcf_t *v;
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t s, rn;
+ int dret;
+ if (bp == 0) return -1;
+ if (!bp->is_vcf) return 0;
+ s.l = s.m = 0; s.s = 0;
+ rn.m = rn.l = h->l_nm; rn.s = h->name;
+ v = (vcf_t*)bp->v;
+ fp = gzopen(fn, "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ bcf_str2id_add(v->refhash, strdup(s.s));
+ kputs(s.s, &rn); kputc('\0', &rn);
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ h->l_nm = rn.l; h->name = rn.s;
+ bcf_hdr_sync(h);
+ free(s.s);
+ return 0;
+}
+
+int vcf_close(bcf_t *bp)
+{
+ vcf_t *v;
+ if (bp == 0) return -1;
+ if (!bp->is_vcf) return bcf_close(bp);
+ v = (vcf_t*)bp->v;
+ if (v->fp) {
+ ks_destroy(v->ks);
+ gzclose(v->fp);
+ }
+ if (v->fpout) fclose(v->fpout);
+ free(v->line.s);
+ bcf_str2id_thorough_destroy(v->refhash);
+ free(v);
+ free(bp);
+ return 0;
+}
+
+int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
+{
+ vcf_t *v = (vcf_t*)bp->v;
+ int i, has_ver = 0;
+ if (!bp->is_vcf) return bcf_hdr_write(bp, h);
+ if (h->l_txt > 0) {
+ if (strstr(h->txt, "##fileformat=")) has_ver = 1;
+ if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
+ fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
+ }
+ if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
+ fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
+ for (i = 0; i < h->n_smpl; ++i)
+ fprintf(v->fpout, "\t%s", h->sns[i]);
+ fputc('\n', v->fpout);
+ return 0;
+}
+
+int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
+{
+ vcf_t *v = (vcf_t*)bp->v;
+ extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s);
+ if (!bp->is_vcf) return bcf_write(bp, h, b);
+ bcf_fmt_core(h, b, &v->line);
+ fwrite(v->line.s, 1, v->line.l, v->fpout);
+ fputc('\n', v->fpout);
+ return v->line.l + 1;
+}
+
+int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
+{
+ int dret, k, i, sync = 0;
+ vcf_t *v = (vcf_t*)bp->v;
+ char *p, *q;
+ kstring_t str, rn;
+ ks_tokaux_t aux, a2;
+ if (!bp->is_vcf) return bcf_read(bp, h, b);
+ v->line.l = 0;
+ str.l = 0; str.m = b->m_str; str.s = b->str;
+ rn.l = rn.m = h->l_nm; rn.s = h->name;
+ if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
+ b->n_smpl = h->n_smpl;
+ for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
+ *(char*)aux.p = 0;
+ if (k == 0) { // ref
+ int tid = bcf_str2id(v->refhash, p);
+ if (tid < 0) {
+ tid = bcf_str2id_add(v->refhash, strdup(p));
+ kputs(p, &rn); kputc('\0', &rn);
+ sync = 1;
+ }
+ b->tid = tid;
+ } else if (k == 1) { // pos
+ b->pos = atoi(p) - 1;
+ } else if (k == 5) { // qual
+ b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
+ } else if (k <= 8) { // variable length strings
+ kputs(p, &str); kputc('\0', &str);
+ b->l_str = str.l; b->m_str = str.m; b->str = str.s;
+ if (k == 8) bcf_sync(b);
+ } else { // k > 9
+ if (strncmp(p, "./.", 3) == 0) {
+ for (i = 0; i < b->n_gi; ++i) {
+ if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
+ ((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
+ ((uint8_t*)b->gi[i].data)[k-9] = 0;
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ ((int32_t*)b->gi[i].data)[k-9] = 0;
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ ((uint16_t*)b->gi[i].data)[k-9] = 0;
+ } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ int y = b->n_alleles * (b->n_alleles + 1) / 2;
+ memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y);
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ int y = b->n_alleles * (b->n_alleles + 1) / 2;
+ memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4);
+ }
+ }
+ goto endblock;
+ }
+ for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
+ if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
+ ((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
+ double _x = strtod(q, &q);
+ int x = (int)(_x + .499);
+ if (x > 255) x = 255;
+ ((uint8_t*)b->gi[i].data)[k-9] = x;
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ int x = strtol(q, &q, 10);
+ if (x > 0xffff) x = 0xffff;
+ ((uint32_t*)b->gi[i].data)[k-9] = x;
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ int x = strtol(q, &q, 10);
+ if (x > 0xffff) x = 0xffff;
+ ((uint16_t*)b->gi[i].data)[k-9] = x;
+ } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ int x, y, j;
+ uint8_t *data = (uint8_t*)b->gi[i].data;
+ y = b->n_alleles * (b->n_alleles + 1) / 2;
+ for (j = 0; j < y; ++j) {
+ x = strtol(q, &q, 10);
+ if (x > 255) x = 255;
+ data[(k-9) * y + j] = x;
+ ++q;
+ }
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ int j, y;
+ float x, *data = (float*)b->gi[i].data;
+ y = b->n_alleles * (b->n_alleles + 1) / 2;
+ for (j = 0; j < y; ++j) {
+ x = strtod(q, &q);
+ data[(k-9) * y + j] = x > 0? -x/10. : x;
+ ++q;
+ }
+ }
+ }
+ endblock: i = i;
+ }
+ }
+ h->l_nm = rn.l; h->name = rn.s;
+ if (sync) bcf_hdr_sync(h);
+ return v->line.l + 1;
+}
diff --git a/src/samtools-0.1.18/bcftools/vcfutils.pl b/src/samtools-0.1.18/bcftools/vcfutils.pl
new file mode 100755
index 0000000..2b7ba0b
--- /dev/null
+++ b/src/samtools-0.1.18/bcftools/vcfutils.pl
@@ -0,0 +1,567 @@
+#!/usr/bin/perl -w
+
+# Author: lh3
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+&main;
+exit;
+
+sub main {
+ &usage if (@ARGV < 1);
+ my $command = shift(@ARGV);
+ my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
+ hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats,
+ gapstats=>\&gapstats, splitchr=>\&splitchr, vcf2fq=>\&vcf2fq);
+ die("Unknown command \"$command\".\n") if (!defined($func{$command}));
+ &{$func{$command}};
+}
+
+sub splitchr {
+ my %opts = (l=>5000000);
+ getopts('l:', \%opts);
+ my $l = $opts{l};
+ die(qq/Usage: vcfutils.pl splitchr [-l $opts{l}] <in.fa.fai>\n/) if (@ARGV == 0 && -t STDIN);
+ while (<>) {
+ my @t = split;
+ my $last = 0;
+ for (my $i = 0; $i < $t[1];) {
+ my $e = ($t[1] - $i) / $l < 1.1? $t[1] : $i + $l;
+ print "$t[0]:".($i+1)."-$e\n";
+ $i = $e;
+ }
+ }
+}
+
+sub subsam {
+ die(qq/Usage: vcfutils.pl subsam <in.vcf> [samples]\n/) if (@ARGV == 0);
+ my ($fh, %h);
+ my $fn = shift(@ARGV);
+ my @col;
+ open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die;
+ $h{$_} = 1 for (@ARGV);
+ while (<$fh>) {
+ if (/^##/) {
+ print;
+ } elsif (/^#/) {
+ my @t = split;
+ my @s = @t[0..8]; # all fixed fields + FORMAT
+ for (9 .. $#t) {
+ if ($h{$t[$_]}) {
+ push(@s, $t[$_]);
+ push(@col, $_);
+ }
+ }
+ pop(@s) if (@s == 9); # no sample selected; remove the FORMAT field
+ print join("\t", @s), "\n";
+ } else {
+ my @t = split;
+ if (@col == 0) {
+ print join("\t", @t[0..7]), "\n";
+ } else {
+ print join("\t", @t[0..8], map {$t[$_]} @col), "\n";
+ }
+ }
+ }
+ close($fh);
+}
+
+sub listsam {
+ die(qq/Usage: vcfutils.pl listsam <in.vcf>\n/) if (@ARGV == 0 && -t STDIN);
+ while (<>) {
+ if (/^#/ && !/^##/) {
+ my @t = split;
+ print join("\n", @t[9..$#t]), "\n";
+ exit;
+ }
+ }
+}
+
+sub fillac {
+ die(qq/Usage: vcfutils.pl fillac <in.vcf>\n\nNote: The GT field MUST BE present and always appear as the first field.\n/) if (@ARGV == 0 && -t STDIN);
+ while (<>) {
+ if (/^#/) {
+ print;
+ } else {
+ my @t = split;
+ my @c = (0, 0);
+ my $n = 0;
+ my $s = -1;
+ @_ = split(":", $t[8]);
+ for (0 .. $#_) {
+ if ($_[$_] eq 'GT') { $s = $_; last; }
+ }
+ if ($s < 0) {
+ print join("\t", @t), "\n";
+ next;
+ }
+ for (9 .. $#t) {
+ if ($t[$_] =~ /^0,0,0/) {
+ } elsif ($t[$_] =~ /^([^\s:]+:){$s}(\d+).(\d+)/) {
+ ++$c[$2]; ++$c[$3];
+ $n += 2;
+ }
+ }
+ my $AC = "AC=" . join("\t", @c[1..$#c]) . ";AN=$n";
+ my $info = $t[7];
+ $info =~ s/(;?)AC=(\d+)//;
+ $info =~ s/(;?)AN=(\d+)//;
+ if ($info eq '.') {
+ $info = $AC;
+ } else {
+ $info .= ";$AC";
+ }
+ $t[7] = $info;
+ print join("\t", @t), "\n";
+ }
+ }
+}
+
+sub ldstats {
+ my %opts = (t=>0.9);
+ getopts('t:', \%opts);
+ die("Usage: vcfutils.pl ldstats [-t $opts{t}] <in.vcf>\n") if (@ARGV == 0 && -t STDIN);
+ my $cutoff = $opts{t};
+ my ($last, $lastchr) = (0x7fffffff, '');
+ my ($x, $y, $n) = (0, 0, 0);
+ while (<>) {
+ if (/^([^#\s]+)\s(\d+)/) {
+ my ($chr, $pos) = ($1, $2);
+ if (/NEIR=([\d\.]+)/) {
+ ++$n;
+ ++$y, $x += $pos - $last if ($lastchr eq $chr && $pos > $last && $1 > $cutoff);
+ }
+ $last = $pos; $lastchr = $chr;
+ }
+ }
+ print "Number of SNP intervals in strong LD (r > $opts{t}): $y\n";
+ print "Fraction: ", $y/$n, "\n";
+ print "Length: $x\n";
+}
+
+sub qstats {
+ my %opts = (r=>'', s=>0.02, v=>undef);
+ getopts('r:s:v', \%opts);
+ die("Usage: vcfutils.pl qstats [-r ref.vcf] <in.vcf>\n
+Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #joint ts/tv #joint/#ref #joint/#non-indel \n") if (@ARGV == 0 && -t STDIN);
+ my %ts = (AG=>1, GA=>1, CT=>1, TC=>1);
+ my %h = ();
+ my $is_vcf = defined($opts{v})? 1 : 0;
+ if ($opts{r}) { # read the reference positions
+ my $fh;
+ open($fh, $opts{r}) || die;
+ while (<$fh>) {
+ next if (/^#/);
+ if ($is_vcf) {
+ my @t = split;
+ $h{$t[0],$t[1]} = $t[4];
+ } else {
+ $h{$1,$2} = 1 if (/^(\S+)\s+(\d+)/);
+ }
+ }
+ close($fh);
+ }
+ my $hsize = scalar(keys %h);
+ my @a;
+ while (<>) {
+ next if (/^#/);
+ my @t = split;
+ next if (length($t[3]) != 1 || uc($t[3]) eq 'N');
+ $t[3] = uc($t[3]); $t[4] = uc($t[4]);
+ my @s = split(',', $t[4]);
+ $t[5] = 3 if ($t[5] eq '.' || $t[5] < 0);
+ next if (length($s[0]) != 1);
+ my $hit;
+ if ($is_vcf) {
+ $hit = 0;
+ my $aa = $h{$t[0],$t[1]};
+ if (defined($aa)) {
+ my @aaa = split(",", $aa);
+ for (@aaa) {
+ $hit = 1 if ($_ eq $s[0]);
+ }
+ }
+ } else {
+ $hit = defined($h{$t[0],$t[1]})? 1 : 0;
+ }
+ push(@a, [$t[5], ($t[4] eq '.' || $t[4] eq $t[3])? 0 : 1, $ts{$t[3].$s[0]}? 1 : 0, $hit]);
+ }
+ push(@a, [-1, 0, 0, 0]); # end marker
+ die("[qstats] No SNP data!\n") if (@a == 0);
+ @a = sort {$b->[0]<=>$a->[0]} @a;
+ my $next = $opts{s};
+ my $last = $a[0];
+ my @c = (0, 0, 0, 0);
+ my @lc;
+ $lc[1] = $lc[2] = 0;
+ for my $p (@a) {
+ if ($p->[0] == -1 || ($p->[0] != $last && $c[0]/@a > $next)) {
+ my @x;
+ $x[0] = sprintf("%.4f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
+ $x[1] = sprintf("%.4f", $hsize? $c[3] / $hsize : 0);
+ $x[2] = sprintf("%.4f", $c[3] / $c[1]);
+ my $a = $c[1] - $lc[1];
+ my $b = $c[2] - $lc[2];
+ $x[3] = sprintf("%.4f", $a-$b? $b / ($a-$b) : 100);
+ print join("\t", $last, @c, @x), "\n";
+ $next = $c[0]/@a + $opts{s};
+ $lc[1] = $c[1]; $lc[2] = $c[2];
+ }
+ ++$c[0]; $c[1] += $p->[1]; $c[2] += $p->[2]; $c[3] += $p->[3];
+ $last = $p->[0];
+ }
+}
+
+sub varFilter {
+ my %opts = (d=>2, D=>10000000, a=>2, W=>10, Q=>10, w=>3, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, G=>0, S=>1000, e=>1e-4);
+ getopts('pd:D:W:Q:w:a:1:2:3:4:G:S:e:', \%opts);
+ die(qq/
+Usage: vcfutils.pl varFilter [options] <in.vcf>
+
+Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}]
+ -d INT minimum read depth [$opts{d}]
+ -D INT maximum read depth [$opts{D}]
+ -a INT minimum number of alternate bases [$opts{a}]
+ -w INT SNP within INT bp around a gap to be filtered [$opts{w}]
+ -W INT window size for filtering adjacent gaps [$opts{W}]
+ -1 FLOAT min P-value for strand bias (given PV4) [$opts{1}]
+ -2 FLOAT min P-value for baseQ bias [$opts{2}]
+ -3 FLOAT min P-value for mapQ bias [$opts{3}]
+ -4 FLOAT min P-value for end distance bias [$opts{4}]
+ -e FLOAT min P-value for HWE (plus F<0) [$opts{e}]
+ -p print filtered variants
+
+Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools.
+\n/) if (@ARGV == 0 && -t STDIN);
+
+ # calculate the window size
+ my ($ol, $ow) = ($opts{W}, $opts{w});
+ my $max_dist = $ol > $ow? $ol : $ow;
+ # the core loop
+ my @staging; # (indel_filtering_score, flt_tag, indel_span; chr, pos, ...)
+ while (<>) {
+ my @t = split;
+ if (/^#/) {
+ print; next;
+ }
+ next if ($t[4] eq '.'); # skip non-var sites
+ next if ($t[3] eq 'N'); # skip sites with unknown ref ('N')
+ # check if the site is a SNP
+ my $type = 1; # SNP
+ if (length($t[3]) > 1) {
+ $type = 2; # MNP
+ my @s = split(',', $t[4]);
+ for (@s) {
+ $type = 3 if (length != length($t[3]));
+ }
+ } else {
+ my @s = split(',', $t[4]);
+ for (@s) {
+ $type = 3 if (length > 1);
+ }
+ }
+ # clear the out-of-range elements
+ while (@staging) {
+ # Still on the same chromosome and the first element's window still affects this position?
+ last if ($staging[0][3] eq $t[0] && $staging[0][4] + $staging[0][2] + $max_dist >= $t[1]);
+ varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much
+ }
+ my $flt = 0;
+ # parse annotations
+ my ($dp, $mq, $dp_alt) = (-1, -1, -1);
+ if ($t[7] =~ /DP4=(\d+),(\d+),(\d+),(\d+)/i) {
+ $dp = $1 + $2 + $3 + $4;
+ $dp_alt = $3 + $4;
+ }
+ if ($t[7] =~ /DP=(\d+)/i) {
+ $dp = $1;
+ }
+ $mq = $1 if ($t[7] =~ /MQ=(\d+)/i);
+ # the depth and mapQ filter
+ if ($dp >= 0) {
+ if ($dp < $opts{d}) {
+ $flt = 2;
+ } elsif ($dp > $opts{D}) {
+ $flt = 3;
+ }
+ }
+ $flt = 4 if ($dp_alt >= 0 && $dp_alt < $opts{a});
+ $flt = 1 if ($flt == 0 && $mq >= 0 && $mq < $opts{Q});
+ $flt = 7 if ($flt == 0 && /PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/
+ && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4}));
+ $flt = 8 if ($flt == 0 && ((/MXGQ=(\d+)/ && $1 < $opts{G}) || (/MXSP=(\d+)/ && $1 >= $opts{S})));
+ # HWE filter
+ if ($t[7] =~ /G3=([^;,]+),([^;,]+),([^;,]+).*HWE=([^;,]+)/ && $4 < $opts{e}) {
+ my $p = 2*$1 + $2;
+ my $f = ($p > 0 && $p < 1)? 1 - $2 / ($p * (1-$p)) : 0;
+ $flt = 9 if ($f < 0);
+ }
+
+ my $score = $t[5] * 100 + $dp_alt;
+ my $rlen = length($t[3]) - 1; # $indel_score<0 for SNPs
+ if ($flt == 0) {
+ if ($type == 3) { # an indel
+ # filtering SNPs and MNPs
+ for my $x (@staging) {
+ next if (($x->[0]&3) == 3 || $x->[1] || $x->[4] + $x->[2] + $ow < $t[1]);
+ $x->[1] = 5;
+ }
+ # check the staging list for indel filtering
+ for my $x (@staging) {
+ next if (($x->[0]&3) != 3 || $x->[1] || $x->[4] + $x->[2] + $ol < $t[1]);
+ if ($x->[0]>>2 < $score) {
+ $x->[1] = 6;
+ } else {
+ $flt = 6; last;
+ }
+ }
+ } else { # SNP or MNP
+ for my $x (@staging) {
+ next if (($x->[0]&3) != 3 || $x->[4] + $x->[2] + $ow < $t[1]);
+ if ($x->[4] + length($x->[7]) - 1 == $t[1] && substr($x->[7], -1, 1) eq substr($t[4], 0, 1)
+ && length($x->[7]) - length($x->[6]) == 1) {
+ $x->[1] = 5;
+ } else { $flt = 5; }
+ last;
+ }
+ # check MNP
+ for my $x (@staging) {
+ next if (($x->[0]&3) == 3 || $x->[4] + $x->[2] < $t[1]);
+ if ($x->[0]>>2 < $score) {
+ $x->[1] = 8;
+ } else {
+ $flt = 8; last;
+ }
+ }
+ }
+ }
+ push(@staging, [$score<<2|$type, $flt, $rlen, @t]);
+ }
+ # output the last few elements in the staging list
+ while (@staging) {
+ varFilter_aux(shift @staging, $opts{p});
+ }
+}
+
+sub varFilter_aux {
+ my ($first, $is_print) = @_;
+ if ($first->[1] == 0) {
+ print join("\t", @$first[3 .. @$first-1]), "\n";
+ } elsif ($is_print) {
+ print STDERR join("\t", substr("UQdDaGgPMS", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
+ }
+}
+
+sub gapstats {
+ my (@c0, @c1);
+ $c0[$_] = $c1[$_] = 0 for (0 .. 10000);
+ while (<>) {
+ next if (/^#/);
+ my @t = split;
+ next if (length($t[3]) == 1 && $t[4] =~ /^[A-Za-z](,[A-Za-z])*$/); # not an indel
+ my @s = split(',', $t[4]);
+ for my $x (@s) {
+ my $l = length($x) - length($t[3]) + 5000;
+ if ($x =~ /^-/) {
+ $l = -(length($x) - 1) + 5000;
+ } elsif ($x =~ /^\+/) {
+ $l = length($x) - 1 + 5000;
+ }
+ $c0[$l] += 1 / @s;
+ }
+ }
+ for (my $i = 0; $i < 10000; ++$i) {
+ next if ($c0[$i] == 0);
+ $c1[0] += $c0[$i];
+ $c1[1] += $c0[$i] if (($i-5000)%3 == 0);
+ printf("C\t%d\t%.2f\n", ($i-5000), $c0[$i]);
+ }
+ printf("3\t%d\t%d\t%.3f\n", $c1[0], $c1[1], $c1[1]/$c1[0]);
+}
+
+sub ucscsnp2vcf {
+ die("Usage: vcfutils.pl <in.ucsc.snp>\n") if (@ARGV == 0 && -t STDIN);
+ print "##fileformat=VCFv4.0\n";
+ print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"), "\n";
+ while (<>) {
+ my @t = split("\t");
+ my $indel = ($t[9] =~ /^[ACGT](\/[ACGT])+$/)? 0 : 1;
+ my $pos = $t[2] + 1;
+ my @alt;
+ push(@alt, $t[7]);
+ if ($t[6] eq '-') {
+ $t[9] = reverse($t[9]);
+ $t[9] =~ tr/ACGTRYMKWSNacgtrymkwsn/TGCAYRKMWSNtgcayrkmwsn/;
+ }
+ my @a = split("/", $t[9]);
+ for (@a) {
+ push(@alt, $_) if ($_ ne $alt[0]);
+ }
+ if ($indel) {
+ --$pos;
+ for (0 .. $#alt) {
+ $alt[$_] =~ tr/-//d;
+ $alt[$_] = "N$alt[$_]";
+ }
+ }
+ my $ref = shift(@alt);
+ my $af = $t[13] > 0? ";AF=$t[13]" : '';
+ my $valid = ($t[12] eq 'unknown')? '' : ";valid=$t[12]";
+ my $info = "molType=$t[10];class=$t[11]$valid$af";
+ print join("\t", $t[1], $pos, $t[4], $ref, join(",", @alt), 0, '.', $info), "\n";
+ }
+}
+
+sub hapmap2vcf {
+ die("Usage: vcfutils.pl <in.ucsc.snp> <in.hapmap>\n") if (@ARGV == 0);
+ my $fn = shift(@ARGV);
+ # parse UCSC SNP
+ warn("Parsing UCSC SNPs...\n");
+ my ($fh, %map);
+ open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die;
+ while (<$fh>) {
+ my @t = split;
+ next if ($t[3] - $t[2] != 1); # not SNP
+ @{$map{$t[4]}} = @t[1,3,7];
+ }
+ close($fh);
+ # write VCF
+ warn("Writing VCF...\n");
+ print "##fileformat=VCFv4.0\n";
+ while (<>) {
+ my @t = split;
+ if ($t[0] eq 'rs#') { # the first line
+ print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", @t[11..$#t]), "\n";
+ } else {
+ next unless ($map{$t[0]});
+ next if (length($t[1]) != 3); # skip non-SNPs
+ my $a = \@{$map{$t[0]}};
+ my $ref = $a->[2];
+ my @u = split('/', $t[1]);
+ if ($u[1] eq $ref) {
+ $u[1] = $u[0]; $u[0] = $ref;
+ } elsif ($u[0] ne $ref) { next; }
+ my $alt = $u[1];
+ my %w;
+ $w{$u[0]} = 0; $w{$u[1]} = 1;
+ my @s = (@$a[0,1], $t[0], $ref, $alt, 0, '.', '.', 'GT');
+ my $is_tri = 0;
+ for (@t[11..$#t]) {
+ if ($_ eq 'NN') {
+ push(@s, './.');
+ } else {
+ my @a = ($w{substr($_,0,1)}, $w{substr($_,1,1)});
+ if (!defined($a[0]) || !defined($a[1])) {
+ $is_tri = 1;
+ last;
+ }
+ push(@s, "$a[0]/$a[1]");
+ }
+ }
+ next if ($is_tri);
+ print join("\t", @s), "\n";
+ }
+ }
+}
+
+sub vcf2fq {
+ my %opts = (d=>3, D=>100000, Q=>10, l=>5);
+ getopts('d:D:Q:l:', \%opts);
+ die(qq/
+Usage: vcfutils.pl vcf2fq [options] <all-site.vcf>
+
+Options: -d INT minimum depth [$opts{d}]
+ -D INT maximum depth [$opts{D}]
+ -Q INT min RMS mapQ [$opts{Q}]
+ -l INT INDEL filtering window [$opts{l}]
+\n/) if (@ARGV == 0 && -t STDIN);
+
+ my ($last_chr, $seq, $qual, $last_pos, @gaps);
+ my $_Q = $opts{Q};
+ my $_d = $opts{d};
+ my $_D = $opts{D};
+
+ my %het = (AC=>'M', AG=>'R', AT=>'W', CA=>'M', CG=>'S', CT=>'Y',
+ GA=>'R', GC=>'S', GT=>'K', TA=>'W', TC=>'Y', TG=>'K');
+
+ $last_chr = '';
+ while (<>) {
+ next if (/^#/);
+ my @t = split;
+ if ($last_chr ne $t[0]) {
+ &v2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l}) if ($last_chr);
+ ($last_chr, $last_pos) = ($t[0], 0);
+ $seq = $qual = '';
+ @gaps = ();
+ }
+ die("[vcf2fq] unsorted input\n") if ($t[1] - $last_pos < 0);
+ if ($t[1] - $last_pos > 1) {
+ $seq .= 'n' x ($t[1] - $last_pos - 1);
+ $qual .= '!' x ($t[1] - $last_pos - 1);
+ }
+ if (length($t[3]) == 1 && $t[7] !~ /INDEL/ && $t[4] =~ /^([A-Za-z.])(,[A-Za-z])*$/) { # a SNP or reference
+ my ($ref, $alt) = ($t[3], $1);
+ my ($b, $q);
+ $q = $1 if ($t[7] =~ /FQ=(-?[\d\.]+)/);
+ if ($q < 0) {
+ $_ = ($t[7] =~ /AF1=([\d\.]+)/)? $1 : 0;
+ $b = ($_ < .5 || $alt eq '.')? $ref : $alt;
+ $q = -$q;
+ } else {
+ $b = $het{"$ref$alt"};
+ $b ||= 'N';
+ }
+ $b = lc($b);
+ $b = uc($b) if (($t[7] =~ /MQ=(\d+)/ && $1 >= $_Q) && ($t[7] =~ /DP=(\d+)/ && $1 >= $_d && $1 <= $_D));
+ $q = int($q + 33 + .499);
+ $q = chr($q <= 126? $q : 126);
+ $seq .= $b;
+ $qual .= $q;
+ } elsif ($t[4] ne '.') { # an INDEL
+ push(@gaps, [$t[1], length($t[3])]);
+ }
+ $last_pos = $t[1];
+ }
+ &v2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l});
+}
+
+sub v2q_post_process {
+ my ($chr, $seq, $qual, $gaps, $l) = @_;
+ for my $g (@$gaps) {
+ my $beg = $g->[0] > $l? $g->[0] - $l : 0;
+ my $end = $g->[0] + $g->[1] + $l;
+ $end = length($$seq) if ($end > length($$seq));
+ substr($$seq, $beg, $end - $beg) = lc(substr($$seq, $beg, $end - $beg));
+ }
+ print "\@$chr\n"; &v2q_print_str($seq);
+ print "+\n"; &v2q_print_str($qual);
+}
+
+sub v2q_print_str {
+ my ($s) = @_;
+ my $l = length($$s);
+ for (my $i = 0; $i < $l; $i += 60) {
+ print substr($$s, $i, 60), "\n";
+ }
+}
+
+sub usage {
+ die(qq/
+Usage: vcfutils.pl <command> [<arguments>]\n
+Command: subsam get a subset of samples
+ listsam list the samples
+ fillac fill the allele count field
+ qstats SNP stats stratified by QUAL
+
+ hapmap2vcf convert the hapmap format to VCF
+ ucscsnp2vcf convert UCSC SNP SQL dump to VCF
+
+ varFilter filtering short variants (*)
+ vcf2fq VCF->fastq (**)
+
+Notes: Commands with description endting with (*) may need bcftools
+ specific annotations.
+\n/);
+}
diff --git a/src/samtools-0.1.18/bedidx.c b/src/samtools-0.1.18/bedidx.c
new file mode 100644
index 0000000..ec75a10
--- /dev/null
+++ b/src/samtools-0.1.18/bedidx.c
@@ -0,0 +1,162 @@
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+
+#ifdef _WIN32
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint64_t)
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 8192)
+
+typedef struct {
+ int n, m;
+ uint64_t *a;
+ int *idx;
+} bed_reglist_t;
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(reg, bed_reglist_t)
+
+#define LIDX_SHIFT 13
+
+typedef kh_reg_t reghash_t;
+
+int *bed_index_core(int n, uint64_t *a, int *n_idx)
+{
+ int i, j, m, *idx;
+ m = *n_idx = 0; idx = 0;
+ for (i = 0; i < n; ++i) {
+ int beg, end;
+ beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT;
+ if (m < end + 1) {
+ int oldm = m;
+ m = end + 1;
+ kroundup32(m);
+ idx = realloc(idx, m * sizeof(int));
+ for (j = oldm; j < m; ++j) idx[j] = -1;
+ }
+ if (beg == end) {
+ if (idx[beg] < 0) idx[beg] = i;
+ } else {
+ for (j = beg; j <= end; ++j)
+ if (idx[j] < 0) idx[j] = i;
+ }
+ *n_idx = end + 1;
+ }
+ return idx;
+}
+
+void bed_index(void *_h)
+{
+ reghash_t *h = (reghash_t*)_h;
+ khint_t k;
+ for (k = 0; k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ bed_reglist_t *p = &kh_val(h, k);
+ if (p->idx) free(p->idx);
+ ks_introsort(uint64_t, p->n, p->a);
+ p->idx = bed_index_core(p->n, p->a, &p->m);
+ }
+ }
+}
+
+int bed_overlap_core(const bed_reglist_t *p, int beg, int end)
+{
+ int i, min_off;
+ if (p->n == 0) return 0;
+ min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT];
+ if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here
+ int n = beg>>LIDX_SHIFT;
+ if (n > p->n) n = p->n;
+ for (i = n - 1; i >= 0; --i)
+ if (p->idx[i] >= 0) break;
+ min_off = i >= 0? p->idx[i] : 0;
+ }
+ for (i = min_off; i < p->n; ++i) {
+ if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed
+ if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end)
+ return 1; // find the overlap; return
+ }
+ return 0;
+}
+
+int bed_overlap(const void *_h, const char *chr, int beg, int end)
+{
+ const reghash_t *h = (const reghash_t*)_h;
+ khint_t k;
+ if (!h) return 0;
+ k = kh_get(reg, h, chr);
+ if (k == kh_end(h)) return 0;
+ return bed_overlap_core(&kh_val(h, k), beg, end);
+}
+
+void *bed_read(const char *fn)
+{
+ reghash_t *h = kh_init(reg);
+ gzFile fp;
+ kstream_t *ks;
+ int dret;
+ kstring_t *str;
+ // read the list
+ fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+ if (fp == 0) return 0;
+ str = calloc(1, sizeof(kstring_t));
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name
+ int beg = -1, end = -1;
+ bed_reglist_t *p;
+ khint_t k = kh_get(reg, h, str->s);
+ if (k == kh_end(h)) { // absent from the hash table
+ int ret;
+ char *s = strdup(str->s);
+ k = kh_put(reg, h, s, &ret);
+ memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
+ }
+ p = &kh_val(h, k);
+ if (dret != '\n') { // if the lines has other characters
+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
+ beg = atoi(str->s); // begin
+ if (dret != '\n') {
+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
+ end = atoi(str->s); // end
+ if (end < beg) end = -1;
+ }
+ }
+ }
+ }
+ if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line
+ if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
+ if (beg >= 0 && end > beg) {
+ if (p->n == p->m) {
+ p->m = p->m? p->m<<1 : 4;
+ p->a = realloc(p->a, p->m * 8);
+ }
+ p->a[p->n++] = (uint64_t)beg<<32 | end;
+ }
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(str->s); free(str);
+ bed_index(h);
+ return h;
+}
+
+void bed_destroy(void *_h)
+{
+ reghash_t *h = (reghash_t*)_h;
+ khint_t k;
+ for (k = 0; k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ free(kh_val(h, k).a);
+ free(kh_val(h, k).idx);
+ free((char*)kh_key(h, k));
+ }
+ }
+ kh_destroy(reg, h);
+}
diff --git a/src/samtools-0.1.18/bgzf.c b/src/samtools-0.1.18/bgzf.c
new file mode 100644
index 0000000..216cd04
--- /dev/null
+++ b/src/samtools-0.1.18/bgzf.c
@@ -0,0 +1,714 @@
+/* The MIT License
+
+ Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+*/
+
+/*
+ 2009-06-29 by lh3: cache recent uncompressed blocks.
+ 2009-06-25 by lh3: optionally use my knetfile library to access file on a FTP.
+ 2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <fcntl.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include "bgzf.h"
+
+#include "khash.h"
+typedef struct {
+ int size;
+ uint8_t *block;
+ int64_t end_offset;
+} cache_t;
+KHASH_MAP_INIT_INT64(cache, cache_t)
+
+#if defined(_WIN32) || defined(_MSC_VER)
+#define ftello(fp) ftell(fp)
+#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
+#else
+extern off_t ftello(FILE *stream);
+extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif
+
+typedef int8_t bgzf_byte_t;
+
+static const int DEFAULT_BLOCK_SIZE = 64 * 1024;
+static const int MAX_BLOCK_SIZE = 64 * 1024;
+
+static const int BLOCK_HEADER_LENGTH = 18;
+static const int BLOCK_FOOTER_LENGTH = 8;
+
+static const int GZIP_ID1 = 31;
+static const int GZIP_ID2 = 139;
+static const int CM_DEFLATE = 8;
+static const int FLG_FEXTRA = 4;
+static const int OS_UNKNOWN = 255;
+static const int BGZF_ID1 = 66; // 'B'
+static const int BGZF_ID2 = 67; // 'C'
+static const int BGZF_LEN = 2;
+static const int BGZF_XLEN = 6; // BGZF_LEN+4
+
+static const int GZIP_WINDOW_BITS = -15; // no zlib header
+static const int Z_DEFAULT_MEM_LEVEL = 8;
+
+
+inline
+void
+packInt16(uint8_t* buffer, uint16_t value)
+{
+ buffer[0] = value;
+ buffer[1] = value >> 8;
+}
+
+inline
+int
+unpackInt16(const uint8_t* buffer)
+{
+ return (buffer[0] | (buffer[1] << 8));
+}
+
+inline
+void
+packInt32(uint8_t* buffer, uint32_t value)
+{
+ buffer[0] = value;
+ buffer[1] = value >> 8;
+ buffer[2] = value >> 16;
+ buffer[3] = value >> 24;
+}
+
+static inline
+int
+bgzf_min(int x, int y)
+{
+ return (x < y) ? x : y;
+}
+
+static
+void
+report_error(BGZF* fp, const char* message) {
+ fp->error = message;
+}
+
+int bgzf_check_bgzf(const char *fn)
+{
+ BGZF *fp;
+ uint8_t buf[10],magic[10]="\037\213\010\4\0\0\0\0\0\377";
+ int n;
+
+ if ((fp = bgzf_open(fn, "r")) == 0)
+ {
+ fprintf(stderr, "[bgzf_check_bgzf] failed to open the file: %s\n",fn);
+ return -1;
+ }
+
+#ifdef _USE_KNETFILE
+ n = knet_read(fp->x.fpr, buf, 10);
+#else
+ n = fread(buf, 1, 10, fp->file);
+#endif
+ bgzf_close(fp);
+
+ if ( n!=10 )
+ return -1;
+
+ if ( !memcmp(magic, buf, 10) ) return 1;
+ return 0;
+}
+
+static BGZF *bgzf_read_init()
+{
+ BGZF *fp;
+ fp = calloc(1, sizeof(BGZF));
+ fp->uncompressed_block_size = MAX_BLOCK_SIZE;
+ fp->uncompressed_block = malloc(MAX_BLOCK_SIZE);
+ fp->compressed_block_size = MAX_BLOCK_SIZE;
+ fp->compressed_block = malloc(MAX_BLOCK_SIZE);
+ fp->cache_size = 0;
+ fp->cache = kh_init(cache);
+ return fp;
+}
+
+static
+BGZF*
+open_read(int fd)
+{
+#ifdef _USE_KNETFILE
+ knetFile *file = knet_dopen(fd, "r");
+#else
+ FILE* file = fdopen(fd, "r");
+#endif
+ BGZF* fp;
+ if (file == 0) return 0;
+ fp = bgzf_read_init();
+ fp->file_descriptor = fd;
+ fp->open_mode = 'r';
+#ifdef _USE_KNETFILE
+ fp->x.fpr = file;
+#else
+ fp->file = file;
+#endif
+ return fp;
+}
+
+static
+BGZF*
+open_write(int fd, int compress_level) // compress_level==-1 for the default level
+{
+ FILE* file = fdopen(fd, "w");
+ BGZF* fp;
+ if (file == 0) return 0;
+ fp = malloc(sizeof(BGZF));
+ fp->file_descriptor = fd;
+ fp->open_mode = 'w';
+ fp->owned_file = 0;
+ fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
+ if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
+#ifdef _USE_KNETFILE
+ fp->x.fpw = file;
+#else
+ fp->file = file;
+#endif
+ fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE;
+ fp->uncompressed_block = NULL;
+ fp->compressed_block_size = MAX_BLOCK_SIZE;
+ fp->compressed_block = malloc(MAX_BLOCK_SIZE);
+ fp->block_address = 0;
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ fp->error = NULL;
+ return fp;
+}
+
+BGZF*
+bgzf_open(const char* __restrict path, const char* __restrict mode)
+{
+ BGZF* fp = NULL;
+ if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
+#ifdef _USE_KNETFILE
+ knetFile *file = knet_open(path, mode);
+ if (file == 0) return 0;
+ fp = bgzf_read_init();
+ fp->file_descriptor = -1;
+ fp->open_mode = 'r';
+ fp->x.fpr = file;
+#else
+ int fd, oflag = O_RDONLY;
+#ifdef _WIN32
+ oflag |= O_BINARY;
+#endif
+ fd = open(path, oflag);
+ if (fd == -1) return 0;
+ fp = open_read(fd);
+#endif
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+ int fd, compress_level = -1, oflag = O_WRONLY | O_CREAT | O_TRUNC;
+#ifdef _WIN32
+ oflag |= O_BINARY;
+#endif
+ fd = open(path, oflag, 0666);
+ if (fd == -1) return 0;
+ { // set compress_level
+ int i;
+ for (i = 0; mode[i]; ++i)
+ if (mode[i] >= '0' && mode[i] <= '9') break;
+ if (mode[i]) compress_level = (int)mode[i] - '0';
+ if (strchr(mode, 'u')) compress_level = 0;
+ }
+ fp = open_write(fd, compress_level);
+ }
+ if (fp != NULL) fp->owned_file = 1;
+ return fp;
+}
+
+BGZF*
+bgzf_fdopen(int fd, const char * __restrict mode)
+{
+ if (fd == -1) return 0;
+ if (mode[0] == 'r' || mode[0] == 'R') {
+ return open_read(fd);
+ } else if (mode[0] == 'w' || mode[0] == 'W') {
+ int i, compress_level = -1;
+ for (i = 0; mode[i]; ++i)
+ if (mode[i] >= '0' && mode[i] <= '9') break;
+ if (mode[i]) compress_level = (int)mode[i] - '0';
+ if (strchr(mode, 'u')) compress_level = 0;
+ return open_write(fd, compress_level);
+ } else {
+ return NULL;
+ }
+}
+
+static
+int
+deflate_block(BGZF* fp, int block_length)
+{
+ // Deflate the block in fp->uncompressed_block into fp->compressed_block.
+ // Also adds an extra field that stores the compressed block length.
+
+ bgzf_byte_t* buffer = fp->compressed_block;
+ int buffer_size = fp->compressed_block_size;
+
+ // Init gzip header
+ buffer[0] = GZIP_ID1;
+ buffer[1] = GZIP_ID2;
+ buffer[2] = CM_DEFLATE;
+ buffer[3] = FLG_FEXTRA;
+ buffer[4] = 0; // mtime
+ buffer[5] = 0;
+ buffer[6] = 0;
+ buffer[7] = 0;
+ buffer[8] = 0;
+ buffer[9] = OS_UNKNOWN;
+ buffer[10] = BGZF_XLEN;
+ buffer[11] = 0;
+ buffer[12] = BGZF_ID1;
+ buffer[13] = BGZF_ID2;
+ buffer[14] = BGZF_LEN;
+ buffer[15] = 0;
+ buffer[16] = 0; // placeholder for block length
+ buffer[17] = 0;
+
+ // loop to retry for blocks that do not compress enough
+ int input_length = block_length;
+ int compressed_length = 0;
+ while (1) {
+ z_stream zs;
+ zs.zalloc = NULL;
+ zs.zfree = NULL;
+ zs.next_in = fp->uncompressed_block;
+ zs.avail_in = input_length;
+ zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
+ zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
+
+ int status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED,
+ GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
+ if (status != Z_OK) {
+ report_error(fp, "deflate init failed");
+ return -1;
+ }
+ status = deflate(&zs, Z_FINISH);
+ if (status != Z_STREAM_END) {
+ deflateEnd(&zs);
+ if (status == Z_OK) {
+ // Not enough space in buffer.
+ // Can happen in the rare case the input doesn't compress enough.
+ // Reduce the amount of input until it fits.
+ input_length -= 1024;
+ if (input_length <= 0) {
+ // should never happen
+ report_error(fp, "input reduction failed");
+ return -1;
+ }
+ continue;
+ }
+ report_error(fp, "deflate failed");
+ return -1;
+ }
+ status = deflateEnd(&zs);
+ if (status != Z_OK) {
+ report_error(fp, "deflate end failed");
+ return -1;
+ }
+ compressed_length = zs.total_out;
+ compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
+ if (compressed_length > MAX_BLOCK_SIZE) {
+ // should never happen
+ report_error(fp, "deflate overflow");
+ return -1;
+ }
+ break;
+ }
+
+ packInt16((uint8_t*)&buffer[16], compressed_length-1);
+ uint32_t crc = crc32(0L, NULL, 0L);
+ crc = crc32(crc, fp->uncompressed_block, input_length);
+ packInt32((uint8_t*)&buffer[compressed_length-8], crc);
+ packInt32((uint8_t*)&buffer[compressed_length-4], input_length);
+
+ int remaining = block_length - input_length;
+ if (remaining > 0) {
+ if (remaining > input_length) {
+ // should never happen (check so we can use memcpy)
+ report_error(fp, "remainder too large");
+ return -1;
+ }
+ memcpy(fp->uncompressed_block,
+ fp->uncompressed_block + input_length,
+ remaining);
+ }
+ fp->block_offset = remaining;
+ return compressed_length;
+}
+
+static
+int
+inflate_block(BGZF* fp, int block_length)
+{
+ // Inflate the block in fp->compressed_block into fp->uncompressed_block
+
+ z_stream zs;
+ int status;
+ zs.zalloc = NULL;
+ zs.zfree = NULL;
+ zs.next_in = fp->compressed_block + 18;
+ zs.avail_in = block_length - 16;
+ zs.next_out = fp->uncompressed_block;
+ zs.avail_out = fp->uncompressed_block_size;
+
+ status = inflateInit2(&zs, GZIP_WINDOW_BITS);
+ if (status != Z_OK) {
+ report_error(fp, "inflate init failed");
+ return -1;
+ }
+ status = inflate(&zs, Z_FINISH);
+ if (status != Z_STREAM_END) {
+ inflateEnd(&zs);
+ report_error(fp, "inflate failed");
+ return -1;
+ }
+ status = inflateEnd(&zs);
+ if (status != Z_OK) {
+ report_error(fp, "inflate failed");
+ return -1;
+ }
+ return zs.total_out;
+}
+
+static
+int
+check_header(const bgzf_byte_t* header)
+{
+ return (header[0] == GZIP_ID1 &&
+ header[1] == (bgzf_byte_t) GZIP_ID2 &&
+ header[2] == Z_DEFLATED &&
+ (header[3] & FLG_FEXTRA) != 0 &&
+ unpackInt16((uint8_t*)&header[10]) == BGZF_XLEN &&
+ header[12] == BGZF_ID1 &&
+ header[13] == BGZF_ID2 &&
+ unpackInt16((uint8_t*)&header[14]) == BGZF_LEN);
+}
+
+static void free_cache(BGZF *fp)
+{
+ khint_t k;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ if (fp->open_mode != 'r') return;
+ for (k = kh_begin(h); k < kh_end(h); ++k)
+ if (kh_exist(h, k)) free(kh_val(h, k).block);
+ kh_destroy(cache, h);
+}
+
+static int load_block_from_cache(BGZF *fp, int64_t block_address)
+{
+ khint_t k;
+ cache_t *p;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ k = kh_get(cache, h, block_address);
+ if (k == kh_end(h)) return 0;
+ p = &kh_val(h, k);
+ if (fp->block_length != 0) fp->block_offset = 0;
+ fp->block_address = block_address;
+ fp->block_length = p->size;
+ memcpy(fp->uncompressed_block, p->block, MAX_BLOCK_SIZE);
+#ifdef _USE_KNETFILE
+ knet_seek(fp->x.fpr, p->end_offset, SEEK_SET);
+#else
+ fseeko(fp->file, p->end_offset, SEEK_SET);
+#endif
+ return p->size;
+}
+
+static void cache_block(BGZF *fp, int size)
+{
+ int ret;
+ khint_t k;
+ cache_t *p;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ if (MAX_BLOCK_SIZE >= fp->cache_size) return;
+ if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) {
+ /* A better way would be to remove the oldest block in the
+ * cache, but here we remove a random one for simplicity. This
+ * should not have a big impact on performance. */
+ for (k = kh_begin(h); k < kh_end(h); ++k)
+ if (kh_exist(h, k)) break;
+ if (k < kh_end(h)) {
+ free(kh_val(h, k).block);
+ kh_del(cache, h, k);
+ }
+ }
+ k = kh_put(cache, h, fp->block_address, &ret);
+ if (ret == 0) return; // if this happens, a bug!
+ p = &kh_val(h, k);
+ p->size = fp->block_length;
+ p->end_offset = fp->block_address + size;
+ p->block = malloc(MAX_BLOCK_SIZE);
+ memcpy(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
+}
+
+int
+bgzf_read_block(BGZF* fp)
+{
+ bgzf_byte_t header[BLOCK_HEADER_LENGTH];
+ int count, size = 0, block_length, remaining;
+#ifdef _USE_KNETFILE
+ int64_t block_address = knet_tell(fp->x.fpr);
+ if (load_block_from_cache(fp, block_address)) return 0;
+ count = knet_read(fp->x.fpr, header, sizeof(header));
+#else
+ int64_t block_address = ftello(fp->file);
+ if (load_block_from_cache(fp, block_address)) return 0;
+ count = fread(header, 1, sizeof(header), fp->file);
+#endif
+ if (count == 0) {
+ fp->block_length = 0;
+ return 0;
+ }
+ size = count;
+ if (count != sizeof(header)) {
+ report_error(fp, "read failed");
+ return -1;
+ }
+ if (!check_header(header)) {
+ report_error(fp, "invalid block header");
+ return -1;
+ }
+ block_length = unpackInt16((uint8_t*)&header[16]) + 1;
+ bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
+ memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
+ remaining = block_length - BLOCK_HEADER_LENGTH;
+#ifdef _USE_KNETFILE
+ count = knet_read(fp->x.fpr, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
+#else
+ count = fread(&compressed_block[BLOCK_HEADER_LENGTH], 1, remaining, fp->file);
+#endif
+ if (count != remaining) {
+ report_error(fp, "read failed");
+ return -1;
+ }
+ size += count;
+ count = inflate_block(fp, block_length);
+ if (count < 0) return -1;
+ if (fp->block_length != 0) {
+ // Do not reset offset if this read follows a seek.
+ fp->block_offset = 0;
+ }
+ fp->block_address = block_address;
+ fp->block_length = count;
+ cache_block(fp, size);
+ return 0;
+}
+
+int
+bgzf_read(BGZF* fp, void* data, int length)
+{
+ if (length <= 0) {
+ return 0;
+ }
+ if (fp->open_mode != 'r') {
+ report_error(fp, "file not open for reading");
+ return -1;
+ }
+
+ int bytes_read = 0;
+ bgzf_byte_t* output = data;
+ while (bytes_read < length) {
+ int copy_length, available = fp->block_length - fp->block_offset;
+ bgzf_byte_t *buffer;
+ if (available <= 0) {
+ if (bgzf_read_block(fp) != 0) {
+ return -1;
+ }
+ available = fp->block_length - fp->block_offset;
+ if (available <= 0) {
+ break;
+ }
+ }
+ copy_length = bgzf_min(length-bytes_read, available);
+ buffer = fp->uncompressed_block;
+ memcpy(output, buffer + fp->block_offset, copy_length);
+ fp->block_offset += copy_length;
+ output += copy_length;
+ bytes_read += copy_length;
+ }
+ if (fp->block_offset == fp->block_length) {
+#ifdef _USE_KNETFILE
+ fp->block_address = knet_tell(fp->x.fpr);
+#else
+ fp->block_address = ftello(fp->file);
+#endif
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ return bytes_read;
+}
+
+int bgzf_flush(BGZF* fp)
+{
+ while (fp->block_offset > 0) {
+ int count, block_length;
+ block_length = deflate_block(fp, fp->block_offset);
+ if (block_length < 0) return -1;
+#ifdef _USE_KNETFILE
+ count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
+#else
+ count = fwrite(fp->compressed_block, 1, block_length, fp->file);
+#endif
+ if (count != block_length) {
+ report_error(fp, "write failed");
+ return -1;
+ }
+ fp->block_address += block_length;
+ }
+ return 0;
+}
+
+int bgzf_flush_try(BGZF *fp, int size)
+{
+ if (fp->block_offset + size > fp->uncompressed_block_size)
+ return bgzf_flush(fp);
+ return -1;
+}
+
+int bgzf_write(BGZF* fp, const void* data, int length)
+{
+ const bgzf_byte_t *input = data;
+ int block_length, bytes_written;
+ if (fp->open_mode != 'w') {
+ report_error(fp, "file not open for writing");
+ return -1;
+ }
+
+ if (fp->uncompressed_block == NULL)
+ fp->uncompressed_block = malloc(fp->uncompressed_block_size);
+
+ input = data;
+ block_length = fp->uncompressed_block_size;
+ bytes_written = 0;
+ while (bytes_written < length) {
+ int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
+ bgzf_byte_t* buffer = fp->uncompressed_block;
+ memcpy(buffer + fp->block_offset, input, copy_length);
+ fp->block_offset += copy_length;
+ input += copy_length;
+ bytes_written += copy_length;
+ if (fp->block_offset == block_length) {
+ if (bgzf_flush(fp) != 0) {
+ break;
+ }
+ }
+ }
+ return bytes_written;
+}
+
+int bgzf_close(BGZF* fp)
+{
+ if (fp->open_mode == 'w') {
+ if (bgzf_flush(fp) != 0) return -1;
+ { // add an empty block
+ int count, block_length = deflate_block(fp, 0);
+#ifdef _USE_KNETFILE
+ count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
+#else
+ count = fwrite(fp->compressed_block, 1, block_length, fp->file);
+#endif
+ }
+#ifdef _USE_KNETFILE
+ if (fflush(fp->x.fpw) != 0) {
+#else
+ if (fflush(fp->file) != 0) {
+#endif
+ report_error(fp, "flush failed");
+ return -1;
+ }
+ }
+ if (fp->owned_file) {
+#ifdef _USE_KNETFILE
+ int ret;
+ if (fp->open_mode == 'w') ret = fclose(fp->x.fpw);
+ else ret = knet_close(fp->x.fpr);
+ if (ret != 0) return -1;
+#else
+ if (fclose(fp->file) != 0) return -1;
+#endif
+ }
+ free(fp->uncompressed_block);
+ free(fp->compressed_block);
+ free_cache(fp);
+ free(fp);
+ return 0;
+}
+
+void bgzf_set_cache_size(BGZF *fp, int cache_size)
+{
+ if (fp) fp->cache_size = cache_size;
+}
+
+int bgzf_check_EOF(BGZF *fp)
+{
+ static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
+ uint8_t buf[28];
+ off_t offset;
+#ifdef _USE_KNETFILE
+ offset = knet_tell(fp->x.fpr);
+ if (knet_seek(fp->x.fpr, -28, SEEK_END) != 0) return -1;
+ knet_read(fp->x.fpr, buf, 28);
+ knet_seek(fp->x.fpr, offset, SEEK_SET);
+#else
+ offset = ftello(fp->file);
+ if (fseeko(fp->file, -28, SEEK_END) != 0) return -1;
+ fread(buf, 1, 28, fp->file);
+ fseeko(fp->file, offset, SEEK_SET);
+#endif
+ return (memcmp(magic, buf, 28) == 0)? 1 : 0;
+}
+
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
+{
+ int block_offset;
+ int64_t block_address;
+
+ if (fp->open_mode != 'r') {
+ report_error(fp, "file not open for read");
+ return -1;
+ }
+ if (where != SEEK_SET) {
+ report_error(fp, "unimplemented seek option");
+ return -1;
+ }
+ block_offset = pos & 0xFFFF;
+ block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
+#ifdef _USE_KNETFILE
+ if (knet_seek(fp->x.fpr, block_address, SEEK_SET) != 0) {
+#else
+ if (fseeko(fp->file, block_address, SEEK_SET) != 0) {
+#endif
+ report_error(fp, "seek failed");
+ return -1;
+ }
+ fp->block_length = 0; // indicates current block is not loaded
+ fp->block_address = block_address;
+ fp->block_offset = block_offset;
+ return 0;
+}
diff --git a/src/samtools-0.1.18/bgzf.h b/src/samtools-0.1.18/bgzf.h
new file mode 100644
index 0000000..7295f37
--- /dev/null
+++ b/src/samtools-0.1.18/bgzf.h
@@ -0,0 +1,157 @@
+/* The MIT License
+
+ Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+*/
+
+#ifndef __BGZF_H
+#define __BGZF_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include <zlib.h>
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+//typedef int8_t bool;
+
+typedef struct {
+ int file_descriptor;
+ char open_mode; // 'r' or 'w'
+ int16_t owned_file, compress_level;
+#ifdef _USE_KNETFILE
+ union {
+ knetFile *fpr;
+ FILE *fpw;
+ } x;
+#else
+ FILE* file;
+#endif
+ int uncompressed_block_size;
+ int compressed_block_size;
+ void* uncompressed_block;
+ void* compressed_block;
+ int64_t block_address;
+ int block_length;
+ int block_offset;
+ int cache_size;
+ const char* error;
+ void *cache; // a pointer to a hash table
+} BGZF;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Open an existing file descriptor for reading or writing.
+ * Mode must be either "r" or "w".
+ * A subsequent bgzf_close will not close the file descriptor.
+ * Returns null on error.
+ */
+BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
+
+/*
+ * Open the specified file for reading or writing.
+ * Mode must be either "r" or "w".
+ * Returns null on error.
+ */
+BGZF* bgzf_open(const char* path, const char* __restrict mode);
+
+/*
+ * Close the BGZ file and free all associated resources.
+ * Does not close the underlying file descriptor if created with bgzf_fdopen.
+ * Returns zero on success, -1 on error.
+ */
+int bgzf_close(BGZF* fp);
+
+/*
+ * Read up to length bytes from the file storing into data.
+ * Returns the number of bytes actually read.
+ * Returns zero on end of file.
+ * Returns -1 on error.
+ */
+int bgzf_read(BGZF* fp, void* data, int length);
+
+/*
+ * Write length bytes from data to the file.
+ * Returns the number of bytes written.
+ * Returns -1 on error.
+ */
+int bgzf_write(BGZF* fp, const void* data, int length);
+
+/*
+ * Return a virtual file pointer to the current location in the file.
+ * No interpetation of the value should be made, other than a subsequent
+ * call to bgzf_seek can be used to position the file at the same point.
+ * Return value is non-negative on success.
+ * Returns -1 on error.
+ */
+#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
+
+/*
+ * Set the file to read from the location specified by pos, which must
+ * be a value previously returned by bgzf_tell for this file (but not
+ * necessarily one returned by this file handle).
+ * The where argument must be SEEK_SET.
+ * Seeking on a file opened for write is not supported.
+ * Returns zero on success, -1 on error.
+ */
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
+
+/*
+ * Set the cache size. Zero to disable. By default, caching is
+ * disabled. The recommended cache size for frequent random access is
+ * about 8M bytes.
+ */
+void bgzf_set_cache_size(BGZF *fp, int cache_size);
+
+int bgzf_check_EOF(BGZF *fp);
+int bgzf_read_block(BGZF* fp);
+int bgzf_flush(BGZF* fp);
+int bgzf_flush_try(BGZF *fp, int size);
+int bgzf_check_bgzf(const char *fn);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline int bgzf_getc(BGZF *fp)
+{
+ int c;
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) return -2; /* error */
+ if (fp->block_length == 0) return -1; /* end-of-file */
+ }
+ c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
+ if (fp->block_offset == fp->block_length) {
+#ifdef _USE_KNETFILE
+ fp->block_address = knet_tell(fp->x.fpr);
+#else
+ fp->block_address = ftello(fp->file);
+#endif
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ return c;
+}
+
+#endif
diff --git a/src/samtools-0.1.18/bgzip.c b/src/samtools-0.1.18/bgzip.c
new file mode 100644
index 0000000..ebcafa2
--- /dev/null
+++ b/src/samtools-0.1.18/bgzip.c
@@ -0,0 +1,206 @@
+/* The MIT License
+
+ Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+*/
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+#include <sys/select.h>
+#include <sys/stat.h>
+#include "bgzf.h"
+
+static const int WINDOW_SIZE = 64 * 1024;
+
+static int bgzip_main_usage()
+{
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: bgzip [options] [file] ...\n\n");
+ fprintf(stderr, "Options: -c write on standard output, keep original files unchanged\n");
+ fprintf(stderr, " -d decompress\n");
+ fprintf(stderr, " -f overwrite files without asking\n");
+ fprintf(stderr, " -b INT decompress at virtual file pointer INT\n");
+ fprintf(stderr, " -s INT decompress INT bytes in the uncompressed file\n");
+ fprintf(stderr, " -h give this help\n");
+ fprintf(stderr, "\n");
+ return 1;
+}
+
+static int write_open(const char *fn, int is_forced)
+{
+ int fd = -1;
+ char c;
+ if (!is_forced) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
+ fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
+ scanf("%c", &c);
+ if (c != 'Y' && c != 'y') {
+ fprintf(stderr, "[bgzip] not overwritten\n");
+ exit(1);
+ }
+ }
+ }
+ if (fd < 0) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
+ fprintf(stderr, "[bgzip] %s: Fail to write\n", fn);
+ exit(1);
+ }
+ }
+ return fd;
+}
+
+static void fail(BGZF* fp)
+{
+ fprintf(stderr, "Error: %s\n", fp->error);
+ exit(1);
+}
+
+int main(int argc, char **argv)
+{
+ int c, compress, pstdout, is_forced;
+ BGZF *fp;
+ void *buffer;
+ long start, end, size;
+
+ compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
+ while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){
+ switch(c){
+ case 'h': return bgzip_main_usage();
+ case 'd': compress = 0; break;
+ case 'c': pstdout = 1; break;
+ case 'b': start = atol(optarg); break;
+ case 's': size = atol(optarg); break;
+ case 'f': is_forced = 1; break;
+ }
+ }
+ if (size >= 0) end = start + size;
+ if (end >= 0 && end < start) {
+ fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
+ return 1;
+ }
+ if (compress == 1) {
+ struct stat sbuf;
+ int f_src = fileno(stdin);
+ int f_dst = fileno(stdout);
+
+ if ( argc>optind )
+ {
+ if ( stat(argv[optind],&sbuf)<0 )
+ {
+ fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+ return 1;
+ }
+
+ if ((f_src = open(argv[optind], O_RDONLY)) < 0) {
+ fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+ return 1;
+ }
+
+ if (pstdout)
+ f_dst = fileno(stdout);
+ else
+ {
+ char *name = malloc(strlen(argv[optind]) + 5);
+ strcpy(name, argv[optind]);
+ strcat(name, ".gz");
+ f_dst = write_open(name, is_forced);
+ if (f_dst < 0) return 1;
+ free(name);
+ }
+ }
+ else if (!pstdout && isatty(fileno((FILE *)stdout)) )
+ return bgzip_main_usage();
+
+ fp = bgzf_fdopen(f_dst, "w");
+ buffer = malloc(WINDOW_SIZE);
+ while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
+ if (bgzf_write(fp, buffer, c) < 0) fail(fp);
+ // f_dst will be closed here
+ if (bgzf_close(fp) < 0) fail(fp);
+ if (argc > optind && !pstdout) unlink(argv[optind]);
+ free(buffer);
+ close(f_src);
+ return 0;
+ } else {
+ struct stat sbuf;
+ int f_dst;
+
+ if ( argc>optind )
+ {
+ if ( stat(argv[optind],&sbuf)<0 )
+ {
+ fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+ return 1;
+ }
+ char *name;
+ int len = strlen(argv[optind]);
+ if ( strcmp(argv[optind]+len-3,".gz") )
+ {
+ fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
+ return 1;
+ }
+ fp = bgzf_open(argv[optind], "r");
+ if (fp == NULL) {
+ fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
+ return 1;
+ }
+
+ if (pstdout) {
+ f_dst = fileno(stdout);
+ }
+ else {
+ name = strdup(argv[optind]);
+ name[strlen(name) - 3] = '\0';
+ f_dst = write_open(name, is_forced);
+ free(name);
+ }
+ }
+ else if (!pstdout && isatty(fileno((FILE *)stdin)) )
+ return bgzip_main_usage();
+ else
+ {
+ f_dst = fileno(stdout);
+ fp = bgzf_fdopen(fileno(stdin), "r");
+ if (fp == NULL) {
+ fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
+ return 1;
+ }
+ }
+ buffer = malloc(WINDOW_SIZE);
+ if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp);
+ while (1) {
+ if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
+ else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
+ if (c == 0) break;
+ if (c < 0) fail(fp);
+ start += c;
+ write(f_dst, buffer, c);
+ if (end >= 0 && start >= end) break;
+ }
+ free(buffer);
+ if (bgzf_close(fp) < 0) fail(fp);
+ if (!pstdout) unlink(argv[optind]);
+ return 0;
+ }
+}
diff --git a/src/samtools-0.1.18/cut_target.c b/src/samtools-0.1.18/cut_target.c
new file mode 100644
index 0000000..26f434f
--- /dev/null
+++ b/src/samtools-0.1.18/cut_target.c
@@ -0,0 +1,193 @@
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include "bam.h"
+#include "errmod.h"
+#include "faidx.h"
+
+#define ERR_DEP 0.83f
+
+typedef struct {
+ int e[2][3], p[2][2];
+} score_param_t;
+
+/* Note that although the two matrics have 10 parameters in total, only 4
+ * (probably 3) are free. Changing the scoring matrices in a sort of symmetric
+ * way will not change the result. */
+static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} };
+
+typedef struct {
+ int min_baseQ, tid, max_bases;
+ uint16_t *bases;
+ bamFile fp;
+ bam_header_t *h;
+ char *ref;
+ faidx_t *fai;
+ errmod_t *em;
+} ct_t;
+
+static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp)
+{
+ int i, j, ret, tmp, k, sum[4], qual;
+ float q[16];
+ if (n > g->max_bases) { // enlarge g->bases
+ g->max_bases = n;
+ kroundup32(g->max_bases);
+ g->bases = realloc(g->bases, g->max_bases * 2);
+ }
+ for (i = k = 0; i < n; ++i) {
+ const bam_pileup1_t *p = plp + i;
+ uint8_t *seq;
+ int q, baseQ, b;
+ if (p->is_refskip || p->is_del) continue;
+ baseQ = bam1_qual(p->b)[p->qpos];
+ if (baseQ < g->min_baseQ) continue;
+ seq = bam1_seq(p->b);
+ b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
+ if (b > 3) continue;
+ q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+ if (q < 4) q = 4;
+ if (q > 63) q = 63;
+ g->bases[k++] = q<<5 | bam1_strand(p->b)<<4 | b;
+ }
+ if (k == 0) return 0;
+ errmod_cal(g->em, k, 4, g->bases, q);
+ for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i;
+ for (i = 1; i < 4; ++i) // insertion sort
+ for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
+ tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
+ qual = (sum[1]>>2) - (sum[0]>>2);
+ k = k < 256? k : 255;
+ ret = (qual < 63? qual : 63) << 2 | (sum[0]&3);
+ return ret<<8|k;
+}
+
+static void process_cns(bam_header_t *h, int tid, int l, uint16_t *cns)
+{
+ int i, f[2][2], *prev, *curr, *swap_tmp, s;
+ uint8_t *b; // backtrack array
+ b = calloc(l, 1);
+ f[0][0] = f[0][1] = 0;
+ prev = f[0]; curr = f[1];
+ // fill the backtrack matrix
+ for (i = 0; i < l; ++i) {
+ int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2;
+ int tmp0, tmp1;
+ // compute f[0]
+ tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0)
+ tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1)
+ if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0;
+ else curr[0] = tmp1, b[i] = 1;
+ // compute f[1]
+ tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0)
+ tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1)
+ if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1;
+ else curr[1] = tmp1, b[i] |= 1<<1;
+ // swap
+ swap_tmp = prev; prev = curr; curr = swap_tmp;
+ }
+ // backtrack
+ s = prev[0] > prev[1]? 0 : 1;
+ for (i = l - 1; i > 0; --i) {
+ b[i] |= s<<2;
+ s = b[i]>>s&1;
+ }
+ // print
+ for (i = 0, s = -1; i <= l; ++i) {
+ if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) {
+ if (s >= 0) {
+ int j;
+ printf("%s:%d-%d\t0\t%s\t%d\t60\t%dM\t*\t0\t0\t", h->target_name[tid], s+1, i, h->target_name[tid], s+1, i-s);
+ for (j = s; j < i; ++j) {
+ int c = cns[j]>>8;
+ if (c == 0) putchar('N');
+ else putchar("ACGT"[c&3]);
+ }
+ putchar('\t');
+ for (j = s; j < i; ++j)
+ putchar(33 + (cns[j]>>8>>2));
+ putchar('\n');
+ }
+ //if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s);
+ s = -1;
+ } else if ((b[i]>>2&3) && s < 0) s = i;
+ }
+ free(b);
+}
+
+static int read_aln(void *data, bam1_t *b)
+{
+ extern int bam_prob_realn_core(bam1_t *b, const char *ref, int flag);
+ ct_t *g = (ct_t*)data;
+ int ret, len;
+ ret = bam_read1(g->fp, b);
+ if (ret >= 0 && g->fai && b->core.tid >= 0 && (b->core.flag&4) == 0) {
+ if (b->core.tid != g->tid) { // then load the sequence
+ free(g->ref);
+ g->ref = fai_fetch(g->fai, g->h->target_name[b->core.tid], &len);
+ g->tid = b->core.tid;
+ }
+ bam_prob_realn_core(b, g->ref, 1<<1|1);
+ }
+ return ret;
+}
+
+int main_cut_target(int argc, char *argv[])
+{
+ int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
+ const bam_pileup1_t *p;
+ bam_plp_t plp;
+ uint16_t *cns;
+ ct_t g;
+
+ memset(&g, 0, sizeof(ct_t));
+ g.min_baseQ = 13; g.tid = -1;
+ while ((c = getopt(argc, argv, "f:Q:i:o:0:1:2:")) >= 0) {
+ switch (c) {
+ case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff
+ case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY
+ case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE
+ case '1': g_param.e[1][1] = atoi(optarg); break;
+ case '2': g_param.e[1][2] = atoi(optarg); break;
+ case 'f': g.fai = fai_load(optarg);
+ if (g.fai == 0) fprintf(stderr, "[%s] fail to load the fasta index.\n", __func__);
+ break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(stderr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>\n");
+ return 1;
+ }
+ l = max_l = 0; cns = 0;
+ g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
+ g.h = bam_header_read(g.fp);
+ g.em = errmod_init(1 - ERR_DEP);
+ plp = bam_plp_init(read_aln, &g);
+ while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
+ if (tid < 0) break;
+ if (tid != lasttid) { // change of chromosome
+ if (cns) process_cns(g.h, lasttid, l, cns);
+ if (max_l < g.h->target_len[tid]) {
+ max_l = g.h->target_len[tid];
+ kroundup32(max_l);
+ cns = realloc(cns, max_l * 2);
+ }
+ l = g.h->target_len[tid];
+ memset(cns, 0, max_l * 2);
+ lasttid = tid;
+ }
+ cns[pos] = gencns(&g, n, p);
+ lastpos = pos;
+ }
+ process_cns(g.h, lasttid, l, cns);
+ free(cns);
+ bam_header_destroy(g.h);
+ bam_plp_destroy(plp);
+ bam_close(g.fp);
+ if (g.fai) {
+ fai_destroy(g.fai); free(g.ref);
+ }
+ errmod_destroy(g.em);
+ free(g.bases);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/errmod.c b/src/samtools-0.1.18/errmod.c
new file mode 100644
index 0000000..fba9a8d
--- /dev/null
+++ b/src/samtools-0.1.18/errmod.c
@@ -0,0 +1,130 @@
+#include <math.h>
+#include "errmod.h"
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint16_t)
+
+typedef struct __errmod_coef_t {
+ double *fk, *beta, *lhet;
+} errmod_coef_t;
+
+typedef struct {
+ double fsum[16], bsum[16];
+ uint32_t c[16];
+} call_aux_t;
+
+static errmod_coef_t *cal_coef(double depcorr, double eta)
+{
+ int k, n, q;
+ long double sum, sum1;
+ double *lC;
+ errmod_coef_t *ec;
+
+ ec = calloc(1, sizeof(errmod_coef_t));
+ // initialize ->fk
+ ec->fk = (double*)calloc(256, sizeof(double));
+ ec->fk[0] = 1.0;
+ for (n = 1; n != 256; ++n)
+ ec->fk[n] = pow(1. - depcorr, n) * (1.0 - eta) + eta;
+ // initialize ->coef
+ ec->beta = (double*)calloc(256 * 256 * 64, sizeof(double));
+ lC = (double*)calloc(256 * 256, sizeof(double));
+ for (n = 1; n != 256; ++n) {
+ double lgn = lgamma(n+1);
+ for (k = 1; k <= n; ++k)
+ lC[n<<8|k] = lgn - lgamma(k+1) - lgamma(n-k+1);
+ }
+ for (q = 1; q != 64; ++q) {
+ double e = pow(10.0, -q/10.0);
+ double le = log(e);
+ double le1 = log(1.0 - e);
+ for (n = 1; n <= 255; ++n) {
+ double *beta = ec->beta + (q<<16|n<<8);
+ sum1 = sum = 0.0;
+ for (k = n; k >= 0; --k, sum1 = sum) {
+ sum = sum1 + expl(lC[n<<8|k] + k*le + (n-k)*le1);
+ beta[k] = -10. / M_LN10 * logl(sum1 / sum);
+ }
+ }
+ }
+ // initialize ->lhet
+ ec->lhet = (double*)calloc(256 * 256, sizeof(double));
+ for (n = 0; n < 256; ++n)
+ for (k = 0; k < 256; ++k)
+ ec->lhet[n<<8|k] = lC[n<<8|k] - M_LN2 * n;
+ free(lC);
+ return ec;
+}
+
+errmod_t *errmod_init(float depcorr)
+{
+ errmod_t *em;
+ em = (errmod_t*)calloc(1, sizeof(errmod_t));
+ em->depcorr = depcorr;
+ em->coef = cal_coef(depcorr, 0.03);
+ return em;
+}
+
+void errmod_destroy(errmod_t *em)
+{
+ if (em == 0) return;
+ free(em->coef->lhet); free(em->coef->fk); free(em->coef->beta);
+ free(em->coef); free(em);
+}
+// qual:6, strand:1, base:4
+int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q)
+{
+ call_aux_t aux;
+ int i, j, k, w[32];
+
+ if (m > m) return -1;
+ memset(q, 0, m * m * sizeof(float));
+ if (n == 0) return 0;
+ // calculate aux.esum and aux.fsum
+ if (n > 255) { // then sample 255 bases
+ ks_shuffle(uint16_t, n, bases);
+ n = 255;
+ }
+ ks_introsort(uint16_t, n, bases);
+ memset(w, 0, 32 * sizeof(int));
+ memset(&aux, 0, sizeof(call_aux_t));
+ for (j = n - 1; j >= 0; --j) { // calculate esum and fsum
+ uint16_t b = bases[j];
+ int q = b>>5 < 4? 4 : b>>5;
+ if (q > 63) q = 63;
+ k = b&0x1f;
+ aux.fsum[k&0xf] += em->coef->fk[w[k]];
+ aux.bsum[k&0xf] += em->coef->fk[w[k]] * em->coef->beta[q<<16|n<<8|aux.c[k&0xf]];
+ ++aux.c[k&0xf];
+ ++w[k];
+ }
+ // generate likelihood
+ for (j = 0; j != m; ++j) {
+ float tmp1, tmp3;
+ int tmp2, bar_e;
+ // homozygous
+ for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != m; ++k) {
+ if (k == j) continue;
+ tmp1 += aux.bsum[k]; tmp2 += aux.c[k]; tmp3 += aux.fsum[k];
+ }
+ if (tmp2) {
+ bar_e = (int)(tmp1 / tmp3 + 0.499);
+ if (bar_e > 63) bar_e = 63;
+ q[j*m+j] = tmp1;
+ }
+ // heterozygous
+ for (k = j + 1; k < m; ++k) {
+ int cjk = aux.c[j] + aux.c[k];
+ for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i < m; ++i) {
+ if (i == j || i == k) continue;
+ tmp1 += aux.bsum[i]; tmp2 += aux.c[i]; tmp3 += aux.fsum[i];
+ }
+ if (tmp2) {
+ bar_e = (int)(tmp1 / tmp3 + 0.499);
+ if (bar_e > 63) bar_e = 63;
+ q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]] + tmp1;
+ } else q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]]; // all the bases are either j or k
+ }
+ for (k = 0; k != m; ++k) if (q[j*m+k] < 0.0) q[j*m+k] = 0.0;
+ }
+ return 0;
+}
diff --git a/src/samtools-0.1.18/errmod.h b/src/samtools-0.1.18/errmod.h
new file mode 100644
index 0000000..32c07b6
--- /dev/null
+++ b/src/samtools-0.1.18/errmod.h
@@ -0,0 +1,24 @@
+#ifndef ERRMOD_H
+#define ERRMOD_H
+
+#include <stdint.h>
+
+struct __errmod_coef_t;
+
+typedef struct {
+ double depcorr;
+ struct __errmod_coef_t *coef;
+} errmod_t;
+
+errmod_t *errmod_init(float depcorr);
+void errmod_destroy(errmod_t *em);
+
+/*
+ n: number of bases
+ m: maximum base
+ bases[i]: qual:6, strand:1, base:4
+ q[i*m+j]: phred-scaled likelihood of (i,j)
+ */
+int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q);
+
+#endif
diff --git a/src/samtools-0.1.18/faidx.c b/src/samtools-0.1.18/faidx.c
new file mode 100644
index 0000000..f0798fc
--- /dev/null
+++ b/src/samtools-0.1.18/faidx.c
@@ -0,0 +1,432 @@
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include "faidx.h"
+#include "khash.h"
+
+typedef struct {
+ int32_t line_len, line_blen;
+ int64_t len;
+ uint64_t offset;
+} faidx1_t;
+KHASH_MAP_INIT_STR(s, faidx1_t)
+
+#ifndef _NO_RAZF
+#include "razf.h"
+#else
+#ifdef _WIN32
+#define ftello(fp) ftell(fp)
+#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
+#else
+extern off_t ftello(FILE *stream);
+extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif
+#define RAZF FILE
+#define razf_read(fp, buf, size) fread(buf, 1, size, fp)
+#define razf_open(fn, mode) fopen(fn, mode)
+#define razf_close(fp) fclose(fp)
+#define razf_seek(fp, offset, whence) fseeko(fp, offset, whence)
+#define razf_tell(fp) ftello(fp)
+#endif
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+struct __faidx_t {
+ RAZF *rz;
+ int n, m;
+ char **name;
+ khash_t(s) *hash;
+};
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+static inline void fai_insert_index(faidx_t *idx, const char *name, int len, int line_len, int line_blen, uint64_t offset)
+{
+ khint_t k;
+ int ret;
+ faidx1_t t;
+ if (idx->n == idx->m) {
+ idx->m = idx->m? idx->m<<1 : 16;
+ idx->name = (char**)realloc(idx->name, sizeof(void*) * idx->m);
+ }
+ idx->name[idx->n] = strdup(name);
+ k = kh_put(s, idx->hash, idx->name[idx->n], &ret);
+ t.len = len; t.line_len = line_len; t.line_blen = line_blen; t.offset = offset;
+ kh_value(idx->hash, k) = t;
+ ++idx->n;
+}
+
+faidx_t *fai_build_core(RAZF *rz)
+{
+ char c, *name;
+ int l_name, m_name, ret;
+ int line_len, line_blen, state;
+ int l1, l2;
+ faidx_t *idx;
+ uint64_t offset;
+ int64_t len;
+
+ idx = (faidx_t*)calloc(1, sizeof(faidx_t));
+ idx->hash = kh_init(s);
+ name = 0; l_name = m_name = 0;
+ len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
+ while (razf_read(rz, &c, 1)) {
+ if (c == '\n') { // an empty line
+ if (state == 1) {
+ offset = razf_tell(rz);
+ continue;
+ } else if ((state == 0 && len < 0) || state == 2) continue;
+ }
+ if (c == '>') { // fasta header
+ if (len >= 0)
+ fai_insert_index(idx, name, len, line_len, line_blen, offset);
+ l_name = 0;
+ while ((ret = razf_read(rz, &c, 1)) != 0 && !isspace(c)) {
+ if (m_name < l_name + 2) {
+ m_name = l_name + 2;
+ kroundup32(m_name);
+ name = (char*)realloc(name, m_name);
+ }
+ name[l_name++] = c;
+ }
+ name[l_name] = '\0';
+ if (ret == 0) {
+ fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
+ free(name); fai_destroy(idx);
+ return 0;
+ }
+ if (c != '\n') while (razf_read(rz, &c, 1) && c != '\n');
+ state = 1; len = 0;
+ offset = razf_tell(rz);
+ } else {
+ if (state == 3) {
+ fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name);
+ free(name); fai_destroy(idx);
+ return 0;
+ }
+ if (state == 2) state = 3;
+ l1 = l2 = 0;
+ do {
+ ++l1;
+ if (isgraph(c)) ++l2;
+ } while ((ret = razf_read(rz, &c, 1)) && c != '\n');
+ if (state == 3 && l2) {
+ fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name);
+ free(name); fai_destroy(idx);
+ return 0;
+ }
+ ++l1; len += l2;
+ if (state == 1) line_len = l1, line_blen = l2, state = 0;
+ else if (state == 0) {
+ if (l1 != line_len || l2 != line_blen) state = 2;
+ }
+ }
+ }
+ fai_insert_index(idx, name, len, line_len, line_blen, offset);
+ free(name);
+ return idx;
+}
+
+void fai_save(const faidx_t *fai, FILE *fp)
+{
+ khint_t k;
+ int i;
+ for (i = 0; i < fai->n; ++i) {
+ faidx1_t x;
+ k = kh_get(s, fai->hash, fai->name[i]);
+ x = kh_value(fai->hash, k);
+#ifdef _WIN32
+ fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len);
+#else
+ fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len);
+#endif
+ }
+}
+
+faidx_t *fai_read(FILE *fp)
+{
+ faidx_t *fai;
+ char *buf, *p;
+ int len, line_len, line_blen;
+#ifdef _WIN32
+ long offset;
+#else
+ long long offset;
+#endif
+ fai = (faidx_t*)calloc(1, sizeof(faidx_t));
+ fai->hash = kh_init(s);
+ buf = (char*)calloc(0x10000, 1);
+ while (!feof(fp) && fgets(buf, 0x10000, fp)) {
+ for (p = buf; *p && isgraph(*p); ++p);
+ *p = 0; ++p;
+#ifdef _WIN32
+ sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len);
+#else
+ sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
+#endif
+ fai_insert_index(fai, buf, len, line_len, line_blen, offset);
+ }
+ free(buf);
+ return fai;
+}
+
+void fai_destroy(faidx_t *fai)
+{
+ int i;
+ for (i = 0; i < fai->n; ++i) free(fai->name[i]);
+ free(fai->name);
+ kh_destroy(s, fai->hash);
+ if (fai->rz) razf_close(fai->rz);
+ free(fai);
+}
+
+int fai_build(const char *fn)
+{
+ char *str;
+ RAZF *rz;
+ FILE *fp;
+ faidx_t *fai;
+ str = (char*)calloc(strlen(fn) + 5, 1);
+ sprintf(str, "%s.fai", fn);
+ rz = razf_open(fn, "r");
+ if (rz == 0) {
+ fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
+ free(str);
+ return -1;
+ }
+ fai = fai_build_core(rz);
+ razf_close(rz);
+ fp = fopen(str, "wb");
+ if (fp == 0) {
+ fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
+ fai_destroy(fai); free(str);
+ return -1;
+ }
+ fai_save(fai, fp);
+ fclose(fp);
+ free(str);
+ fai_destroy(fai);
+ return 0;
+}
+
+#ifdef _USE_KNETFILE
+FILE *download_and_open(const char *fn)
+{
+ const int buf_size = 1 * 1024 * 1024;
+ uint8_t *buf;
+ FILE *fp;
+ knetFile *fp_remote;
+ const char *url = fn;
+ const char *p;
+ int l = strlen(fn);
+ for (p = fn + l - 1; p >= fn; --p)
+ if (*p == '/') break;
+ fn = p + 1;
+
+ // First try to open a local copy
+ fp = fopen(fn, "r");
+ if (fp)
+ return fp;
+
+ // If failed, download from remote and open
+ fp_remote = knet_open(url, "rb");
+ if (fp_remote == 0) {
+ fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url);
+ return NULL;
+ }
+ if ((fp = fopen(fn, "wb")) == 0) {
+ fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn);
+ knet_close(fp_remote);
+ return NULL;
+ }
+ buf = (uint8_t*)calloc(buf_size, 1);
+ while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+ fwrite(buf, 1, l, fp);
+ free(buf);
+ fclose(fp);
+ knet_close(fp_remote);
+
+ return fopen(fn, "r");
+}
+#endif
+
+faidx_t *fai_load(const char *fn)
+{
+ char *str;
+ FILE *fp;
+ faidx_t *fai;
+ str = (char*)calloc(strlen(fn) + 5, 1);
+ sprintf(str, "%s.fai", fn);
+
+#ifdef _USE_KNETFILE
+ if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
+ {
+ fp = download_and_open(str);
+ if ( !fp )
+ {
+ fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
+ free(str);
+ return 0;
+ }
+ }
+ else
+#endif
+ fp = fopen(str, "rb");
+ if (fp == 0) {
+ fprintf(stderr, "[fai_load] build FASTA index.\n");
+ fai_build(fn);
+ fp = fopen(str, "rb");
+ if (fp == 0) {
+ fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
+ free(str);
+ return 0;
+ }
+ }
+
+ fai = fai_read(fp);
+ fclose(fp);
+
+ fai->rz = razf_open(fn, "rb");
+ free(str);
+ if (fai->rz == 0) {
+ fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
+ return 0;
+ }
+ return fai;
+}
+
+char *fai_fetch(const faidx_t *fai, const char *str, int *len)
+{
+ char *s, c;
+ int i, l, k, name_end;
+ khiter_t iter;
+ faidx1_t val;
+ khash_t(s) *h;
+ int beg, end;
+
+ beg = end = -1;
+ h = fai->hash;
+ name_end = l = strlen(str);
+ s = (char*)malloc(l+1);
+ // remove space
+ for (i = k = 0; i < l; ++i)
+ if (!isspace(str[i])) s[k++] = str[i];
+ s[k] = 0; l = k;
+ // determine the sequence name
+ for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+ if (i >= 0) name_end = i;
+ if (name_end < l) { // check if this is really the end
+ int n_hyphen = 0;
+ for (i = name_end + 1; i < l; ++i) {
+ if (s[i] == '-') ++n_hyphen;
+ else if (!isdigit(s[i]) && s[i] != ',') break;
+ }
+ if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+ s[name_end] = 0;
+ iter = kh_get(s, h, s);
+ if (iter == kh_end(h)) { // cannot find the sequence name
+ iter = kh_get(s, h, str); // try str as the name
+ if (iter == kh_end(h)) {
+ *len = 0;
+ free(s); return 0;
+ } else s[name_end] = ':', name_end = l;
+ }
+ } else iter = kh_get(s, h, str);
+ val = kh_value(h, iter);
+ // parse the interval
+ if (name_end < l) {
+ for (i = k = name_end + 1; i < l; ++i)
+ if (s[i] != ',') s[k++] = s[i];
+ s[k] = 0;
+ beg = atoi(s + name_end + 1);
+ for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+ end = i < k? atoi(s + i + 1) : val.len;
+ if (beg > 0) --beg;
+ } else beg = 0, end = val.len;
+ if (beg >= val.len) beg = val.len;
+ if (end >= val.len) end = val.len;
+ if (beg > end) beg = end;
+ free(s);
+
+ // now retrieve the sequence
+ l = 0;
+ s = (char*)malloc(end - beg + 2);
+ razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
+ while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg && !fai->rz->z_err)
+ if (isgraph(c)) s[l++] = c;
+ s[l] = '\0';
+ *len = l;
+ return s;
+}
+
+int faidx_main(int argc, char *argv[])
+{
+ if (argc == 1) {
+ fprintf(stderr, "Usage: faidx <in.fasta> [<reg> [...]]\n");
+ return 1;
+ } else {
+ if (argc == 2) fai_build(argv[1]);
+ else {
+ int i, j, k, l;
+ char *s;
+ faidx_t *fai;
+ fai = fai_load(argv[1]);
+ if (fai == 0) return 1;
+ for (i = 2; i != argc; ++i) {
+ printf(">%s\n", argv[i]);
+ s = fai_fetch(fai, argv[i], &l);
+ for (j = 0; j < l; j += 60) {
+ for (k = 0; k < 60 && k < l - j; ++k)
+ putchar(s[j + k]);
+ putchar('\n');
+ }
+ free(s);
+ }
+ fai_destroy(fai);
+ }
+ }
+ return 0;
+}
+
+int faidx_fetch_nseq(const faidx_t *fai)
+{
+ return fai->n;
+}
+
+char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len)
+{
+ int l;
+ char c;
+ khiter_t iter;
+ faidx1_t val;
+ char *seq=NULL;
+
+ // Adjust position
+ iter = kh_get(s, fai->hash, c_name);
+ if(iter == kh_end(fai->hash)) return 0;
+ val = kh_value(fai->hash, iter);
+ if(p_end_i < p_beg_i) p_beg_i = p_end_i;
+ if(p_beg_i < 0) p_beg_i = 0;
+ else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
+ if(p_end_i < 0) p_end_i = 0;
+ else if(val.len <= p_end_i) p_end_i = val.len - 1;
+
+ // Now retrieve the sequence
+ l = 0;
+ seq = (char*)malloc(p_end_i - p_beg_i + 2);
+ razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
+ while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1)
+ if (isgraph(c)) seq[l++] = c;
+ seq[l] = '\0';
+ *len = l;
+ return seq;
+}
+
+#ifdef FAIDX_MAIN
+int main(int argc, char *argv[]) { return faidx_main(argc, argv); }
+#endif
diff --git a/src/samtools-0.1.18/faidx.h b/src/samtools-0.1.18/faidx.h
new file mode 100644
index 0000000..1fb1b1f
--- /dev/null
+++ b/src/samtools-0.1.18/faidx.h
@@ -0,0 +1,103 @@
+/* The MIT License
+
+ Copyright (c) 2008 Genome Research Ltd (GRL).
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3 at sanger.ac.uk> */
+
+#ifndef FAIDX_H
+#define FAIDX_H
+
+/*!
+ @header
+
+ Index FASTA files and extract subsequence.
+
+ @copyright The Wellcome Trust Sanger Institute.
+ */
+
+struct __faidx_t;
+typedef struct __faidx_t faidx_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ /*!
+ @abstract Build index for a FASTA or razip compressed FASTA file.
+ @param fn FASTA file name
+ @return 0 on success; or -1 on failure
+ @discussion File "fn.fai" will be generated.
+ */
+ int fai_build(const char *fn);
+
+ /*!
+ @abstract Distroy a faidx_t struct.
+ @param fai Pointer to the struct to be destroyed
+ */
+ void fai_destroy(faidx_t *fai);
+
+ /*!
+ @abstract Load index from "fn.fai".
+ @param fn File name of the FASTA file
+ */
+ faidx_t *fai_load(const char *fn);
+
+ /*!
+ @abstract Fetch the sequence in a region.
+ @param fai Pointer to the faidx_t struct
+ @param reg Region in the format "chr2:20,000-30,000"
+ @param len Length of the region
+ @return Pointer to the sequence; null on failure
+
+ @discussion The returned sequence is allocated by malloc family
+ and should be destroyed by end users by calling free() on it.
+ */
+ char *fai_fetch(const faidx_t *fai, const char *reg, int *len);
+
+ /*!
+ @abstract Fetch the number of sequences.
+ @param fai Pointer to the faidx_t struct
+ @return The number of sequences
+ */
+ int faidx_fetch_nseq(const faidx_t *fai);
+
+ /*!
+ @abstract Fetch the sequence in a region.
+ @param fai Pointer to the faidx_t struct
+ @param c_name Region name
+ @param p_beg_i Beginning position number (zero-based)
+ @param p_end_i End position number (zero-based)
+ @param len Length of the region
+ @return Pointer to the sequence; null on failure
+
+ @discussion The returned sequence is allocated by malloc family
+ and should be destroyed by end users by calling free() on it.
+ */
+ char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/samtools-0.1.18/kaln.c b/src/samtools-0.1.18/kaln.c
new file mode 100644
index 0000000..9c0bbaa
--- /dev/null
+++ b/src/samtools-0.1.18/kaln.c
@@ -0,0 +1,486 @@
+/* The MIT License
+
+ Copyright (c) 2003-2006, 2008, 2009, by Heng Li <lh3lh3 at gmail.com>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdint.h>
+#include <math.h>
+#include "kaln.h"
+
+#define FROM_M 0
+#define FROM_I 1
+#define FROM_D 2
+
+typedef struct {
+ int i, j;
+ unsigned char ctype;
+} path_t;
+
+int aln_sm_blosum62[] = {
+/* A R N D C Q E G H I L K M F P S T W Y V * X */
+ 4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-4, 0,
+ -1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-4,-1,
+ -2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3,-4,-1,
+ -2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3,-4,-1,
+ 0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-4,-2,
+ -1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2,-4,-1,
+ -1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2,-4,-1,
+ 0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-4,-1,
+ -2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3,-4,-1,
+ -1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-4,-1,
+ -1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-1,
+ -1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2,-4,-1,
+ -1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-4,-1,
+ -2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-4,-1,
+ -1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-4,-2,
+ 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2,-4, 0,
+ 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-4, 0,
+ -3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-2,
+ -2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-4,-1,
+ 0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-4,-1,
+ -4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1,-4,
+ 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-4,-1
+};
+
+int aln_sm_blast[] = {
+ 1, -3, -3, -3, -2,
+ -3, 1, -3, -3, -2,
+ -3, -3, 1, -3, -2,
+ -3, -3, -3, 1, -2,
+ -2, -2, -2, -2, -2
+};
+
+int aln_sm_qual[] = {
+ 0, -23, -23, -23, 0,
+ -23, 0, -23, -23, 0,
+ -23, -23, 0, -23, 0,
+ -23, -23, -23, 0, 0,
+ 0, 0, 0, 0, 0
+};
+
+ka_param_t ka_param_blast = { 5, 2, 5, 2, aln_sm_blast, 5, 50 };
+ka_param_t ka_param_aa2aa = { 10, 2, 10, 2, aln_sm_blosum62, 22, 50 };
+
+ka_param2_t ka_param2_qual = { 37, 11, 37, 11, 37, 11, 0, 0, aln_sm_qual, 5, 50 };
+
+static uint32_t *ka_path2cigar32(const path_t *path, int path_len, int *n_cigar)
+{
+ int i, n;
+ uint32_t *cigar;
+ unsigned char last_type;
+
+ if (path_len == 0 || path == 0) {
+ *n_cigar = 0;
+ return 0;
+ }
+
+ last_type = path->ctype;
+ for (i = n = 1; i < path_len; ++i) {
+ if (last_type != path[i].ctype) ++n;
+ last_type = path[i].ctype;
+ }
+ *n_cigar = n;
+ cigar = (uint32_t*)calloc(*n_cigar, 4);
+
+ cigar[0] = 1u << 4 | path[path_len-1].ctype;
+ last_type = path[path_len-1].ctype;
+ for (i = path_len - 2, n = 0; i >= 0; --i) {
+ if (path[i].ctype == last_type) cigar[n] += 1u << 4;
+ else {
+ cigar[++n] = 1u << 4 | path[i].ctype;
+ last_type = path[i].ctype;
+ }
+ }
+
+ return cigar;
+}
+
+/***************************/
+/* START OF common_align.c */
+/***************************/
+
+#define SET_INF(s) (s).M = (s).I = (s).D = MINOR_INF;
+
+#define set_M(MM, cur, p, sc) \
+{ \
+ if ((p)->M >= (p)->I) { \
+ if ((p)->M >= (p)->D) { \
+ (MM) = (p)->M + (sc); (cur)->Mt = FROM_M; \
+ } else { \
+ (MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \
+ } \
+ } else { \
+ if ((p)->I > (p)->D) { \
+ (MM) = (p)->I + (sc); (cur)->Mt = FROM_I; \
+ } else { \
+ (MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \
+ } \
+ } \
+}
+#define set_I(II, cur, p) \
+{ \
+ if ((p)->M - gap_open > (p)->I) { \
+ (cur)->It = FROM_M; \
+ (II) = (p)->M - gap_open - gap_ext; \
+ } else { \
+ (cur)->It = FROM_I; \
+ (II) = (p)->I - gap_ext; \
+ } \
+}
+#define set_end_I(II, cur, p) \
+{ \
+ if (gap_end_ext >= 0) { \
+ if ((p)->M - gap_end_open > (p)->I) { \
+ (cur)->It = FROM_M; \
+ (II) = (p)->M - gap_end_open - gap_end_ext; \
+ } else { \
+ (cur)->It = FROM_I; \
+ (II) = (p)->I - gap_end_ext; \
+ } \
+ } else set_I(II, cur, p); \
+}
+#define set_D(DD, cur, p) \
+{ \
+ if ((p)->M - gap_open > (p)->D) { \
+ (cur)->Dt = FROM_M; \
+ (DD) = (p)->M - gap_open - gap_ext; \
+ } else { \
+ (cur)->Dt = FROM_D; \
+ (DD) = (p)->D - gap_ext; \
+ } \
+}
+#define set_end_D(DD, cur, p) \
+{ \
+ if (gap_end_ext >= 0) { \
+ if ((p)->M - gap_end_open > (p)->D) { \
+ (cur)->Dt = FROM_M; \
+ (DD) = (p)->M - gap_end_open - gap_end_ext; \
+ } else { \
+ (cur)->Dt = FROM_D; \
+ (DD) = (p)->D - gap_end_ext; \
+ } \
+ } else set_D(DD, cur, p); \
+}
+
+typedef struct {
+ uint8_t Mt:3, It:2, Dt:3;
+} dpcell_t;
+
+typedef struct {
+ int M, I, D;
+} dpscore_t;
+
+/***************************
+ * banded global alignment *
+ ***************************/
+uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar)
+{
+ int i, j;
+ dpcell_t **dpcell, *q;
+ dpscore_t *curr, *last, *s;
+ int b1, b2, tmp_end;
+ int *mat, end, max = 0;
+ uint8_t type, ctype;
+ uint32_t *cigar = 0;
+
+ int gap_open, gap_ext, gap_end_open, gap_end_ext, b;
+ int *score_matrix, N_MATRIX_ROW;
+
+ /* initialize some align-related parameters. just for compatibility */
+ gap_open = ap->gap_open;
+ gap_ext = ap->gap_ext;
+ gap_end_open = ap->gap_end_open;
+ gap_end_ext = ap->gap_end_ext;
+ b = ap->band_width;
+ score_matrix = ap->matrix;
+ N_MATRIX_ROW = ap->row;
+
+ if (n_cigar) *n_cigar = 0;
+ if (len1 == 0 || len2 == 0) return 0;
+
+ /* calculate b1 and b2 */
+ if (len1 > len2) {
+ b1 = len1 - len2 + b;
+ b2 = b;
+ } else {
+ b1 = b;
+ b2 = len2 - len1 + b;
+ }
+ if (b1 > len1) b1 = len1;
+ if (b2 > len2) b2 = len2;
+ --seq1; --seq2;
+
+ /* allocate memory */
+ end = (b1 + b2 <= len1)? (b1 + b2 + 1) : (len1 + 1);
+ dpcell = (dpcell_t**)malloc(sizeof(dpcell_t*) * (len2 + 1));
+ for (j = 0; j <= len2; ++j)
+ dpcell[j] = (dpcell_t*)malloc(sizeof(dpcell_t) * end);
+ for (j = b2 + 1; j <= len2; ++j)
+ dpcell[j] -= j - b2;
+ curr = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
+ last = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
+
+ /* set first row */
+ SET_INF(*curr); curr->M = 0;
+ for (i = 1, s = curr + 1; i < b1; ++i, ++s) {
+ SET_INF(*s);
+ set_end_D(s->D, dpcell[0] + i, s - 1);
+ }
+ s = curr; curr = last; last = s;
+
+ /* core dynamic programming, part 1 */
+ tmp_end = (b2 < len2)? b2 : len2 - 1;
+ for (j = 1; j <= tmp_end; ++j) {
+ q = dpcell[j]; s = curr; SET_INF(*s);
+ set_end_I(s->I, q, last);
+ end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ ++s; ++q;
+ for (i = 1; i != end; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
+ set_I(s->I, q, last + i);
+ set_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_D(s->D, q, s - 1);
+ if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
+ set_end_I(s->I, q, last + i);
+ } else s->I = MINOR_INF;
+ s = curr; curr = last; last = s;
+ }
+ /* last row for part 1, use set_end_D() instead of set_D() */
+ if (j == len2 && b2 != len2 - 1) {
+ q = dpcell[j]; s = curr; SET_INF(*s);
+ set_end_I(s->I, q, last);
+ end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ ++s; ++q;
+ for (i = 1; i != end; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
+ set_I(s->I, q, last + i);
+ set_end_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_end_D(s->D, q, s - 1);
+ if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
+ set_end_I(s->I, q, last + i);
+ } else s->I = MINOR_INF;
+ s = curr; curr = last; last = s;
+ ++j;
+ }
+
+ /* core dynamic programming, part 2 */
+ for (; j <= len2 - b2 + 1; ++j) {
+ SET_INF(curr[j - b2]);
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ end = j + b1 - 1;
+ for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i != end; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_I(s->I, q, last + i);
+ set_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_D(s->D, q, s - 1);
+ s->I = MINOR_INF;
+ s = curr; curr = last; last = s;
+ }
+
+ /* core dynamic programming, part 3 */
+ for (; j < len2; ++j) {
+ SET_INF(curr[j - b2]);
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_I(s->I, q, last + i);
+ set_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
+ set_end_I(s->I, q, last + i);
+ set_D(s->D, q, s - 1);
+ s = curr; curr = last; last = s;
+ }
+ /* last row */
+ if (j == len2) {
+ SET_INF(curr[j - b2]);
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_I(s->I, q, last + i);
+ set_end_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
+ set_end_I(s->I, q, last + i);
+ set_end_D(s->D, q, s - 1);
+ s = curr; curr = last; last = s;
+ }
+
+ *_score = last[len1].M;
+ if (n_cigar) { /* backtrace */
+ path_t *p, *path = (path_t*)malloc(sizeof(path_t) * (len1 + len2 + 2));
+ i = len1; j = len2;
+ q = dpcell[j] + i;
+ s = last + len1;
+ max = s->M; type = q->Mt; ctype = FROM_M;
+ if (s->I > max) { max = s->I; type = q->It; ctype = FROM_I; }
+ if (s->D > max) { max = s->D; type = q->Dt; ctype = FROM_D; }
+
+ p = path;
+ p->ctype = ctype; p->i = i; p->j = j; /* bug fixed 040408 */
+ ++p;
+ do {
+ switch (ctype) {
+ case FROM_M: --i; --j; break;
+ case FROM_I: --j; break;
+ case FROM_D: --i; break;
+ }
+ q = dpcell[j] + i;
+ ctype = type;
+ switch (type) {
+ case FROM_M: type = q->Mt; break;
+ case FROM_I: type = q->It; break;
+ case FROM_D: type = q->Dt; break;
+ }
+ p->ctype = ctype; p->i = i; p->j = j;
+ ++p;
+ } while (i || j);
+ cigar = ka_path2cigar32(path, p - path - 1, n_cigar);
+ free(path);
+ }
+
+ /* free memory */
+ for (j = b2 + 1; j <= len2; ++j)
+ dpcell[j] += j - b2;
+ for (j = 0; j <= len2; ++j)
+ free(dpcell[j]);
+ free(dpcell);
+ free(curr); free(last);
+
+ return cigar;
+}
+
+typedef struct {
+ int M, I, D;
+} score_aux_t;
+
+#define MINUS_INF -0x40000000
+
+// matrix: len2 rows and len1 columns
+int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap)
+{
+
+#define __score_aux(_p, _q0, _sc, _io, _ie, _do, _de) { \
+ int t1, t2; \
+ score_aux_t *_q; \
+ _q = _q0; \
+ _p->M = _q->M >= _q->I? _q->M : _q->I; \
+ _p->M = _p->M >= _q->D? _p->M : _q->D; \
+ _p->M += (_sc); \
+ ++_q; t1 = _q->M - _io - _ie; t2 = _q->I - _ie; _p->I = t1 >= t2? t1 : t2; \
+ _q = _p-1; t1 = _q->M - _do - _de; t2 = _q->D - _de; _p->D = t1 >= t2? t1 : t2; \
+ }
+
+ int i, j, bw, scmat_size = ap->row, *scmat = ap->matrix, ret;
+ const uint8_t *seq1, *seq2;
+ score_aux_t *curr, *last, *swap;
+ bw = abs(len1 - len2) + ap->band_width;
+ i = len1 > len2? len1 : len2;
+ if (bw > i + 1) bw = i + 1;
+ seq1 = _seq1 - 1; seq2 = _seq2 - 1;
+ curr = calloc(len1 + 2, sizeof(score_aux_t));
+ last = calloc(len1 + 2, sizeof(score_aux_t));
+ { // the zero-th row
+ int x, end = len1;
+ score_aux_t *p;
+ j = 0;
+ x = j + bw; end = len1 < x? len1 : x; // band end
+ p = curr;
+ p->M = 0; p->I = p->D = MINUS_INF;
+ for (i = 1, p = &curr[1]; i <= end; ++i, ++p)
+ p->M = p->I = MINUS_INF, p->D = -(ap->edo + ap->ede * i);
+ p->M = p->I = p->D = MINUS_INF;
+ swap = curr; curr = last; last = swap;
+ }
+ for (j = 1; j < len2; ++j) {
+ int x, beg = 0, end = len1, *scrow, col_end;
+ score_aux_t *p;
+ x = j - bw; beg = 0 > x? 0 : x; // band start
+ x = j + bw; end = len1 < x? len1 : x; // band end
+ if (beg == 0) { // from zero-th column
+ p = curr;
+ p->M = p->D = MINUS_INF; p->I = -(ap->eio + ap->eie * j);
+ ++beg; // then beg = 1
+ }
+ scrow = scmat + seq2[j] * scmat_size;
+ if (end == len1) col_end = 1, --end;
+ else col_end = 0;
+ for (i = beg, p = &curr[beg]; i <= end; ++i, ++p)
+ __score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->iio, ap->iie, ap->ido, ap->ide);
+ if (col_end) {
+ __score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->eio, ap->eie, ap->ido, ap->ide);
+ ++p;
+ }
+ p->M = p->I = p->D = MINUS_INF;
+// for (i = 0; i <= len1; ++i) printf("(%d,%d,%d) ", curr[i].M, curr[i].I, curr[i].D); putchar('\n');
+ swap = curr; curr = last; last = swap;
+ }
+ { // the last row
+ int x, beg = 0, *scrow;
+ score_aux_t *p;
+ j = len2;
+ x = j - bw; beg = 0 > x? 0 : x; // band start
+ if (beg == 0) { // from zero-th column
+ p = curr;
+ p->M = p->D = MINUS_INF; p->I = -(ap->eio + ap->eie * j);
+ ++beg; // then beg = 1
+ }
+ scrow = scmat + seq2[j] * scmat_size;
+ for (i = beg, p = &curr[beg]; i < len1; ++i, ++p)
+ __score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->iio, ap->iie, ap->edo, ap->ede);
+ __score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->eio, ap->eie, ap->edo, ap->ede);
+// for (i = 0; i <= len1; ++i) printf("(%d,%d,%d) ", curr[i].M, curr[i].I, curr[i].D); putchar('\n');
+ }
+ ret = curr[len1].M >= curr[len1].I? curr[len1].M : curr[len1].I;
+ ret = ret >= curr[len1].D? ret : curr[len1].D;
+ free(curr); free(last);
+ return ret;
+}
+
+#ifdef _MAIN
+int main(int argc, char *argv[])
+{
+// int len1 = 35, len2 = 35;
+// uint8_t *seq1 = (uint8_t*)"\0\0\3\3\2\0\0\0\1\0\2\1\2\1\3\2\3\3\3\0\2\3\2\1\1\3\3\3\2\3\3\1\0\0\1";
+// uint8_t *seq2 = (uint8_t*)"\0\0\3\3\2\0\0\0\1\0\2\1\2\1\3\2\3\3\3\0\2\3\2\1\1\3\3\3\2\3\3\1\0\1\0";
+ int len1 = 4, len2 = 4;
+ uint8_t *seq1 = (uint8_t*)"\1\0\0\1";
+ uint8_t *seq2 = (uint8_t*)"\1\0\1\0";
+ int sc;
+// ka_global_core(seq1, 2, seq2, 1, &ka_param_qual, &sc, 0);
+ sc = ka_global_score(seq1, len1, seq2, len2, &ka_param2_qual);
+ printf("%d\n", sc);
+ return 0;
+}
+#endif
diff --git a/src/samtools-0.1.18/kaln.h b/src/samtools-0.1.18/kaln.h
new file mode 100644
index 0000000..1ece132
--- /dev/null
+++ b/src/samtools-0.1.18/kaln.h
@@ -0,0 +1,67 @@
+/* The MIT License
+
+ Copyright (c) 2003-2006, 2008, 2009 by Heng Li <lh3 at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#ifndef LH3_KALN_H_
+#define LH3_KALN_H_
+
+#include <stdint.h>
+
+#define MINOR_INF -1073741823
+
+typedef struct {
+ int gap_open;
+ int gap_ext;
+ int gap_end_open;
+ int gap_end_ext;
+
+ int *matrix;
+ int row;
+ int band_width;
+} ka_param_t;
+
+typedef struct {
+ int iio, iie, ido, ide;
+ int eio, eie, edo, ede;
+ int *matrix;
+ int row;
+ int band_width;
+} ka_param2_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap,
+ int *_score, int *n_cigar);
+ int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap);
+#ifdef __cplusplus
+}
+#endif
+
+extern ka_param_t ka_param_blast; /* = { 5, 2, 5, 2, aln_sm_blast, 5, 50 }; */
+extern ka_param_t ka_param_qual; // only use this for global alignment!!!
+extern ka_param2_t ka_param2_qual; // only use this for global alignment!!!
+
+#endif
diff --git a/src/samtools-0.1.18/khash.h b/src/samtools-0.1.18/khash.h
new file mode 100644
index 0000000..a7e8056
--- /dev/null
+++ b/src/samtools-0.1.18/khash.h
@@ -0,0 +1,528 @@
+/* The MIT License
+
+ Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/*
+ An example:
+
+#include "khash.h"
+KHASH_MAP_INIT_INT(32, char)
+int main() {
+ int ret, is_missing;
+ khiter_t k;
+ khash_t(32) *h = kh_init(32);
+ k = kh_put(32, h, 5, &ret);
+ if (!ret) kh_del(32, h, k);
+ kh_value(h, k) = 10;
+ k = kh_get(32, h, 10);
+ is_missing = (k == kh_end(h));
+ k = kh_get(32, h, 5);
+ kh_del(32, h, k);
+ for (k = kh_begin(h); k != kh_end(h); ++k)
+ if (kh_exist(h, k)) kh_value(h, k) = 1;
+ kh_destroy(32, h);
+ return 0;
+}
+*/
+
+/*
+ 2011-02-14 (0.2.5):
+
+ * Allow to declare global functions.
+
+ 2009-09-26 (0.2.4):
+
+ * Improve portability
+
+ 2008-09-19 (0.2.3):
+
+ * Corrected the example
+ * Improved interfaces
+
+ 2008-09-11 (0.2.2):
+
+ * Improved speed a little in kh_put()
+
+ 2008-09-10 (0.2.1):
+
+ * Added kh_clear()
+ * Fixed a compiling error
+
+ 2008-09-02 (0.2.0):
+
+ * Changed to token concatenation which increases flexibility.
+
+ 2008-08-31 (0.1.2):
+
+ * Fixed a bug in kh_get(), which has not been tested previously.
+
+ 2008-08-31 (0.1.1):
+
+ * Added destructor
+*/
+
+
+#ifndef __AC_KHASH_H
+#define __AC_KHASH_H
+
+/*!
+ @header
+
+ Generic hash table library.
+
+ @copyright Heng Li
+ */
+
+#define AC_VERSION_KHASH_H "0.2.5"
+
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+
+/* compipler specific configuration */
+
+#if UINT_MAX == 0xffffffffu
+typedef unsigned int khint32_t;
+#elif ULONG_MAX == 0xffffffffu
+typedef unsigned long khint32_t;
+#endif
+
+#if ULONG_MAX == ULLONG_MAX
+typedef unsigned long khint64_t;
+#else
+typedef unsigned long long khint64_t;
+#endif
+
+#ifdef _MSC_VER
+#define inline __inline
+#endif
+
+typedef khint32_t khint_t;
+typedef khint_t khiter_t;
+
+#define __ac_HASH_PRIME_SIZE 32
+static const khint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] =
+{
+ 0ul, 3ul, 11ul, 23ul, 53ul,
+ 97ul, 193ul, 389ul, 769ul, 1543ul,
+ 3079ul, 6151ul, 12289ul, 24593ul, 49157ul,
+ 98317ul, 196613ul, 393241ul, 786433ul, 1572869ul,
+ 3145739ul, 6291469ul, 12582917ul, 25165843ul, 50331653ul,
+ 100663319ul, 201326611ul, 402653189ul, 805306457ul, 1610612741ul,
+ 3221225473ul, 4294967291ul
+};
+
+#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
+#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
+#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
+#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
+#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
+#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
+#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))
+
+static const double __ac_HASH_UPPER = 0.77;
+
+#define KHASH_DECLARE(name, khkey_t, khval_t) \
+ typedef struct { \
+ khint_t n_buckets, size, n_occupied, upper_bound; \
+ khint32_t *flags; \
+ khkey_t *keys; \
+ khval_t *vals; \
+ } kh_##name##_t; \
+ extern kh_##name##_t *kh_init_##name(); \
+ extern void kh_destroy_##name(kh_##name##_t *h); \
+ extern void kh_clear_##name(kh_##name##_t *h); \
+ extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \
+ extern void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \
+ extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \
+ extern void kh_del_##name(kh_##name##_t *h, khint_t x);
+
+#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+ typedef struct { \
+ khint_t n_buckets, size, n_occupied, upper_bound; \
+ khint32_t *flags; \
+ khkey_t *keys; \
+ khval_t *vals; \
+ } kh_##name##_t; \
+ SCOPE kh_##name##_t *kh_init_##name() { \
+ return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \
+ } \
+ SCOPE void kh_destroy_##name(kh_##name##_t *h) \
+ { \
+ if (h) { \
+ free(h->keys); free(h->flags); \
+ free(h->vals); \
+ free(h); \
+ } \
+ } \
+ SCOPE void kh_clear_##name(kh_##name##_t *h) \
+ { \
+ if (h && h->flags) { \
+ memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(khint32_t)); \
+ h->size = h->n_occupied = 0; \
+ } \
+ } \
+ SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
+ { \
+ if (h->n_buckets) { \
+ khint_t inc, k, i, last; \
+ k = __hash_func(key); i = k % h->n_buckets; \
+ inc = 1 + k % (h->n_buckets - 1); last = i; \
+ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+ if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
+ else i += inc; \
+ if (i == last) return h->n_buckets; \
+ } \
+ return __ac_iseither(h->flags, i)? h->n_buckets : i; \
+ } else return 0; \
+ } \
+ SCOPE void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
+ { \
+ khint32_t *new_flags = 0; \
+ khint_t j = 1; \
+ { \
+ khint_t t = __ac_HASH_PRIME_SIZE - 1; \
+ while (__ac_prime_list[t] > new_n_buckets) --t; \
+ new_n_buckets = __ac_prime_list[t+1]; \
+ if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; \
+ else { \
+ new_flags = (khint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
+ memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
+ if (h->n_buckets < new_n_buckets) { \
+ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
+ if (kh_is_map) \
+ h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
+ } \
+ } \
+ } \
+ if (j) { \
+ for (j = 0; j != h->n_buckets; ++j) { \
+ if (__ac_iseither(h->flags, j) == 0) { \
+ khkey_t key = h->keys[j]; \
+ khval_t val; \
+ if (kh_is_map) val = h->vals[j]; \
+ __ac_set_isdel_true(h->flags, j); \
+ while (1) { \
+ khint_t inc, k, i; \
+ k = __hash_func(key); \
+ i = k % new_n_buckets; \
+ inc = 1 + k % (new_n_buckets - 1); \
+ while (!__ac_isempty(new_flags, i)) { \
+ if (i + inc >= new_n_buckets) i = i + inc - new_n_buckets; \
+ else i += inc; \
+ } \
+ __ac_set_isempty_false(new_flags, i); \
+ if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { \
+ { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
+ if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
+ __ac_set_isdel_true(h->flags, i); \
+ } else { \
+ h->keys[i] = key; \
+ if (kh_is_map) h->vals[i] = val; \
+ break; \
+ } \
+ } \
+ } \
+ } \
+ if (h->n_buckets > new_n_buckets) { \
+ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
+ if (kh_is_map) \
+ h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
+ } \
+ free(h->flags); \
+ h->flags = new_flags; \
+ h->n_buckets = new_n_buckets; \
+ h->n_occupied = h->size; \
+ h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
+ } \
+ } \
+ SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
+ { \
+ khint_t x; \
+ if (h->n_occupied >= h->upper_bound) { \
+ if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); \
+ else kh_resize_##name(h, h->n_buckets + 1); \
+ } \
+ { \
+ khint_t inc, k, i, site, last; \
+ x = site = h->n_buckets; k = __hash_func(key); i = k % h->n_buckets; \
+ if (__ac_isempty(h->flags, i)) x = i; \
+ else { \
+ inc = 1 + k % (h->n_buckets - 1); last = i; \
+ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+ if (__ac_isdel(h->flags, i)) site = i; \
+ if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
+ else i += inc; \
+ if (i == last) { x = site; break; } \
+ } \
+ if (x == h->n_buckets) { \
+ if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
+ else x = i; \
+ } \
+ } \
+ } \
+ if (__ac_isempty(h->flags, x)) { \
+ h->keys[x] = key; \
+ __ac_set_isboth_false(h->flags, x); \
+ ++h->size; ++h->n_occupied; \
+ *ret = 1; \
+ } else if (__ac_isdel(h->flags, x)) { \
+ h->keys[x] = key; \
+ __ac_set_isboth_false(h->flags, x); \
+ ++h->size; \
+ *ret = 2; \
+ } else *ret = 0; \
+ return x; \
+ } \
+ SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
+ { \
+ if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \
+ __ac_set_isdel_true(h->flags, x); \
+ --h->size; \
+ } \
+ }
+
+#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+ KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
+
+/* --- BEGIN OF HASH FUNCTIONS --- */
+
+/*! @function
+ @abstract Integer hash function
+ @param key The integer [khint32_t]
+ @return The hash value [khint_t]
+ */
+#define kh_int_hash_func(key) (khint32_t)(key)
+/*! @function
+ @abstract Integer comparison function
+ */
+#define kh_int_hash_equal(a, b) ((a) == (b))
+/*! @function
+ @abstract 64-bit integer hash function
+ @param key The integer [khint64_t]
+ @return The hash value [khint_t]
+ */
+#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
+/*! @function
+ @abstract 64-bit integer comparison function
+ */
+#define kh_int64_hash_equal(a, b) ((a) == (b))
+/*! @function
+ @abstract const char* hash function
+ @param s Pointer to a null terminated string
+ @return The hash value
+ */
+static inline khint_t __ac_X31_hash_string(const char *s)
+{
+ khint_t h = *s;
+ if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
+ return h;
+}
+/*! @function
+ @abstract Another interface to const char* hash function
+ @param key Pointer to a null terminated string [const char*]
+ @return The hash value [khint_t]
+ */
+#define kh_str_hash_func(key) __ac_X31_hash_string(key)
+/*! @function
+ @abstract Const char* comparison function
+ */
+#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)
+
+/* --- END OF HASH FUNCTIONS --- */
+
+/* Other necessary macros... */
+
+/*!
+ @abstract Type of the hash table.
+ @param name Name of the hash table [symbol]
+ */
+#define khash_t(name) kh_##name##_t
+
+/*! @function
+ @abstract Initiate a hash table.
+ @param name Name of the hash table [symbol]
+ @return Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_init(name) kh_init_##name()
+
+/*! @function
+ @abstract Destroy a hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_destroy(name, h) kh_destroy_##name(h)
+
+/*! @function
+ @abstract Reset a hash table without deallocating memory.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_clear(name, h) kh_clear_##name(h)
+
+/*! @function
+ @abstract Resize a hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param s New size [khint_t]
+ */
+#define kh_resize(name, h, s) kh_resize_##name(h, s)
+
+/*! @function
+ @abstract Insert a key to the hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param k Key [type of keys]
+ @param r Extra return code: 0 if the key is present in the hash table;
+ 1 if the bucket is empty (never used); 2 if the element in
+ the bucket has been deleted [int*]
+ @return Iterator to the inserted element [khint_t]
+ */
+#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
+
+/*! @function
+ @abstract Retrieve a key from the hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param k Key [type of keys]
+ @return Iterator to the found element, or kh_end(h) is the element is absent [khint_t]
+ */
+#define kh_get(name, h, k) kh_get_##name(h, k)
+
+/*! @function
+ @abstract Remove a key from the hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param k Iterator to the element to be deleted [khint_t]
+ */
+#define kh_del(name, h, k) kh_del_##name(h, k)
+
+
+/*! @function
+ @abstract Test whether a bucket contains data.
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param x Iterator to the bucket [khint_t]
+ @return 1 if containing data; 0 otherwise [int]
+ */
+#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))
+
+/*! @function
+ @abstract Get key given an iterator
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param x Iterator to the bucket [khint_t]
+ @return Key [type of keys]
+ */
+#define kh_key(h, x) ((h)->keys[x])
+
+/*! @function
+ @abstract Get value given an iterator
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param x Iterator to the bucket [khint_t]
+ @return Value [type of values]
+ @discussion For hash sets, calling this results in segfault.
+ */
+#define kh_val(h, x) ((h)->vals[x])
+
+/*! @function
+ @abstract Alias of kh_val()
+ */
+#define kh_value(h, x) ((h)->vals[x])
+
+/*! @function
+ @abstract Get the start iterator
+ @param h Pointer to the hash table [khash_t(name)*]
+ @return The start iterator [khint_t]
+ */
+#define kh_begin(h) (khint_t)(0)
+
+/*! @function
+ @abstract Get the end iterator
+ @param h Pointer to the hash table [khash_t(name)*]
+ @return The end iterator [khint_t]
+ */
+#define kh_end(h) ((h)->n_buckets)
+
+/*! @function
+ @abstract Get the number of elements in the hash table
+ @param h Pointer to the hash table [khash_t(name)*]
+ @return Number of elements in the hash table [khint_t]
+ */
+#define kh_size(h) ((h)->size)
+
+/*! @function
+ @abstract Get the number of buckets in the hash table
+ @param h Pointer to the hash table [khash_t(name)*]
+ @return Number of buckets in the hash table [khint_t]
+ */
+#define kh_n_buckets(h) ((h)->n_buckets)
+
+/* More conenient interfaces */
+
+/*! @function
+ @abstract Instantiate a hash set containing integer keys
+ @param name Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT(name) \
+ KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+ @abstract Instantiate a hash map containing integer keys
+ @param name Name of the hash table [symbol]
+ @param khval_t Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT(name, khval_t) \
+ KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+ @abstract Instantiate a hash map containing 64-bit integer keys
+ @param name Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT64(name) \
+ KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
+
+/*! @function
+ @abstract Instantiate a hash map containing 64-bit integer keys
+ @param name Name of the hash table [symbol]
+ @param khval_t Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT64(name, khval_t) \
+ KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
+
+typedef const char *kh_cstr_t;
+/*! @function
+ @abstract Instantiate a hash map containing const char* keys
+ @param name Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_STR(name) \
+ KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
+
+/*! @function
+ @abstract Instantiate a hash map containing const char* keys
+ @param name Name of the hash table [symbol]
+ @param khval_t Type of values [type]
+ */
+#define KHASH_MAP_INIT_STR(name, khval_t) \
+ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
+
+#endif /* __AC_KHASH_H */
diff --git a/src/samtools-0.1.18/klist.h b/src/samtools-0.1.18/klist.h
new file mode 100644
index 0000000..2f17016
--- /dev/null
+++ b/src/samtools-0.1.18/klist.h
@@ -0,0 +1,96 @@
+#ifndef _LH3_KLIST_H
+#define _LH3_KLIST_H
+
+#include <stdlib.h>
+
+#define KMEMPOOL_INIT(name, kmptype_t, kmpfree_f) \
+ typedef struct { \
+ size_t cnt, n, max; \
+ kmptype_t **buf; \
+ } kmp_##name##_t; \
+ static inline kmp_##name##_t *kmp_init_##name() { \
+ return calloc(1, sizeof(kmp_##name##_t)); \
+ } \
+ static inline void kmp_destroy_##name(kmp_##name##_t *mp) { \
+ size_t k; \
+ for (k = 0; k < mp->n; ++k) { \
+ kmpfree_f(mp->buf[k]); free(mp->buf[k]); \
+ } \
+ free(mp->buf); free(mp); \
+ } \
+ static inline kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) { \
+ ++mp->cnt; \
+ if (mp->n == 0) return calloc(1, sizeof(kmptype_t)); \
+ return mp->buf[--mp->n]; \
+ } \
+ static inline void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) { \
+ --mp->cnt; \
+ if (mp->n == mp->max) { \
+ mp->max = mp->max? mp->max<<1 : 16; \
+ mp->buf = realloc(mp->buf, sizeof(void*) * mp->max); \
+ } \
+ mp->buf[mp->n++] = p; \
+ }
+
+#define kmempool_t(name) kmp_##name##_t
+#define kmp_init(name) kmp_init_##name()
+#define kmp_destroy(name, mp) kmp_destroy_##name(mp)
+#define kmp_alloc(name, mp) kmp_alloc_##name(mp)
+#define kmp_free(name, mp, p) kmp_free_##name(mp, p)
+
+#define KLIST_INIT(name, kltype_t, kmpfree_t) \
+ struct __kl1_##name { \
+ kltype_t data; \
+ struct __kl1_##name *next; \
+ }; \
+ typedef struct __kl1_##name kl1_##name; \
+ KMEMPOOL_INIT(name, kl1_##name, kmpfree_t) \
+ typedef struct { \
+ kl1_##name *head, *tail; \
+ kmp_##name##_t *mp; \
+ size_t size; \
+ } kl_##name##_t; \
+ static inline kl_##name##_t *kl_init_##name() { \
+ kl_##name##_t *kl = calloc(1, sizeof(kl_##name##_t)); \
+ kl->mp = kmp_init(name); \
+ kl->head = kl->tail = kmp_alloc(name, kl->mp); \
+ kl->head->next = 0; \
+ return kl; \
+ } \
+ static inline void kl_destroy_##name(kl_##name##_t *kl) { \
+ kl1_##name *p; \
+ for (p = kl->head; p != kl->tail; p = p->next) \
+ kmp_free(name, kl->mp, p); \
+ kmp_free(name, kl->mp, p); \
+ kmp_destroy(name, kl->mp); \
+ free(kl); \
+ } \
+ static inline kltype_t *kl_pushp_##name(kl_##name##_t *kl) { \
+ kl1_##name *q, *p = kmp_alloc(name, kl->mp); \
+ q = kl->tail; p->next = 0; kl->tail->next = p; kl->tail = p; \
+ ++kl->size; \
+ return &q->data; \
+ } \
+ static inline int kl_shift_##name(kl_##name##_t *kl, kltype_t *d) { \
+ kl1_##name *p; \
+ if (kl->head->next == 0) return -1; \
+ --kl->size; \
+ p = kl->head; kl->head = kl->head->next; \
+ if (d) *d = p->data; \
+ kmp_free(name, kl->mp, p); \
+ return 0; \
+ }
+
+#define kliter_t(name) kl1_##name
+#define klist_t(name) kl_##name##_t
+#define kl_val(iter) ((iter)->data)
+#define kl_next(iter) ((iter)->next)
+#define kl_begin(kl) ((kl)->head)
+#define kl_end(kl) ((kl)->tail)
+
+#define kl_init(name) kl_init_##name()
+#define kl_destroy(name, kl) kl_destroy_##name(kl)
+#define kl_pushp(name, kl) kl_pushp_##name(kl)
+#define kl_shift(name, kl, d) kl_shift_##name(kl, d)
+
+#endif
diff --git a/src/samtools-0.1.18/knetfile.c b/src/samtools-0.1.18/knetfile.c
new file mode 100644
index 0000000..af09146
--- /dev/null
+++ b/src/samtools-0.1.18/knetfile.c
@@ -0,0 +1,632 @@
+/* The MIT License
+
+ Copyright (c) 2008 by Genome Research Ltd (GRL).
+ 2010 by Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* Probably I will not do socket programming in the next few years and
+ therefore I decide to heavily annotate this file, for Linux and
+ Windows as well. -ac */
+
+#include <time.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <unistd.h>
+#include <sys/types.h>
+
+#ifndef _WIN32
+#include <netdb.h>
+#include <arpa/inet.h>
+#include <sys/socket.h>
+#endif
+
+#include "knetfile.h"
+
+/* In winsock.h, the type of a socket is SOCKET, which is: "typedef
+ * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed
+ * integer -1. In knetfile.c, I use "int" for socket type
+ * throughout. This should be improved to avoid confusion.
+ *
+ * In Linux/Mac, recv() and read() do almost the same thing. You can see
+ * in the header file that netread() is simply an alias of read(). In
+ * Windows, however, they are different and using recv() is mandatory.
+ */
+
+/* This function tests if the file handler is ready for reading (or
+ * writing if is_read==0). */
+static int socket_wait(int fd, int is_read)
+{
+ fd_set fds, *fdr = 0, *fdw = 0;
+ struct timeval tv;
+ int ret;
+ tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
+ FD_ZERO(&fds);
+ FD_SET(fd, &fds);
+ if (is_read) fdr = &fds;
+ else fdw = &fds;
+ ret = select(fd+1, fdr, fdw, 0, &tv);
+#ifndef _WIN32
+ if (ret == -1) perror("select");
+#else
+ if (ret == 0)
+ fprintf(stderr, "select time-out\n");
+ else if (ret == SOCKET_ERROR)
+ fprintf(stderr, "select: %d\n", WSAGetLastError());
+#endif
+ return ret;
+}
+
+#ifndef _WIN32
+/* This function does not work with Windows due to the lack of
+ * getaddrinfo() in winsock. It is addapted from an example in "Beej's
+ * Guide to Network Programming" (http://beej.us/guide/bgnet/). */
+static int socket_connect(const char *host, const char *port)
+{
+#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
+
+ int on = 1, fd;
+ struct linger lng = { 0, 0 };
+ struct addrinfo hints, *res = 0;
+ memset(&hints, 0, sizeof(struct addrinfo));
+ hints.ai_family = AF_UNSPEC;
+ hints.ai_socktype = SOCK_STREAM;
+ /* In Unix/Mac, getaddrinfo() is the most convenient way to get
+ * server information. */
+ if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
+ if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
+ /* The following two setsockopt() are used by ftplib
+ * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they
+ * necessary. */
+ if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
+ if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
+ if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
+ freeaddrinfo(res);
+ return fd;
+}
+#else
+/* MinGW's printf has problem with "%lld" */
+char *int64tostr(char *buf, int64_t x)
+{
+ int cnt;
+ int i = 0;
+ do {
+ buf[i++] = '0' + x % 10;
+ x /= 10;
+ } while (x);
+ buf[i] = 0;
+ for (cnt = i, i = 0; i < cnt/2; ++i) {
+ int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c;
+ }
+ return buf;
+}
+
+int64_t strtoint64(const char *buf)
+{
+ int64_t x;
+ for (x = 0; *buf != '\0'; ++buf)
+ x = x * 10 + ((int64_t) *buf - 48);
+ return x;
+}
+/* In windows, the first thing is to establish the TCP connection. */
+int knet_win32_init()
+{
+ WSADATA wsaData;
+ return WSAStartup(MAKEWORD(2, 2), &wsaData);
+}
+void knet_win32_destroy()
+{
+ WSACleanup();
+}
+/* A slightly modfied version of the following function also works on
+ * Mac (and presummably Linux). However, this function is not stable on
+ * my Mac. It sometimes works fine but sometimes does not. Therefore for
+ * non-Windows OS, I do not use this one. */
+static SOCKET socket_connect(const char *host, const char *port)
+{
+#define __err_connect(func) \
+ do { \
+ fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \
+ return -1; \
+ } while (0)
+
+ int on = 1;
+ SOCKET fd;
+ struct linger lng = { 0, 0 };
+ struct sockaddr_in server;
+ struct hostent *hp = 0;
+ // open socket
+ if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket");
+ if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt");
+ if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt");
+ // get host info
+ if (isalpha(host[0])) hp = gethostbyname(host);
+ else {
+ struct in_addr addr;
+ addr.s_addr = inet_addr(host);
+ hp = gethostbyaddr((char*)&addr, 4, AF_INET);
+ }
+ if (hp == 0) __err_connect("gethost");
+ // connect
+ server.sin_addr.s_addr = *((unsigned long*)hp->h_addr);
+ server.sin_family= AF_INET;
+ server.sin_port = htons(atoi(port));
+ if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");
+ // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)
+ return fd;
+}
+#endif
+
+static off_t my_netread(int fd, void *buf, off_t len)
+{
+ off_t rest = len, curr, l = 0;
+ /* recv() and read() may not read the required length of data with
+ * one call. They have to be called repeatedly. */
+ while (rest) {
+ if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading
+ curr = netread(fd, buf + l, rest);
+ /* According to the glibc manual, section 13.2, a zero returned
+ * value indicates end-of-file (EOF), which should mean that
+ * read() will not return zero if EOF has not been met but data
+ * are not immediately available. */
+ if (curr == 0) break;
+ l += curr; rest -= curr;
+ }
+ return l;
+}
+
+/*************************
+ * FTP specific routines *
+ *************************/
+
+static int kftp_get_response(knetFile *ftp)
+{
+#ifndef _WIN32
+ unsigned char c;
+#else
+ char c;
+#endif
+ int n = 0;
+ char *p;
+ if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
+ while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
+ //fputc(c, stderr);
+ if (n >= ftp->max_response) {
+ ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
+ ftp->response = realloc(ftp->response, ftp->max_response);
+ }
+ ftp->response[n++] = c;
+ if (c == '\n') {
+ if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2])
+ && ftp->response[3] != '-') break;
+ n = 0;
+ continue;
+ }
+ }
+ if (n < 2) return -1;
+ ftp->response[n-2] = 0;
+ return strtol(ftp->response, &p, 0);
+}
+
+static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get)
+{
+ if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
+ netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
+ return is_get? kftp_get_response(ftp) : 0;
+}
+
+static int kftp_pasv_prep(knetFile *ftp)
+{
+ char *p;
+ int v[6];
+ kftp_send_cmd(ftp, "PASV\r\n", 1);
+ for (p = ftp->response; *p && *p != '('; ++p);
+ if (*p != '(') return -1;
+ ++p;
+ sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
+ memcpy(ftp->pasv_ip, v, 4 * sizeof(int));
+ ftp->pasv_port = (v[4]<<8&0xff00) + v[5];
+ return 0;
+}
+
+
+static int kftp_pasv_connect(knetFile *ftp)
+{
+ char host[80], port[10];
+ if (ftp->pasv_port == 0) {
+ fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
+ return -1;
+ }
+ sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
+ sprintf(port, "%d", ftp->pasv_port);
+ ftp->fd = socket_connect(host, port);
+ if (ftp->fd == -1) return -1;
+ return 0;
+}
+
+int kftp_connect(knetFile *ftp)
+{
+ ftp->ctrl_fd = socket_connect(ftp->host, ftp->port);
+ if (ftp->ctrl_fd == -1) return -1;
+ kftp_get_response(ftp);
+ kftp_send_cmd(ftp, "USER anonymous\r\n", 1);
+ kftp_send_cmd(ftp, "PASS kftp@\r\n", 1);
+ kftp_send_cmd(ftp, "TYPE I\r\n", 1);
+ return 0;
+}
+
+int kftp_reconnect(knetFile *ftp)
+{
+ if (ftp->ctrl_fd != -1) {
+ netclose(ftp->ctrl_fd);
+ ftp->ctrl_fd = -1;
+ }
+ netclose(ftp->fd);
+ ftp->fd = -1;
+ return kftp_connect(ftp);
+}
+
+// initialize ->type, ->host, ->retr and ->size
+knetFile *kftp_parse_url(const char *fn, const char *mode)
+{
+ knetFile *fp;
+ char *p;
+ int l;
+ if (strstr(fn, "ftp://") != fn) return 0;
+ for (p = (char*)fn + 6; *p && *p != '/'; ++p);
+ if (*p != '/') return 0;
+ l = p - fn - 6;
+ fp = calloc(1, sizeof(knetFile));
+ fp->type = KNF_TYPE_FTP;
+ fp->fd = -1;
+ /* the Linux/Mac version of socket_connect() also recognizes a port
+ * like "ftp", but the Windows version does not. */
+ fp->port = strdup("21");
+ fp->host = calloc(l + 1, 1);
+ if (strchr(mode, 'c')) fp->no_reconnect = 1;
+ strncpy(fp->host, fn + 6, l);
+ fp->retr = calloc(strlen(p) + 8, 1);
+ sprintf(fp->retr, "RETR %s\r\n", p);
+ fp->size_cmd = calloc(strlen(p) + 8, 1);
+ sprintf(fp->size_cmd, "SIZE %s\r\n", p);
+ fp->seek_offset = 0;
+ return fp;
+}
+// place ->fd at offset off
+int kftp_connect_file(knetFile *fp)
+{
+ int ret;
+ long long file_size;
+ if (fp->fd != -1) {
+ netclose(fp->fd);
+ if (fp->no_reconnect) kftp_get_response(fp);
+ }
+ kftp_pasv_prep(fp);
+ kftp_send_cmd(fp, fp->size_cmd, 1);
+#ifndef _WIN32
+ if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 )
+ {
+ fprintf(stderr,"[kftp_connect_file] %s\n", fp->response);
+ return -1;
+ }
+#else
+ const char *p = fp->response;
+ while (*p != ' ') ++p;
+ while (*p < '0' || *p > '9') ++p;
+ file_size = strtoint64(p);
+#endif
+ fp->file_size = file_size;
+ if (fp->offset>=0) {
+ char tmp[32];
+#ifndef _WIN32
+ sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
+#else
+ strcpy(tmp, "REST ");
+ int64tostr(tmp + 5, fp->offset);
+ strcat(tmp, "\r\n");
+#endif
+ kftp_send_cmd(fp, tmp, 1);
+ }
+ kftp_send_cmd(fp, fp->retr, 0);
+ kftp_pasv_connect(fp);
+ ret = kftp_get_response(fp);
+ if (ret != 150) {
+ fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
+ netclose(fp->fd);
+ fp->fd = -1;
+ return -1;
+ }
+ fp->is_ready = 1;
+ return 0;
+}
+
+
+/**************************
+ * HTTP specific routines *
+ **************************/
+
+knetFile *khttp_parse_url(const char *fn, const char *mode)
+{
+ knetFile *fp;
+ char *p, *proxy, *q;
+ int l;
+ if (strstr(fn, "http://") != fn) return 0;
+ // set ->http_host
+ for (p = (char*)fn + 7; *p && *p != '/'; ++p);
+ l = p - fn - 7;
+ fp = calloc(1, sizeof(knetFile));
+ fp->http_host = calloc(l + 1, 1);
+ strncpy(fp->http_host, fn + 7, l);
+ fp->http_host[l] = 0;
+ for (q = fp->http_host; *q && *q != ':'; ++q);
+ if (*q == ':') *q++ = 0;
+ // get http_proxy
+ proxy = getenv("http_proxy");
+ // set ->host, ->port and ->path
+ if (proxy == 0) {
+ fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name.
+ fp->port = strdup(*q? q : "80");
+ fp->path = strdup(*p? p : "/");
+ } else {
+ fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
+ for (q = fp->host; *q && *q != ':'; ++q);
+ if (*q == ':') *q++ = 0;
+ fp->port = strdup(*q? q : "80");
+ fp->path = strdup(fn);
+ }
+ fp->type = KNF_TYPE_HTTP;
+ fp->ctrl_fd = fp->fd = -1;
+ fp->seek_offset = 0;
+ return fp;
+}
+
+int khttp_connect_file(knetFile *fp)
+{
+ int ret, l = 0;
+ char *buf, *p;
+ if (fp->fd != -1) netclose(fp->fd);
+ fp->fd = socket_connect(fp->host, fp->port);
+ buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
+ l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
+ l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
+ l += sprintf(buf + l, "\r\n");
+ netwrite(fp->fd, buf, l);
+ l = 0;
+ while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
+ if (buf[l] == '\n' && l >= 3)
+ if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
+ ++l;
+ }
+ buf[l] = 0;
+ if (l < 14) { // prematured header
+ netclose(fp->fd);
+ fp->fd = -1;
+ return -1;
+ }
+ ret = strtol(buf + 8, &p, 0); // HTTP return code
+ if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file
+ off_t rest = fp->offset;
+ while (rest) {
+ off_t l = rest < 0x10000? rest : 0x10000;
+ rest -= my_netread(fp->fd, buf, l);
+ }
+ } else if (ret != 206 && ret != 200) {
+ free(buf);
+ fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret);
+ netclose(fp->fd);
+ fp->fd = -1;
+ return -1;
+ }
+ free(buf);
+ fp->is_ready = 1;
+ return 0;
+}
+
+/********************
+ * Generic routines *
+ ********************/
+
+knetFile *knet_open(const char *fn, const char *mode)
+{
+ knetFile *fp = 0;
+ if (mode[0] != 'r') {
+ fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n");
+ return 0;
+ }
+ if (strstr(fn, "ftp://") == fn) {
+ fp = kftp_parse_url(fn, mode);
+ if (fp == 0) return 0;
+ if (kftp_connect(fp) == -1) {
+ knet_close(fp);
+ return 0;
+ }
+ kftp_connect_file(fp);
+ } else if (strstr(fn, "http://") == fn) {
+ fp = khttp_parse_url(fn, mode);
+ if (fp == 0) return 0;
+ khttp_connect_file(fp);
+ } else { // local file
+#ifdef _WIN32
+ /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may
+ * be undefined on some systems, although it is defined on my
+ * Mac and the Linux I have tested on. */
+ int fd = open(fn, O_RDONLY | O_BINARY);
+#else
+ int fd = open(fn, O_RDONLY);
+#endif
+ if (fd == -1) {
+ perror("open");
+ return 0;
+ }
+ fp = (knetFile*)calloc(1, sizeof(knetFile));
+ fp->type = KNF_TYPE_LOCAL;
+ fp->fd = fd;
+ fp->ctrl_fd = -1;
+ }
+ if (fp && fp->fd == -1) {
+ knet_close(fp);
+ return 0;
+ }
+ return fp;
+}
+
+knetFile *knet_dopen(int fd, const char *mode)
+{
+ knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile));
+ fp->type = KNF_TYPE_LOCAL;
+ fp->fd = fd;
+ return fp;
+}
+
+off_t knet_read(knetFile *fp, void *buf, off_t len)
+{
+ off_t l = 0;
+ if (fp->fd == -1) return 0;
+ if (fp->type == KNF_TYPE_FTP) {
+ if (fp->is_ready == 0) {
+ if (!fp->no_reconnect) kftp_reconnect(fp);
+ kftp_connect_file(fp);
+ }
+ } else if (fp->type == KNF_TYPE_HTTP) {
+ if (fp->is_ready == 0)
+ khttp_connect_file(fp);
+ }
+ if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX
+ off_t rest = len, curr;
+ while (rest) {
+ do {
+ curr = read(fp->fd, buf + l, rest);
+ } while (curr < 0 && EINTR == errno);
+ if (curr < 0) return -1;
+ if (curr == 0) break;
+ l += curr; rest -= curr;
+ }
+ } else l = my_netread(fp->fd, buf, len);
+ fp->offset += l;
+ return l;
+}
+
+off_t knet_seek(knetFile *fp, int64_t off, int whence)
+{
+ if (whence == SEEK_SET && off == fp->offset) return 0;
+ if (fp->type == KNF_TYPE_LOCAL) {
+ /* Be aware that lseek() returns the offset after seeking,
+ * while fseek() returns zero on success. */
+ off_t offset = lseek(fp->fd, off, whence);
+ if (offset == -1) {
+ // Be silent, it is OK for knet_seek to fail when the file is streamed
+ // fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
+ return -1;
+ }
+ fp->offset = offset;
+ return 0;
+ }
+ else if (fp->type == KNF_TYPE_FTP)
+ {
+ if (whence==SEEK_CUR)
+ fp->offset += off;
+ else if (whence==SEEK_SET)
+ fp->offset = off;
+ else if ( whence==SEEK_END)
+ fp->offset = fp->file_size+off;
+ fp->is_ready = 0;
+ return 0;
+ }
+ else if (fp->type == KNF_TYPE_HTTP)
+ {
+ if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
+ fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
+ errno = ESPIPE;
+ return -1;
+ }
+ if (whence==SEEK_CUR)
+ fp->offset += off;
+ else if (whence==SEEK_SET)
+ fp->offset = off;
+ fp->is_ready = 0;
+ return 0;
+ }
+ errno = EINVAL;
+ fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
+ return -1;
+}
+
+int knet_close(knetFile *fp)
+{
+ if (fp == 0) return 0;
+ if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific
+ if (fp->fd != -1) {
+ /* On Linux/Mac, netclose() is an alias of close(), but on
+ * Windows, it is an alias of closesocket(). */
+ if (fp->type == KNF_TYPE_LOCAL) close(fp->fd);
+ else netclose(fp->fd);
+ }
+ free(fp->host); free(fp->port);
+ free(fp->response); free(fp->retr); // FTP specific
+ free(fp->path); free(fp->http_host); // HTTP specific
+ free(fp);
+ return 0;
+}
+
+#ifdef KNETFILE_MAIN
+int main(void)
+{
+ char *buf;
+ knetFile *fp;
+ int type = 4, l;
+#ifdef _WIN32
+ knet_win32_init();
+#endif
+ buf = calloc(0x100000, 1);
+ if (type == 0) {
+ fp = knet_open("knetfile.c", "r");
+ knet_seek(fp, 1000, SEEK_SET);
+ } else if (type == 1) { // NCBI FTP, large file
+ fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r");
+ knet_seek(fp, 2500000000ll, SEEK_SET);
+ l = knet_read(fp, buf, 255);
+ } else if (type == 2) {
+ fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
+ knet_seek(fp, 1000, SEEK_SET);
+ } else if (type == 3) {
+ fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
+ knet_seek(fp, 1000, SEEK_SET);
+ } else if (type == 4) {
+ fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
+ knet_read(fp, buf, 10000);
+ knet_seek(fp, 20000, SEEK_SET);
+ knet_seek(fp, 10000, SEEK_SET);
+ l = knet_read(fp, buf+10000, 10000000) + 10000;
+ }
+ if (type != 4 && type != 1) {
+ knet_read(fp, buf, 255);
+ buf[255] = 0;
+ printf("%s\n", buf);
+ } else write(fileno(stdout), buf, l);
+ knet_close(fp);
+ free(buf);
+ return 0;
+}
+#endif
diff --git a/src/samtools-0.1.18/knetfile.h b/src/samtools-0.1.18/knetfile.h
new file mode 100644
index 0000000..0a0e66f
--- /dev/null
+++ b/src/samtools-0.1.18/knetfile.h
@@ -0,0 +1,75 @@
+#ifndef KNETFILE_H
+#define KNETFILE_H
+
+#include <stdint.h>
+#include <fcntl.h>
+
+#ifndef _WIN32
+#define netread(fd, ptr, len) read(fd, ptr, len)
+#define netwrite(fd, ptr, len) write(fd, ptr, len)
+#define netclose(fd) close(fd)
+#else
+#include <winsock2.h>
+#define netread(fd, ptr, len) recv(fd, ptr, len, 0)
+#define netwrite(fd, ptr, len) send(fd, ptr, len, 0)
+#define netclose(fd) closesocket(fd)
+#endif
+
+// FIXME: currently I/O is unbuffered
+
+#define KNF_TYPE_LOCAL 1
+#define KNF_TYPE_FTP 2
+#define KNF_TYPE_HTTP 3
+
+typedef struct knetFile_s {
+ int type, fd;
+ int64_t offset;
+ char *host, *port;
+
+ // the following are for FTP only
+ int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready;
+ char *response, *retr, *size_cmd;
+ int64_t seek_offset; // for lazy seek
+ int64_t file_size;
+
+ // the following are for HTTP only
+ char *path, *http_host;
+} knetFile;
+
+#define knet_tell(fp) ((fp)->offset)
+#define knet_fileno(fp) ((fp)->fd)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#ifdef _WIN32
+ int knet_win32_init();
+ void knet_win32_destroy();
+#endif
+
+ knetFile *knet_open(const char *fn, const char *mode);
+
+ /*
+ This only works with local files.
+ */
+ knetFile *knet_dopen(int fd, const char *mode);
+
+ /*
+ If ->is_ready==0, this routine updates ->fd; otherwise, it simply
+ reads from ->fd.
+ */
+ off_t knet_read(knetFile *fp, void *buf, off_t len);
+
+ /*
+ This routine only sets ->offset and ->is_ready=0. It does not
+ communicate with the FTP server.
+ */
+ off_t knet_seek(knetFile *fp, int64_t off, int whence);
+ int knet_close(knetFile *fp);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/samtools-0.1.18/kprobaln.c b/src/samtools-0.1.18/kprobaln.c
new file mode 100644
index 0000000..894a2ae
--- /dev/null
+++ b/src/samtools-0.1.18/kprobaln.c
@@ -0,0 +1,278 @@
+/* The MIT License
+
+ Copyright (c) 2003-2006, 2008-2010, by Heng Li <lh3lh3 at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdint.h>
+#include <math.h>
+#include "kprobaln.h"
+
+/*****************************************
+ * Probabilistic banded glocal alignment *
+ *****************************************/
+
+#define EI .25
+#define EM .33333333333
+
+static float g_qual2prob[256];
+
+#define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; }
+
+kpa_par_t kpa_par_def = { 0.001, 0.1, 10 };
+kpa_par_t kpa_par_alt = { 0.0001, 0.01, 10 };
+
+/*
+ The topology of the profile HMM:
+
+ /\ /\ /\ /\
+ I[1] I[k-1] I[k] I[L]
+ ^ \ \ ^ \ ^ \ \ ^
+ | \ \ | \ | \ \ |
+ M[0] M[1] -> ... -> M[k-1] -> M[k] -> ... -> M[L] M[L+1]
+ \ \/ \/ \/ /
+ \ /\ /\ /\ /
+ -> D[k-1] -> D[k] ->
+
+ M[0] points to every {M,I}[k] and every {M,I}[k] points M[L+1].
+
+ On input, _ref is the reference sequence and _query is the query
+ sequence. Both are sequences of 0/1/2/3/4 where 4 stands for an
+ ambiguous residue. iqual is the base quality. c sets the gap open
+ probability, gap extension probability and band width.
+
+ On output, state and q are arrays of length l_query. The higher 30
+ bits give the reference position the query base is matched to and the
+ lower two bits can be 0 (an alignment match) or 1 (an
+ insertion). q[i] gives the phred scaled posterior probability of
+ state[i] being wrong.
+ */
+int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual,
+ const kpa_par_t *c, int *state, uint8_t *q)
+{
+ double **f, **b = 0, *s, m[9], sI, sM, bI, bM, pb;
+ float *qual, *_qual;
+ const uint8_t *ref, *query;
+ int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
+
+ /*** initialization ***/
+ is_backward = state && q? 1 : 0;
+ ref = _ref - 1; query = _query - 1; // change to 1-based coordinate
+ bw = l_ref > l_query? l_ref : l_query;
+ if (bw > c->bw) bw = c->bw;
+ if (bw < abs(l_ref - l_query)) bw = abs(l_ref - l_query);
+ bw2 = bw * 2 + 1;
+ // allocate the forward and backward matrices f[][] and b[][] and the scaling array s[]
+ f = calloc(l_query+1, sizeof(void*));
+ if (is_backward) b = calloc(l_query+1, sizeof(void*));
+ for (i = 0; i <= l_query; ++i) {
+ f[i] = calloc(bw2 * 3 + 6, sizeof(double)); // FIXME: this is over-allocated for very short seqs
+ if (is_backward) b[i] = calloc(bw2 * 3 + 6, sizeof(double));
+ }
+ s = calloc(l_query+2, sizeof(double)); // s[] is the scaling factor to avoid underflow
+ // initialize qual
+ _qual = calloc(l_query, sizeof(float));
+ if (g_qual2prob[0] == 0)
+ for (i = 0; i < 256; ++i)
+ g_qual2prob[i] = pow(10, -i/10.);
+ for (i = 0; i < l_query; ++i) _qual[i] = g_qual2prob[iqual? iqual[i] : 30];
+ qual = _qual - 1;
+ // initialize transition probability
+ sM = sI = 1. / (2 * l_query + 2); // the value here seems not to affect results; FIXME: need proof
+ m[0*3+0] = (1 - c->d - c->d) * (1 - sM); m[0*3+1] = m[0*3+2] = c->d * (1 - sM);
+ m[1*3+0] = (1 - c->e) * (1 - sI); m[1*3+1] = c->e * (1 - sI); m[1*3+2] = 0.;
+ m[2*3+0] = 1 - c->e; m[2*3+1] = 0.; m[2*3+2] = c->e;
+ bM = (1 - c->d) / l_ref; bI = c->d / l_ref; // (bM+bI)*l_ref==1
+ /*** forward ***/
+ // f[0]
+ set_u(k, bw, 0, 0);
+ f[0][k] = s[0] = 1.;
+ { // f[1]
+ double *fi = f[1], sum;
+ int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1, _beg, _end;
+ for (k = beg, sum = 0.; k <= end; ++k) {
+ int u;
+ double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] * EM;
+ set_u(u, bw, 1, k);
+ fi[u+0] = e * bM; fi[u+1] = EI * bI;
+ sum += fi[u] + fi[u+1];
+ }
+ // rescale
+ s[1] = sum;
+ set_u(_beg, bw, 1, beg); set_u(_end, bw, 1, end); _end += 2;
+ for (k = _beg; k <= _end; ++k) fi[k] /= sum;
+ }
+ // f[2..l_query]
+ for (i = 2; i <= l_query; ++i) {
+ double *fi = f[i], *fi1 = f[i-1], sum, qli = qual[i];
+ int beg = 1, end = l_ref, x, _beg, _end;
+ uint8_t qyi = query[i];
+ x = i - bw; beg = beg > x? beg : x; // band start
+ x = i + bw; end = end < x? end : x; // band end
+ for (k = beg, sum = 0.; k <= end; ++k) {
+ int u, v11, v01, v10;
+ double e;
+ e = (ref[k] > 3 || qyi > 3)? 1. : ref[k] == qyi? 1. - qli : qli * EM;
+ set_u(u, bw, i, k); set_u(v11, bw, i-1, k-1); set_u(v10, bw, i-1, k); set_u(v01, bw, i, k-1);
+ fi[u+0] = e * (m[0] * fi1[v11+0] + m[3] * fi1[v11+1] + m[6] * fi1[v11+2]);
+ fi[u+1] = EI * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]);
+ fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2];
+ sum += fi[u] + fi[u+1] + fi[u+2];
+// fprintf(stderr, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG
+ }
+ // rescale
+ s[i] = sum;
+ set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
+ for (k = _beg, sum = 1./sum; k <= _end; ++k) fi[k] *= sum;
+ }
+ { // f[l_query+1]
+ double sum;
+ for (k = 1, sum = 0.; k <= l_ref; ++k) {
+ int u;
+ set_u(u, bw, l_query, k);
+ if (u < 3 || u >= bw2*3+3) continue;
+ sum += f[l_query][u+0] * sM + f[l_query][u+1] * sI;
+ }
+ s[l_query+1] = sum; // the last scaling factor
+ }
+ { // compute likelihood
+ double p = 1., Pr1 = 0.;
+ for (i = 0; i <= l_query + 1; ++i) {
+ p *= s[i];
+ if (p < 1e-100) Pr1 += -4.343 * log(p), p = 1.;
+ }
+ Pr1 += -4.343 * log(p * l_ref * l_query);
+ Pr = (int)(Pr1 + .499);
+ if (!is_backward) { // skip backward and MAP
+ for (i = 0; i <= l_query; ++i) free(f[i]);
+ free(f); free(s); free(_qual);
+ return Pr;
+ }
+ }
+ /*** backward ***/
+ // b[l_query] (b[l_query+1][0]=1 and thus \tilde{b}[][]=1/s[l_query+1]; this is where s[l_query+1] comes from)
+ for (k = 1; k <= l_ref; ++k) {
+ int u;
+ double *bi = b[l_query];
+ set_u(u, bw, l_query, k);
+ if (u < 3 || u >= bw2*3+3) continue;
+ bi[u+0] = sM / s[l_query] / s[l_query+1]; bi[u+1] = sI / s[l_query] / s[l_query+1];
+ }
+ // b[l_query-1..1]
+ for (i = l_query - 1; i >= 1; --i) {
+ int beg = 1, end = l_ref, x, _beg, _end;
+ double *bi = b[i], *bi1 = b[i+1], y = (i > 1), qli1 = qual[i+1];
+ uint8_t qyi1 = query[i+1];
+ x = i - bw; beg = beg > x? beg : x;
+ x = i + bw; end = end < x? end : x;
+ for (k = end; k >= beg; --k) {
+ int u, v11, v01, v10;
+ double e;
+ set_u(u, bw, i, k); set_u(v11, bw, i+1, k+1); set_u(v10, bw, i+1, k); set_u(v01, bw, i, k+1);
+ e = (k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 * EM) * bi1[v11];
+ bi[u+0] = e * m[0] + EI * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e.
+ bi[u+1] = e * m[3] + EI * m[4] * bi1[v10+1];
+ bi[u+2] = (e * m[6] + m[8] * bi[v01+2]) * y;
+// fprintf(stderr, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG
+ }
+ // rescale
+ set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
+ for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y;
+ }
+ { // b[0]
+ int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1;
+ double sum = 0.;
+ for (k = end; k >= beg; --k) {
+ int u;
+ double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] * EM;
+ set_u(u, bw, 1, k);
+ if (u < 3 || u >= bw2*3+3) continue;
+ sum += e * b[1][u+0] * bM + EI * b[1][u+1] * bI;
+ }
+ set_u(k, bw, 0, 0);
+ pb = b[0][k] = sum / s[0]; // if everything works as is expected, pb == 1.0
+ }
+ is_diff = fabs(pb - 1.) > 1e-7? 1 : 0;
+ /*** MAP ***/
+ for (i = 1; i <= l_query; ++i) {
+ double sum = 0., *fi = f[i], *bi = b[i], max = 0.;
+ int beg = 1, end = l_ref, x, max_k = -1;
+ x = i - bw; beg = beg > x? beg : x;
+ x = i + bw; end = end < x? end : x;
+ for (k = beg; k <= end; ++k) {
+ int u;
+ double z;
+ set_u(u, bw, i, k);
+ z = fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = (k-1)<<2 | 0; sum += z;
+ z = fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = (k-1)<<2 | 1; sum += z;
+ }
+ max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0
+ if (state) state[i-1] = max_k;
+ if (q) k = (int)(-4.343 * log(1. - max) + .499), q[i-1] = k > 100? 99 : k;
+#ifdef _MAIN
+ fprintf(stderr, "(%.10lg,%.10lg) (%d,%d:%c,%c:%d) %lg\n", pb, sum, i-1, max_k>>2,
+ "ACGT"[query[i]], "ACGT"[ref[(max_k>>2)+1]], max_k&3, max); // DEBUG
+#endif
+ }
+ /*** free ***/
+ for (i = 0; i <= l_query; ++i) {
+ free(f[i]); free(b[i]);
+ }
+ free(f); free(b); free(s); free(_qual);
+ return Pr;
+}
+
+#ifdef _MAIN
+#include <unistd.h>
+int main(int argc, char *argv[])
+{
+ uint8_t conv[256], *iqual, *ref, *query;
+ int c, l_ref, l_query, i, q = 30, b = 10, P;
+ while ((c = getopt(argc, argv, "b:q:")) >= 0) {
+ switch (c) {
+ case 'b': b = atoi(optarg); break;
+ case 'q': q = atoi(optarg); break;
+ }
+ }
+ if (optind + 2 > argc) {
+ fprintf(stderr, "Usage: %s [-q %d] [-b %d] <ref> <query>\n", argv[0], q, b); // example: acttc attc
+ return 1;
+ }
+ memset(conv, 4, 256);
+ conv['a'] = conv['A'] = 0; conv['c'] = conv['C'] = 1;
+ conv['g'] = conv['G'] = 2; conv['t'] = conv['T'] = 3;
+ ref = (uint8_t*)argv[optind]; query = (uint8_t*)argv[optind+1];
+ l_ref = strlen((char*)ref); l_query = strlen((char*)query);
+ for (i = 0; i < l_ref; ++i) ref[i] = conv[ref[i]];
+ for (i = 0; i < l_query; ++i) query[i] = conv[query[i]];
+ iqual = malloc(l_query);
+ memset(iqual, q, l_query);
+ kpa_par_def.bw = b;
+ P = kpa_glocal(ref, l_ref, query, l_query, iqual, &kpa_par_alt, 0, 0);
+ fprintf(stderr, "%d\n", P);
+ free(iqual);
+ return 0;
+}
+#endif
diff --git a/src/samtools-0.1.18/kprobaln.h b/src/samtools-0.1.18/kprobaln.h
new file mode 100644
index 0000000..0357dcc
--- /dev/null
+++ b/src/samtools-0.1.18/kprobaln.h
@@ -0,0 +1,49 @@
+/* The MIT License
+
+ Copyright (c) 2003-2006, 2008, 2009 by Heng Li <lh3 at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#ifndef LH3_KPROBALN_H_
+#define LH3_KPROBALN_H_
+
+#include <stdint.h>
+
+typedef struct {
+ float d, e;
+ int bw;
+} kpa_par_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual,
+ const kpa_par_t *c, int *state, uint8_t *q);
+
+#ifdef __cplusplus
+}
+#endif
+
+extern kpa_par_t kpa_par_def, kpa_par_alt;
+
+#endif
diff --git a/src/samtools-0.1.18/kseq.h b/src/samtools-0.1.18/kseq.h
new file mode 100644
index 0000000..0bbc7dc
--- /dev/null
+++ b/src/samtools-0.1.18/kseq.h
@@ -0,0 +1,224 @@
+/* The MIT License
+
+ Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* Last Modified: 18AUG2011 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB 1 // isspace() && !' '
+#define KS_SEP_MAX 1
+
+#define __KS_TYPE(type_t) \
+ typedef struct __kstream_t { \
+ unsigned char *buf; \
+ int begin, end, is_eof; \
+ type_t f; \
+ } kstream_t;
+
+#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
+#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
+
+#define __KS_BASIC(type_t, __bufsize) \
+ static inline kstream_t *ks_init(type_t f) \
+ { \
+ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
+ ks->f = f; \
+ ks->buf = malloc(__bufsize); \
+ return ks; \
+ } \
+ static inline void ks_destroy(kstream_t *ks) \
+ { \
+ if (ks) { \
+ free(ks->buf); \
+ free(ks); \
+ } \
+ }
+
+#define __KS_GETC(__read, __bufsize) \
+ static inline int ks_getc(kstream_t *ks) \
+ { \
+ if (ks->is_eof && ks->begin >= ks->end) return -1; \
+ if (ks->begin >= ks->end) { \
+ ks->begin = 0; \
+ ks->end = __read(ks->f, ks->buf, __bufsize); \
+ if (ks->end < __bufsize) ks->is_eof = 1; \
+ if (ks->end == 0) return -1; \
+ } \
+ return (int)ks->buf[ks->begin++]; \
+ }
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+ size_t l, m;
+ char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(__read, __bufsize) \
+ static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
+ { \
+ if (dret) *dret = 0; \
+ str->l = append? str->l : 0; \
+ if (ks->begin >= ks->end && ks->is_eof) return -1; \
+ for (;;) { \
+ int i; \
+ if (ks->begin >= ks->end) { \
+ if (!ks->is_eof) { \
+ ks->begin = 0; \
+ ks->end = __read(ks->f, ks->buf, __bufsize); \
+ if (ks->end < __bufsize) ks->is_eof = 1; \
+ if (ks->end == 0) break; \
+ } else break; \
+ } \
+ if (delimiter > KS_SEP_MAX) { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (ks->buf[i] == delimiter) break; \
+ } else if (delimiter == KS_SEP_SPACE) { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (isspace(ks->buf[i])) break; \
+ } else if (delimiter == KS_SEP_TAB) { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
+ } else i = 0; /* never come to here! */ \
+ if (str->m - str->l < i - ks->begin + 1) { \
+ str->m = str->l + (i - ks->begin) + 1; \
+ kroundup32(str->m); \
+ str->s = (char*)realloc(str->s, str->m); \
+ } \
+ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
+ str->l = str->l + (i - ks->begin); \
+ ks->begin = i + 1; \
+ if (i < ks->end) { \
+ if (dret) *dret = ks->buf[i]; \
+ break; \
+ } \
+ } \
+ if (str->s == 0) { \
+ str->m = 1; \
+ str->s = (char*)calloc(1, 1); \
+ } \
+ str->s[str->l] = '\0'; \
+ return str->l; \
+ } \
+ static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+ { return ks_getuntil2(ks, delimiter, str, dret, 0); }
+
+#define KSTREAM_INIT(type_t, __read, __bufsize) \
+ __KS_TYPE(type_t) \
+ __KS_BASIC(type_t, __bufsize) \
+ __KS_GETC(__read, __bufsize) \
+ __KS_GETUNTIL(__read, __bufsize)
+
+#define __KSEQ_BASIC(type_t) \
+ static inline kseq_t *kseq_init(type_t fd) \
+ { \
+ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
+ s->f = ks_init(fd); \
+ return s; \
+ } \
+ static inline void kseq_rewind(kseq_t *ks) \
+ { \
+ ks->last_char = 0; \
+ ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
+ } \
+ static inline void kseq_destroy(kseq_t *ks) \
+ { \
+ if (!ks) return; \
+ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
+ ks_destroy(ks->f); \
+ free(ks); \
+ }
+
+/* Return value:
+ >=0 length of the sequence (normal)
+ -1 end-of-file
+ -2 truncated quality string
+ */
+#define __KSEQ_READ \
+ static int kseq_read(kseq_t *seq) \
+ { \
+ int c; \
+ kstream_t *ks = seq->f; \
+ if (seq->last_char == 0) { /* then jump to the next header line */ \
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
+ if (c == -1) return -1; /* end of file */ \
+ seq->last_char = c; \
+ } /* else: the first header char has been read in the previous call */ \
+ seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
+ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
+ if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); /* read FASTA/Q comment */ \
+ if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
+ seq->seq.m = 256; \
+ seq->seq.s = (char*)malloc(seq->seq.m); \
+ } \
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+ seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
+ ks_getuntil2(ks, '\n', &seq->seq, 0, 1); /* read the rest of the line */ \
+ } \
+ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
+ if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
+ seq->seq.m = seq->seq.l + 2; \
+ kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
+ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+ } \
+ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
+ if (c != '+') return seq->seq.l; /* FASTA */ \
+ if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \
+ seq->qual.m = seq->seq.m; \
+ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
+ } \
+ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+ if (c == -1) return -2; /* error: no quality string */ \
+ while (ks_getuntil2(ks, '\n', &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
+ seq->last_char = 0; /* we have not come to the next header line */ \
+ if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
+ return seq->seq.l; \
+ }
+
+#define __KSEQ_TYPE(type_t) \
+ typedef struct { \
+ kstring_t name, comment, seq, qual; \
+ int last_char; \
+ kstream_t *f; \
+ } kseq_t;
+
+#define KSEQ_INIT(type_t, __read) \
+ KSTREAM_INIT(type_t, __read, 16384) \
+ __KSEQ_TYPE(type_t) \
+ __KSEQ_BASIC(type_t) \
+ __KSEQ_READ
+
+#endif
diff --git a/src/samtools-0.1.18/ksort.h b/src/samtools-0.1.18/ksort.h
new file mode 100644
index 0000000..fa850ab
--- /dev/null
+++ b/src/samtools-0.1.18/ksort.h
@@ -0,0 +1,281 @@
+/* The MIT License
+
+ Copyright (c) 2008 Genome Research Ltd (GRL).
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3 at sanger.ac.uk> */
+
+/*
+ 2008-11-16 (0.1.4):
+
+ * Fixed a bug in introsort() that happens in rare cases.
+
+ 2008-11-05 (0.1.3):
+
+ * Fixed a bug in introsort() for complex comparisons.
+
+ * Fixed a bug in mergesort(). The previous version is not stable.
+
+ 2008-09-15 (0.1.2):
+
+ * Accelerated introsort. On my Mac (not on another Linux machine),
+ my implementation is as fast as std::sort on random input.
+
+ * Added combsort and in introsort, switch to combsort if the
+ recursion is too deep.
+
+ 2008-09-13 (0.1.1):
+
+ * Added k-small algorithm
+
+ 2008-09-05 (0.1.0):
+
+ * Initial version
+
+*/
+
+#ifndef AC_KSORT_H
+#define AC_KSORT_H
+
+#include <stdlib.h>
+#include <string.h>
+
+typedef struct {
+ void *left, *right;
+ int depth;
+} ks_isort_stack_t;
+
+#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
+
+#define KSORT_INIT(name, type_t, __sort_lt) \
+ void ks_mergesort_##name(size_t n, type_t array[], type_t temp[]) \
+ { \
+ type_t *a2[2], *a, *b; \
+ int curr, shift; \
+ \
+ a2[0] = array; \
+ a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n); \
+ for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) { \
+ a = a2[curr]; b = a2[1-curr]; \
+ if (shift == 0) { \
+ type_t *p = b, *i, *eb = a + n; \
+ for (i = a; i < eb; i += 2) { \
+ if (i == eb - 1) *p++ = *i; \
+ else { \
+ if (__sort_lt(*(i+1), *i)) { \
+ *p++ = *(i+1); *p++ = *i; \
+ } else { \
+ *p++ = *i; *p++ = *(i+1); \
+ } \
+ } \
+ } \
+ } else { \
+ size_t i, step = 1ul<<shift; \
+ for (i = 0; i < n; i += step<<1) { \
+ type_t *p, *j, *k, *ea, *eb; \
+ if (n < i + step) { \
+ ea = a + n; eb = a; \
+ } else { \
+ ea = a + i + step; \
+ eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
+ } \
+ j = a + i; k = a + i + step; p = b + i; \
+ while (j < ea && k < eb) { \
+ if (__sort_lt(*k, *j)) *p++ = *k++; \
+ else *p++ = *j++; \
+ } \
+ while (j < ea) *p++ = *j++; \
+ while (k < eb) *p++ = *k++; \
+ } \
+ } \
+ curr = 1 - curr; \
+ } \
+ if (curr == 1) { \
+ type_t *p = a2[0], *i = a2[1], *eb = array + n; \
+ for (; p < eb; ++i) *p++ = *i; \
+ } \
+ if (temp == 0) free(a2[1]); \
+ } \
+ void ks_heapadjust_##name(size_t i, size_t n, type_t l[]) \
+ { \
+ size_t k = i; \
+ type_t tmp = l[i]; \
+ while ((k = (k << 1) + 1) < n) { \
+ if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k; \
+ if (__sort_lt(l[k], tmp)) break; \
+ l[i] = l[k]; i = k; \
+ } \
+ l[i] = tmp; \
+ } \
+ void ks_heapmake_##name(size_t lsize, type_t l[]) \
+ { \
+ size_t i; \
+ for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i) \
+ ks_heapadjust_##name(i, lsize, l); \
+ } \
+ void ks_heapsort_##name(size_t lsize, type_t l[]) \
+ { \
+ size_t i; \
+ for (i = lsize - 1; i > 0; --i) { \
+ type_t tmp; \
+ tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
+ } \
+ } \
+ inline void __ks_insertsort_##name(type_t *s, type_t *t) \
+ { \
+ type_t *i, *j, swap_tmp; \
+ for (i = s + 1; i < t; ++i) \
+ for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \
+ swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp; \
+ } \
+ } \
+ void ks_combsort_##name(size_t n, type_t a[]) \
+ { \
+ const double shrink_factor = 1.2473309501039786540366528676643; \
+ int do_swap; \
+ size_t gap = n; \
+ type_t tmp, *i, *j; \
+ do { \
+ if (gap > 2) { \
+ gap = (size_t)(gap / shrink_factor); \
+ if (gap == 9 || gap == 10) gap = 11; \
+ } \
+ do_swap = 0; \
+ for (i = a; i < a + n - gap; ++i) { \
+ j = i + gap; \
+ if (__sort_lt(*j, *i)) { \
+ tmp = *i; *i = *j; *j = tmp; \
+ do_swap = 1; \
+ } \
+ } \
+ } while (do_swap || gap > 2); \
+ if (gap != 1) __ks_insertsort_##name(a, a + n); \
+ } \
+ void ks_introsort_##name(size_t n, type_t a[]) \
+ { \
+ int d; \
+ ks_isort_stack_t *top, *stack; \
+ type_t rp, swap_tmp; \
+ type_t *s, *t, *i, *j, *k; \
+ \
+ if (n < 1) return; \
+ else if (n == 2) { \
+ if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
+ return; \
+ } \
+ for (d = 2; 1ul<<d < n; ++d); \
+ stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
+ top = stack; s = a; t = a + (n-1); d <<= 1; \
+ while (1) { \
+ if (s < t) { \
+ if (--d == 0) { \
+ ks_combsort_##name(t - s + 1, s); \
+ t = s; \
+ continue; \
+ } \
+ i = s; j = t; k = i + ((j-i)>>1) + 1; \
+ if (__sort_lt(*k, *i)) { \
+ if (__sort_lt(*k, *j)) k = j; \
+ } else k = __sort_lt(*j, *i)? i : j; \
+ rp = *k; \
+ if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; } \
+ for (;;) { \
+ do ++i; while (__sort_lt(*i, rp)); \
+ do --j; while (i <= j && __sort_lt(rp, *j)); \
+ if (j <= i) break; \
+ swap_tmp = *i; *i = *j; *j = swap_tmp; \
+ } \
+ swap_tmp = *i; *i = *t; *t = swap_tmp; \
+ if (i-s > t-i) { \
+ if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
+ s = t-i > 16? i+1 : t; \
+ } else { \
+ if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
+ t = i-s > 16? i-1 : s; \
+ } \
+ } else { \
+ if (top == stack) { \
+ free(stack); \
+ __ks_insertsort_##name(a, a+n); \
+ return; \
+ } else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
+ } \
+ } \
+ } \
+ /* This function is adapted from: http://ndevilla.free.fr/median/ */ \
+ /* 0 <= kk < n */ \
+ type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk) \
+ { \
+ type_t *low, *high, *k, *ll, *hh, *mid; \
+ low = arr; high = arr + n - 1; k = arr + kk; \
+ for (;;) { \
+ if (high <= low) return *k; \
+ if (high == low + 1) { \
+ if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
+ return *k; \
+ } \
+ mid = low + (high - low) / 2; \
+ if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
+ if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
+ if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
+ KSORT_SWAP(type_t, *mid, *(low+1)); \
+ ll = low + 1; hh = high; \
+ for (;;) { \
+ do ++ll; while (__sort_lt(*ll, *low)); \
+ do --hh; while (__sort_lt(*low, *hh)); \
+ if (hh < ll) break; \
+ KSORT_SWAP(type_t, *ll, *hh); \
+ } \
+ KSORT_SWAP(type_t, *low, *hh); \
+ if (hh <= k) low = ll; \
+ if (hh >= k) high = hh - 1; \
+ } \
+ } \
+ void ks_shuffle_##name(size_t n, type_t a[]) \
+ { \
+ int i, j; \
+ for (i = n; i > 1; --i) { \
+ type_t tmp; \
+ j = (int)(drand48() * i); \
+ tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; \
+ } \
+ }
+
+#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
+#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
+#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
+#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
+#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
+#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
+#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
+#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)
+
+#define ks_lt_generic(a, b) ((a) < (b))
+#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)
+
+typedef const char *ksstr_t;
+
+#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
+#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)
+
+#endif
diff --git a/src/samtools-0.1.18/kstring.c b/src/samtools-0.1.18/kstring.c
new file mode 100644
index 0000000..b2a0dab
--- /dev/null
+++ b/src/samtools-0.1.18/kstring.c
@@ -0,0 +1,212 @@
+#include <stdarg.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdint.h>
+#include "kstring.h"
+
+int ksprintf(kstring_t *s, const char *fmt, ...)
+{
+ va_list ap;
+ int l;
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'.
+ va_end(ap);
+ if (l + 1 > s->m - s->l) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+ }
+ va_end(ap);
+ s->l += l;
+ return l;
+}
+
+char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux)
+{
+ const char *p, *start;
+ if (sep) { // set up the table
+ if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished
+ aux->finished = 0;
+ if (sep[1]) {
+ aux->sep = -1;
+ aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
+ for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f);
+ } else aux->sep = sep[0];
+ }
+ if (aux->finished) return 0;
+ else if (str) aux->p = str - 1, aux->finished = 0;
+ if (aux->sep < 0) {
+ for (p = start = aux->p + 1; *p; ++p)
+ if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;
+ } else {
+ for (p = start = aux->p + 1; *p; ++p)
+ if (*p == aux->sep) break;
+ }
+ aux->p = p; // end of token
+ if (*p == 0) aux->finished = 1; // no more tokens
+ return (char*)start;
+}
+
+// s MUST BE a null terminated string; l = strlen(s)
+int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
+{
+ int i, n, max, last_char, last_start, *offsets, l;
+ n = 0; max = *_max; offsets = *_offsets;
+ l = strlen(s);
+
+#define __ksplit_aux do { \
+ if (_offsets) { \
+ s[i] = 0; \
+ if (n == max) { \
+ max = max? max<<1 : 2; \
+ offsets = (int*)realloc(offsets, sizeof(int) * max); \
+ } \
+ offsets[n++] = last_start; \
+ } else ++n; \
+ } while (0)
+
+ for (i = 0, last_char = last_start = 0; i <= l; ++i) {
+ if (delimiter == 0) {
+ if (isspace(s[i]) || s[i] == 0) {
+ if (isgraph(last_char)) __ksplit_aux; // the end of a field
+ } else {
+ if (isspace(last_char) || last_char == 0) last_start = i;
+ }
+ } else {
+ if (s[i] == delimiter || s[i] == 0) {
+ if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field
+ } else {
+ if (last_char == delimiter || last_char == 0) last_start = i;
+ }
+ }
+ last_char = s[i];
+ }
+ *_max = max; *_offsets = offsets;
+ return n;
+}
+
+/**********************
+ * Boyer-Moore search *
+ **********************/
+
+typedef unsigned char ubyte_t;
+
+// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
+static int *ksBM_prep(const ubyte_t *pat, int m)
+{
+ int i, *suff, *prep, *bmGs, *bmBc;
+ prep = calloc(m + 256, sizeof(int));
+ bmGs = prep; bmBc = prep + m;
+ { // preBmBc()
+ for (i = 0; i < 256; ++i) bmBc[i] = m;
+ for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
+ }
+ suff = calloc(m, sizeof(int));
+ { // suffixes()
+ int f = 0, g;
+ suff[m - 1] = m;
+ g = m - 1;
+ for (i = m - 2; i >= 0; --i) {
+ if (i > g && suff[i + m - 1 - f] < i - g)
+ suff[i] = suff[i + m - 1 - f];
+ else {
+ if (i < g) g = i;
+ f = i;
+ while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g;
+ suff[i] = f - g;
+ }
+ }
+ }
+ { // preBmGs()
+ int j = 0;
+ for (i = 0; i < m; ++i) bmGs[i] = m;
+ for (i = m - 1; i >= 0; --i)
+ if (suff[i] == i + 1)
+ for (; j < m - 1 - i; ++j)
+ if (bmGs[j] == m)
+ bmGs[j] = m - 1 - i;
+ for (i = 0; i <= m - 2; ++i)
+ bmGs[m - 1 - suff[i]] = m - 1 - i;
+ }
+ free(suff);
+ return prep;
+}
+
+void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep)
+{
+ int i, j, *prep = 0, *bmGs, *bmBc;
+ const ubyte_t *str, *pat;
+ str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat;
+ prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep;
+ if (_prep && *_prep == 0) *_prep = prep;
+ bmGs = prep; bmBc = prep + m;
+ j = 0;
+ while (j <= n - m) {
+ for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i);
+ if (i >= 0) {
+ int max = bmBc[str[i+j]] - m + 1 + i;
+ if (max < bmGs[i]) max = bmGs[i];
+ j += max;
+ } else return (void*)(str + j);
+ }
+ if (_prep == 0) free(prep);
+ return 0;
+}
+
+char *kstrstr(const char *str, const char *pat, int **_prep)
+{
+ return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
+}
+
+char *kstrnstr(const char *str, const char *pat, int n, int **_prep)
+{
+ return (char*)kmemmem(str, n, pat, strlen(pat), _prep);
+}
+
+/***********************
+ * The main() function *
+ ***********************/
+
+#ifdef KSTRING_MAIN
+#include <stdio.h>
+int main()
+{
+ kstring_t *s;
+ int *fields, n, i;
+ ks_tokaux_t aux;
+ char *p;
+ s = (kstring_t*)calloc(1, sizeof(kstring_t));
+ // test ksprintf()
+ ksprintf(s, " abcdefg: %d ", 100);
+ printf("'%s'\n", s->s);
+ // test ksplit()
+ fields = ksplit(s, 0, &n);
+ for (i = 0; i < n; ++i)
+ printf("field[%d] = '%s'\n", i, s->s + fields[i]);
+ // test kstrtok()
+ s->l = 0;
+ for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) {
+ kputsn(p, aux.p - p, s);
+ kputc('\n', s);
+ }
+ printf("%s", s->s);
+ // free
+ free(s->s); free(s); free(fields);
+
+ {
+ static char *str = "abcdefgcdgcagtcakcdcd";
+ static char *pat = "cd";
+ char *ret, *s = str;
+ int *prep = 0;
+ while ((ret = kstrstr(s, pat, &prep)) != 0) {
+ printf("match: %s\n", ret);
+ s = ret + prep[0];
+ }
+ free(prep);
+ }
+ return 0;
+}
+#endif
diff --git a/src/samtools-0.1.18/kstring.h b/src/samtools-0.1.18/kstring.h
new file mode 100644
index 0000000..ec5775b
--- /dev/null
+++ b/src/samtools-0.1.18/kstring.h
@@ -0,0 +1,117 @@
+#ifndef KSTRING_H
+#define KSTRING_H
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdint.h>
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+ size_t l, m;
+ char *s;
+} kstring_t;
+#endif
+
+typedef struct {
+ uint64_t tab[4];
+ int sep, finished;
+ const char *p; // end of the current token
+} ks_tokaux_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ int ksprintf(kstring_t *s, const char *fmt, ...);
+ int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
+ char *kstrstr(const char *str, const char *pat, int **_prep);
+ char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
+ void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);
+
+ /* kstrtok() is similar to strtok_r() except that str is not
+ * modified and both str and sep can be NULL. For efficiency, it is
+ * actually recommended to set both to NULL in the subsequent calls
+ * if sep is not changed. */
+ char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline int kputsn(const char *p, int l, kstring_t *s)
+{
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ memcpy(s->s + s->l, p, l);
+ s->l += l;
+ s->s[s->l] = 0;
+ return l;
+}
+
+static inline int kputs(const char *p, kstring_t *s)
+{
+ return kputsn(p, strlen(p), s);
+}
+
+static inline int kputc(int c, kstring_t *s)
+{
+ if (s->l + 1 >= s->m) {
+ s->m = s->l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ s->s[s->l++] = c;
+ s->s[s->l] = 0;
+ return c;
+}
+
+static inline int kputw(int c, kstring_t *s)
+{
+ char buf[16];
+ int l, x;
+ if (c == 0) return kputc('0', s);
+ for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+ if (c < 0) buf[l++] = '-';
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
+ s->s[s->l] = 0;
+ return 0;
+}
+
+static inline int kputuw(unsigned c, kstring_t *s)
+{
+ char buf[16];
+ int l, i;
+ unsigned x;
+ if (c == 0) return kputc('0', s);
+ for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
+ s->s[s->l] = 0;
+ return 0;
+}
+
+static inline int *ksplit(kstring_t *s, int delimiter, int *n)
+{
+ int max = 0, *offsets = 0;
+ *n = ksplit_core(s->s, delimiter, &max, &offsets);
+ return offsets;
+}
+
+#endif
diff --git a/src/samtools-0.1.18/phase.c b/src/samtools-0.1.18/phase.c
new file mode 100644
index 0000000..ef4eff9
--- /dev/null
+++ b/src/samtools-0.1.18/phase.c
@@ -0,0 +1,687 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+#include <math.h>
+#include <zlib.h>
+#include "bam.h"
+#include "errmod.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define MAX_VARS 256
+#define FLIP_PENALTY 2
+#define FLIP_THRES 4
+#define MASK_THRES 3
+
+#define FLAG_FIX_CHIMERA 0x1
+#define FLAG_LIST_EXCL 0x4
+#define FLAG_DROP_AMBI 0x8
+
+typedef struct {
+ // configurations, initialized in the main function
+ int flag, k, min_baseQ, min_varLOD, max_depth;
+ // other global variables
+ int vpos_shift;
+ bamFile fp;
+ char *pre;
+ bamFile out[3];
+ // alignment queue
+ int n, m;
+ bam1_t **b;
+} phaseg_t;
+
+typedef struct {
+ int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation!
+ int vpos, beg, end;
+ uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1;
+ uint32_t in:16, out:16; // in-phase and out-phase
+} frag_t, *frag_p;
+
+#define rseq_lt(a,b) ((a)->vpos < (b)->vpos)
+
+#include "khash.h"
+KHASH_SET_INIT_INT64(set64)
+KHASH_MAP_INIT_INT64(64, frag_t)
+
+typedef khash_t(64) nseq_t;
+
+#include "ksort.h"
+KSORT_INIT(rseq, frag_p, rseq_lt)
+
+static char nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+
+static inline uint64_t X31_hash_string(const char *s)
+{
+ uint64_t h = *s;
+ if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
+ return h;
+}
+
+static void count1(int l, const uint8_t *seq, int *cnt)
+{
+ int i, j, n_ambi;
+ uint32_t z, x;
+ if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous
+ for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases
+ if (seq[i] == 0) ++n_ambi;
+ if (l - n_ambi <= 1) return; // only one SNP
+ for (x = 0; x < 1u<<n_ambi; ++x) { // count
+ for (i = j = 0, z = 0; i < l; ++i) {
+ int c;
+ if (seq[i]) c = seq[i] - 1;
+ else {
+ c = x>>j&1;
+ ++j;
+ }
+ z = z<<1 | c;
+ }
+ ++cnt[z];
+ }
+}
+
+static int **count_all(int l, int vpos, nseq_t *hash)
+{
+ khint_t k;
+ int i, j, **cnt;
+ uint8_t *seq;
+ seq = calloc(l, 1);
+ cnt = calloc(vpos, sizeof(void*));
+ for (i = 0; i < vpos; ++i) cnt[i] = calloc(1<<l, sizeof(int));
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ frag_t *f = &kh_val(hash, k);
+ if (f->vpos >= vpos || f->single) continue; // out of region; or singleton
+ if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right
+ f->single = 1;
+ continue;
+ }
+ for (j = 1; j < f->vlen; ++j) {
+ for (i = 0; i < l; ++i)
+ seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)];
+ count1(l, seq, cnt[f->vpos + j]);
+ }
+ }
+ }
+ free(seq);
+ return cnt;
+}
+
+// phasing
+static int8_t *dynaprog(int l, int vpos, int **w)
+{
+ int *f[2], *curr, *prev, max, i;
+ int8_t **b, *h = 0;
+ uint32_t x, z = 1u<<(l-1), mask = (1u<<l) - 1;
+ f[0] = calloc(z, sizeof(int));
+ f[1] = calloc(z, sizeof(int));
+ b = calloc(vpos, sizeof(void*));
+ prev = f[0]; curr = f[1];
+ // fill the backtrack matrix
+ for (i = 0; i < vpos; ++i) {
+ int *wi = w[i], *tmp;
+ int8_t *bi;
+ bi = b[i] = calloc(z, 1);
+ /* In the following, x is the current state, which is the
+ * lexicographically smaller local haplotype. xc is the complement of
+ * x, or the larger local haplotype; y0 and y1 are the two predecessors
+ * of x. */
+ for (x = 0; x < z; ++x) { // x0 is the smaller
+ uint32_t y0, y1, xc;
+ int c0, c1;
+ xc = ~x&mask; y0 = x>>1; y1 = xc>>1;
+ c0 = prev[y0] + wi[x] + wi[xc];
+ c1 = prev[y1] + wi[x] + wi[xc];
+ if (c0 > c1) bi[x] = 0, curr[x] = c0;
+ else bi[x] = 1, curr[x] = c1;
+ }
+ tmp = prev; prev = curr; curr = tmp; // swap
+ }
+ { // backtrack
+ uint32_t max_x = 0;
+ int which = 0;
+ h = calloc(vpos, 1);
+ for (x = 0, max = 0, max_x = 0; x < z; ++x)
+ if (prev[x] > max) max = prev[x], max_x = x;
+ for (i = vpos - 1, x = max_x; i >= 0; --i) {
+ h[i] = which? (~x&1) : (x&1);
+ which = b[i][x]? !which : which;
+ x = b[i][x]? (~x&mask)>>1 : x>>1;
+ }
+ }
+ // free
+ for (i = 0; i < vpos; ++i) free(b[i]);
+ free(f[0]); free(f[1]); free(b);
+ return h;
+}
+
+// phase each fragment
+static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip)
+{
+ khint_t k;
+ uint64_t *pcnt;
+ uint32_t *left, *rght, max;
+ left = rght = 0; max = 0;
+ pcnt = calloc(vpos, 8);
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ int i, c[2];
+ frag_t *f = &kh_val(hash, k);
+ if (f->vpos >= vpos) continue;
+ // get the phase
+ c[0] = c[1] = 0;
+ for (i = 0; i < f->vlen; ++i) {
+ if (f->seq[i] == 0) continue;
+ ++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1];
+ }
+ f->phase = c[0] > c[1]? 0 : 1;
+ f->in = c[f->phase]; f->out = c[1 - f->phase];
+ f->phased = f->in == f->out? 0 : 1;
+ f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0;
+ // fix chimera
+ f->flip = 0;
+ if (flip && c[0] >= 3 && c[1] >= 3) {
+ int sum[2], m, mi, md;
+ if (f->vlen > max) { // enlarge the array
+ max = f->vlen;
+ kroundup32(max);
+ left = realloc(left, max * 4);
+ rght = realloc(rght, max * 4);
+ }
+ for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts
+ if (f->seq[i]) {
+ int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+ ++sum[c == path[f->vpos + i]? 0 : 1];
+ }
+ left[i] = sum[1]<<16 | sum[0];
+ }
+ for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts
+ if (f->seq[i]) {
+ int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+ ++sum[c == path[f->vpos + i]? 0 : 1];
+ }
+ rght[i] = sum[1]<<16 | sum[0];
+ }
+ // find the best flip point
+ for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) {
+ int a[2];
+ a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY;
+ a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY;
+ if (a[0] > a[1]) {
+ if (a[0] > m) m = a[0], md = 0, mi = i;
+ } else {
+ if (a[1] > m) m = a[1], md = 1, mi = i;
+ }
+ }
+ if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip
+ f->flip = 1;
+ if (md == 0) { // flip the tail
+ for (i = mi + 1; i < f->vlen; ++i)
+ if (f->seq[i] == 1) f->seq[i] = 2;
+ else if (f->seq[i] == 2) f->seq[i] = 1;
+ } else { // flip the head
+ for (i = 0; i <= mi; ++i)
+ if (f->seq[i] == 1) f->seq[i] = 2;
+ else if (f->seq[i] == 2) f->seq[i] = 1;
+ }
+ }
+ }
+ // update pcnt[]
+ if (!f->single) {
+ for (i = 0; i < f->vlen; ++i) {
+ int c;
+ if (f->seq[i] == 0) continue;
+ c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+ if (c == path[f->vpos + i]) {
+ if (f->phase == 0) ++pcnt[f->vpos + i];
+ else pcnt[f->vpos + i] += 1ull<<32;
+ } else {
+ if (f->phase == 0) pcnt[f->vpos + i] += 1<<16;
+ else pcnt[f->vpos + i] += 1ull<<48;
+ }
+ }
+ }
+ }
+ }
+ free(left); free(rght);
+ return pcnt;
+}
+
+static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n)
+{
+ int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0;
+ uint64_t *list = 0;
+ for (i = 0; i < vpos; ++i) {
+ uint64_t x = pcnt[i];
+ int c[4], pre = score, s;
+ c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff;
+ s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1);
+ if (c[3] > c[2]) s += c[3] - c[2];
+ if (c[1] > c[0]) s += c[1] - c[0];
+ score += s;
+ if (score < 0) score = 0;
+ if (pre == 0 && score > 0) beg = i; // change from zero to non-zero
+ if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) {
+ if (n == m) {
+ m = m? m<<1 : 4;
+ list = realloc(list, m * 8);
+ }
+ list[n++] = (uint64_t)beg<<32 | max_i;
+ i = max_i; // reset i to max_i
+ score = 0;
+ } else if (score > max) max = score, max_i = i;
+ if (score == 0) max = 0;
+ }
+ *_n = n;
+ return list;
+}
+
+// trim heading and tailing ambiguous bases; mark deleted and remove sequence
+static int clean_seqs(int vpos, nseq_t *hash)
+{
+ khint_t k;
+ int ret = 0;
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ frag_t *f = &kh_val(hash, k);
+ int beg, end, i;
+ if (f->vpos >= vpos) {
+ ret = 1;
+ continue;
+ }
+ for (i = 0; i < f->vlen; ++i)
+ if (f->seq[i] != 0) break;
+ beg = i;
+ for (i = f->vlen - 1; i >= 0; --i)
+ if (f->seq[i] != 0) break;
+ end = i + 1;
+ if (end - beg <= 0) kh_del(64, hash, k);
+ else {
+ if (beg != 0) memmove(f->seq, f->seq + beg, end - beg);
+ f->vpos += beg; f->vlen = end - beg;
+ f->single = f->vlen == 1? 1 : 0;
+ }
+ }
+ }
+ return ret;
+}
+
+static void dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash)
+{
+ int i, is_flip, drop_ambi;
+ drop_ambi = g->flag & FLAG_DROP_AMBI;
+ is_flip = (drand48() < 0.5);
+ for (i = 0; i < g->n; ++i) {
+ int end, which;
+ uint64_t key;
+ khint_t k;
+ bam1_t *b = g->b[i];
+ key = X31_hash_string(bam1_qname(b));
+ end = bam_calend(&b->core, bam1_cigar(b));
+ if (end > min_pos) break;
+ k = kh_get(64, hash, key);
+ if (k == kh_end(hash)) which = 3;
+ else {
+ frag_t *f = &kh_val(hash, k);
+ if (f->ambig) which = drop_ambi? 2 : 3;
+ else if (f->phased && f->flip) which = 2;
+ else if (f->phased == 0) which = 3;
+ else { // phased and not flipped
+ char c = 'Y';
+ which = f->phase;
+ bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c);
+ }
+ if (which < 2 && is_flip) which = 1 - which; // increase the randomness
+ }
+ if (which == 3) which = (drand48() < 0.5);
+ bam_write1(g->out[which], b);
+ bam_destroy1(b);
+ g->b[i] = 0;
+ }
+ memmove(g->b, g->b + i, (g->n - i) * sizeof(void*));
+ g->n -= i;
+}
+
+static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash)
+{
+ int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos;
+ khint_t k;
+ frag_t **seqs;
+ int8_t *path, *sitemask;
+ uint64_t *pcnt, *regmask;
+
+ if (vpos == 0) return 0;
+ i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos
+ min_pos = i? cns[vpos]>>32 : 0x7fffffff;
+ if (vpos == 1) {
+ printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1);
+ printf("M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1,
+ "ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1);
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ frag_t *f = &kh_val(hash, k);
+ if (f->vpos) continue;
+ f->flip = 0;
+ if (f->seq[0] == 0) f->phased = 0;
+ else f->phased = 1, f->phase = f->seq[0] - 1;
+ }
+ }
+ dump_aln(g, min_pos, hash);
+ ++g->vpos_shift;
+ return 1;
+ }
+ { // phase
+ int **cnt;
+ uint64_t *mask;
+ printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1);
+ sitemask = calloc(vpos, 1);
+ cnt = count_all(g->k, vpos, hash);
+ path = dynaprog(g->k, vpos, cnt);
+ for (i = 0; i < vpos; ++i) free(cnt[i]);
+ free(cnt);
+ pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking
+ mask = genmask(vpos, pcnt, &n_masked);
+ regmask = calloc(n_masked, 8);
+ for (i = 0; i < n_masked; ++i) {
+ regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32;
+ for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j)
+ sitemask[j] = 1;
+ }
+ free(mask);
+ if (g->flag & FLAG_FIX_CHIMERA) {
+ free(pcnt);
+ pcnt = fragphase(vpos, path, hash, 1);
+ }
+ }
+ for (i = 0; i < n_masked; ++i)
+ printf("FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1);
+ for (i = 0; i < vpos; ++i) {
+ uint64_t x = pcnt[i];
+ int8_t c[2];
+ c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3);
+ c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3);
+ printf("M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]],
+ i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff));
+ }
+ free(path); free(pcnt); free(regmask); free(sitemask);
+ seqs = calloc(n_seqs, sizeof(void*));
+ for (k = 0, i = 0; k < kh_end(hash); ++k)
+ if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single)
+ seqs[i++] = &kh_val(hash, k);
+ n_seqs = i;
+ ks_introsort_rseq(n_seqs, seqs);
+ for (i = 0; i < n_seqs; ++i) {
+ frag_t *f = seqs[i];
+ printf("EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen);
+ for (j = 0; j < f->vlen; ++j) {
+ uint32_t c = cns[f->vpos + j];
+ if (f->seq[j] == 0) putchar('N');
+ else putchar("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)]);
+ }
+ printf("\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1);
+ }
+ free(seqs);
+ printf("//\n");
+ fflush(stdout);
+ g->vpos_shift += vpos;
+ dump_aln(g, min_pos, hash);
+ return vpos;
+}
+
+static void update_vpos(int vpos, nseq_t *hash)
+{
+ khint_t k;
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ frag_t *f = &kh_val(hash, k);
+ if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it
+ else f->vpos -= vpos;
+ }
+ }
+}
+
+static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement
+{
+ return hash;
+}
+
+static int readaln(void *data, bam1_t *b)
+{
+ phaseg_t *g = (phaseg_t*)data;
+ int ret;
+ ret = bam_read1(g->fp, b);
+ if (ret < 0) return ret;
+ if (!(b->core.flag & (BAM_FUNMAP|BAM_FSECONDARY|BAM_FQCFAIL|BAM_FDUP)) && g->pre) {
+ if (g->n == g->m) {
+ g->m = g->m? g->m<<1 : 16;
+ g->b = realloc(g->b, g->m * sizeof(void*));
+ }
+ g->b[g->n++] = bam_dup1(b);
+ }
+ return ret;
+}
+
+static khash_t(set64) *loadpos(const char *fn, bam_header_t *h)
+{
+ gzFile fp;
+ kstream_t *ks;
+ int ret, dret;
+ kstring_t *str;
+ khash_t(set64) *hash;
+
+ hash = kh_init(set64);
+ str = calloc(1, sizeof(kstring_t));
+ fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ int tid = bam_get_tid(h, str->s);
+ if (tid >= 0 && dret != '\n') {
+ if (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
+ kh_put(set64, hash, x, &ret);
+ } else break;
+ }
+ if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
+ if (dret < 0) break;
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(str->s); free(str);
+ return hash;
+}
+
+static int gl2cns(float q[16])
+{
+ int i, j, min_ij;
+ float min, min2;
+ min = min2 = 1e30; min_ij = -1;
+ for (i = 0; i < 4; ++i) {
+ for (j = i; j < 4; ++j) {
+ if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j];
+ else if (q[i<<2|j] < min2) min2 = q[i<<2|j];
+ }
+ }
+ return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2;
+}
+
+int main_phase(int argc, char *argv[])
+{
+ extern void bam_init_header_hash(bam_header_t *header);
+ int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0;
+ const bam_pileup1_t *plp;
+ bam_plp_t iter;
+ bam_header_t *h;
+ nseq_t *seqs;
+ uint64_t *cns = 0;
+ phaseg_t g;
+ char *fn_list = 0;
+ khash_t(set64) *set = 0;
+ errmod_t *em;
+ uint16_t *bases;
+
+ memset(&g, 0, sizeof(phaseg_t));
+ g.flag = FLAG_FIX_CHIMERA;
+ g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256;
+ while ((c = getopt(argc, argv, "Q:eFq:k:b:l:D:A:")) >= 0) {
+ switch (c) {
+ case 'D': g.max_depth = atoi(optarg); break;
+ case 'q': g.min_varLOD = atoi(optarg); break;
+ case 'Q': g.min_baseQ = atoi(optarg); break;
+ case 'k': g.k = atoi(optarg); break;
+ case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break;
+ case 'e': g.flag |= FLAG_LIST_EXCL; break;
+ case 'A': g.flag |= FLAG_DROP_AMBI; break;
+ case 'b': g.pre = strdup(optarg); break;
+ case 'l': fn_list = strdup(optarg); break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools phase [options] <in.bam>\n\n");
+ fprintf(stderr, "Options: -k INT block length [%d]\n", g.k);
+ fprintf(stderr, " -b STR prefix of BAMs to output [null]\n");
+ fprintf(stderr, " -q INT min het phred-LOD [%d]\n", g.min_varLOD);
+ fprintf(stderr, " -Q INT min base quality in het calling [%d]\n", g.min_baseQ);
+ fprintf(stderr, " -D INT max read depth [%d]\n", g.max_depth);
+// fprintf(stderr, " -l FILE list of sites to phase [null]\n");
+ fprintf(stderr, " -F do not attempt to fix chimeras\n");
+ fprintf(stderr, " -A drop reads with ambiguous phase\n");
+// fprintf(stderr, " -e do not discover SNPs (effective with -l)\n");
+ fprintf(stderr, "\n");
+ return 1;
+ }
+ g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
+ h = bam_header_read(g.fp);
+ if (fn_list) { // read the list of sites to phase
+ bam_init_header_hash(h);
+ set = loadpos(fn_list, h);
+ free(fn_list);
+ } else g.flag &= ~FLAG_LIST_EXCL;
+ if (g.pre) { // open BAMs to write
+ char *s = malloc(strlen(g.pre) + 20);
+ strcpy(s, g.pre); strcat(s, ".0.bam"); g.out[0] = bam_open(s, "w");
+ strcpy(s, g.pre); strcat(s, ".1.bam"); g.out[1] = bam_open(s, "w");
+ strcpy(s, g.pre); strcat(s, ".chimera.bam"); g.out[2] = bam_open(s, "w");
+ for (c = 0; c <= 2; ++c) bam_header_write(g.out[c], h);
+ free(s);
+ }
+
+ iter = bam_plp_init(readaln, &g);
+ g.vpos_shift = 0;
+ seqs = kh_init(64);
+ em = errmod_init(1. - 0.83);
+ bases = calloc(g.max_depth, 2);
+ printf("CC\n");
+ printf("CC\tDescriptions:\nCC\n");
+ printf("CC\t CC comments\n");
+ printf("CC\t PS start of a phase set\n");
+ printf("CC\t FL filtered region\n");
+ printf("CC\t M[012] markers; 0 for singletons, 1 for phased and 2 for filtered\n");
+ printf("CC\t EV supporting reads; SAM format\n");
+ printf("CC\t // end of a phase set\nCC\n");
+ printf("CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n");
+ printf("CC\t PS chr phaseSetStart phaseSetEnd\n");
+ printf("CC\t FL chr filterStart filterEnd\n");
+ printf("CC\t M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1\n");
+ printf("CC\nCC\n");
+ fflush(stdout);
+ while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) {
+ int i, k, c, tmp, dophase = 1, in_set = 0;
+ float q[16];
+ if (tid < 0) break;
+ if (tid != lasttid) { // change of chromosome
+ g.vpos_shift = 0;
+ if (lasttid >= 0) {
+ seqs = shrink_hash(seqs);
+ phase(&g, h->target_name[lasttid], vpos, cns, seqs);
+ update_vpos(0x7fffffff, seqs);
+ }
+ lasttid = tid;
+ vpos = 0;
+ }
+ if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1;
+ if (n > g.max_depth) continue; // do not proceed if the depth is too high
+ // fill the bases array and check if there is a variant
+ for (i = k = 0; i < n; ++i) {
+ const bam_pileup1_t *p = plp + i;
+ uint8_t *seq;
+ int q, baseQ, b;
+ if (p->is_del || p->is_refskip) continue;
+ baseQ = bam1_qual(p->b)[p->qpos];
+ if (baseQ < g.min_baseQ) continue;
+ seq = bam1_seq(p->b);
+ b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
+ if (b > 3) continue;
+ q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+ if (q < 4) q = 4;
+ if (q > 63) q = 63;
+ bases[k++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
+ }
+ if (k == 0) continue;
+ errmod_cal(em, k, 4, bases, q); // compute genotype likelihood
+ c = gl2cns(q); // get the consensus
+ // tell if to proceed
+ if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list
+ if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant
+ // add the variant
+ if (vpos == max_vpos) {
+ max_vpos = max_vpos? max_vpos<<1 : 128;
+ cns = realloc(cns, max_vpos * 8);
+ }
+ cns[vpos] = (uint64_t)pos<<32 | c;
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = plp + i;
+ uint64_t key;
+ khint_t k;
+ uint8_t *seq = bam1_seq(p->b);
+ frag_t *f;
+ if (p->is_del || p->is_refskip) continue;
+ if (p->b->core.qual == 0) continue;
+ // get the base code
+ c = nt16_nt4_table[(int)bam1_seqi(seq, p->qpos)];
+ if (c == (cns[vpos]&3)) c = 1;
+ else if (c == (cns[vpos]>>16&3)) c = 2;
+ else c = 0;
+ // write to seqs
+ key = X31_hash_string(bam1_qname(p->b));
+ k = kh_put(64, seqs, key, &tmp);
+ f = &kh_val(seqs, k);
+ if (tmp == 0) { // present in the hash table
+ if (vpos - f->vpos + 1 < MAX_VARS) {
+ f->vlen = vpos - f->vpos + 1;
+ f->seq[f->vlen-1] = c;
+ f->end = bam_calend(&p->b->core, bam1_cigar(p->b));
+ }
+ dophase = 0;
+ } else { // absent
+ memset(f->seq, 0, MAX_VARS);
+ f->beg = p->b->core.pos;
+ f->end = bam_calend(&p->b->core, bam1_cigar(p->b));
+ f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0;
+ }
+ }
+ if (dophase) {
+ seqs = shrink_hash(seqs);
+ phase(&g, h->target_name[tid], vpos, cns, seqs);
+ update_vpos(vpos, seqs);
+ cns[0] = cns[vpos];
+ vpos = 0;
+ }
+ ++vpos;
+ }
+ if (tid >= 0) phase(&g, h->target_name[tid], vpos, cns, seqs);
+ bam_header_destroy(h);
+ bam_plp_destroy(iter);
+ bam_close(g.fp);
+ kh_destroy(64, seqs);
+ kh_destroy(set64, set);
+ free(cns);
+ errmod_destroy(em);
+ free(bases);
+ if (g.pre) {
+ for (c = 0; c <= 2; ++c) bam_close(g.out[c]);
+ free(g.pre); free(g.b);
+ }
+ return 0;
+}
diff --git a/src/samtools-0.1.18/razf.c b/src/samtools-0.1.18/razf.c
new file mode 100644
index 0000000..e7499f9
--- /dev/null
+++ b/src/samtools-0.1.18/razf.c
@@ -0,0 +1,853 @@
+/*
+ * RAZF : Random Access compressed(Z) File
+ * Version: 1.0
+ * Release Date: 2008-10-27
+ *
+ * Copyright 2008, Jue Ruan <ruanjue at gmail.com>, Heng Li <lh3 at sanger.ac.uk>
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+
+#ifndef _NO_RAZF
+
+#include <fcntl.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include "razf.h"
+
+
+#if ZLIB_VERNUM < 0x1221
+struct _gz_header_s {
+ int text;
+ uLong time;
+ int xflags;
+ int os;
+ Bytef *extra;
+ uInt extra_len;
+ uInt extra_max;
+ Bytef *name;
+ uInt name_max;
+ Bytef *comment;
+ uInt comm_max;
+ int hcrc;
+ int done;
+};
+#warning "zlib < 1.2.2.1; RAZF writing is disabled."
+#endif
+
+#define DEF_MEM_LEVEL 8
+
+static inline uint32_t byte_swap_4(uint32_t v){
+ v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
+ return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
+}
+
+static inline uint64_t byte_swap_8(uint64_t v){
+ v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
+ v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
+ return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
+}
+
+static inline int is_big_endian(){
+ int x = 0x01;
+ char *c = (char*)&x;
+ return (c[0] != 0x01);
+}
+
+#ifndef _RZ_READONLY
+static void add_zindex(RAZF *rz, int64_t in, int64_t out){
+ if(rz->index->size == rz->index->cap){
+ rz->index->cap = rz->index->cap * 1.5 + 2;
+ rz->index->cell_offsets = realloc(rz->index->cell_offsets, sizeof(int) * rz->index->cap);
+ rz->index->bin_offsets = realloc(rz->index->bin_offsets, sizeof(int64_t) * (rz->index->cap/RZ_BIN_SIZE + 1));
+ }
+ if(rz->index->size % RZ_BIN_SIZE == 0) rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE] = out;
+ rz->index->cell_offsets[rz->index->size] = out - rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE];
+ rz->index->size ++;
+}
+
+static void save_zindex(RAZF *rz, int fd){
+ int32_t i, v32;
+ int is_be;
+ is_be = is_big_endian();
+ if(is_be) write(fd, &rz->index->size, sizeof(int));
+ else {
+ v32 = byte_swap_4((uint32_t)rz->index->size);
+ write(fd, &v32, sizeof(uint32_t));
+ }
+ v32 = rz->index->size / RZ_BIN_SIZE + 1;
+ if(!is_be){
+ for(i=0;i<v32;i++) rz->index->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
+ for(i=0;i<rz->index->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
+ }
+ write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
+ write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
+}
+#endif
+
+#ifdef _USE_KNETFILE
+static void load_zindex(RAZF *rz, knetFile *fp){
+#else
+static void load_zindex(RAZF *rz, int fd){
+#endif
+ int32_t i, v32;
+ int is_be;
+ if(!rz->load_index) return;
+ if(rz->index == NULL) rz->index = malloc(sizeof(ZBlockIndex));
+ is_be = is_big_endian();
+#ifdef _USE_KNETFILE
+ knet_read(fp, &rz->index->size, sizeof(int));
+#else
+ read(fd, &rz->index->size, sizeof(int));
+#endif
+ if(!is_be) rz->index->size = byte_swap_4((uint32_t)rz->index->size);
+ rz->index->cap = rz->index->size;
+ v32 = rz->index->size / RZ_BIN_SIZE + 1;
+ rz->index->bin_offsets = malloc(sizeof(int64_t) * v32);
+#ifdef _USE_KNETFILE
+ knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32);
+#else
+ read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
+#endif
+ rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size);
+#ifdef _USE_KNETFILE
+ knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size);
+#else
+ read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
+#endif
+ if(!is_be){
+ for(i=0;i<v32;i++) rz->index->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
+ for(i=0;i<rz->index->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
+ }
+}
+
+#ifdef _RZ_READONLY
+static RAZF* razf_open_w(int fd)
+{
+ fprintf(stderr, "[razf_open_w] Writing is not available with zlib ver < 1.2.2.1\n");
+ return 0;
+}
+#else
+static RAZF* razf_open_w(int fd){
+ RAZF *rz;
+#ifdef _WIN32
+ setmode(fd, O_BINARY);
+#endif
+ rz = calloc(1, sizeof(RAZF));
+ rz->mode = 'w';
+#ifdef _USE_KNETFILE
+ rz->x.fpw = fd;
+#else
+ rz->filedes = fd;
+#endif
+ rz->stream = calloc(sizeof(z_stream), 1);
+ rz->inbuf = malloc(RZ_BUFFER_SIZE);
+ rz->outbuf = malloc(RZ_BUFFER_SIZE);
+ rz->index = calloc(sizeof(ZBlockIndex), 1);
+ deflateInit2(rz->stream, RZ_COMPRESS_LEVEL, Z_DEFLATED, WINDOW_BITS + 16, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY);
+ rz->stream->avail_out = RZ_BUFFER_SIZE;
+ rz->stream->next_out = rz->outbuf;
+ rz->header = calloc(sizeof(gz_header), 1);
+ rz->header->os = 0x03; //Unix
+ rz->header->text = 0;
+ rz->header->time = 0;
+ rz->header->extra = malloc(7);
+ strncpy((char*)rz->header->extra, "RAZF", 4);
+ rz->header->extra[4] = 1; // obsolete field
+ // block size = RZ_BLOCK_SIZE, Big-Endian
+ rz->header->extra[5] = RZ_BLOCK_SIZE >> 8;
+ rz->header->extra[6] = RZ_BLOCK_SIZE & 0xFF;
+ rz->header->extra_len = 7;
+ rz->header->name = rz->header->comment = 0;
+ rz->header->hcrc = 0;
+ deflateSetHeader(rz->stream, rz->header);
+ rz->block_pos = rz->block_off = 0;
+ return rz;
+}
+
+static void _razf_write(RAZF* rz, const void *data, int size){
+ int tout;
+ rz->stream->avail_in = size;
+ rz->stream->next_in = (void*)data;
+ while(1){
+ tout = rz->stream->avail_out;
+ deflate(rz->stream, Z_NO_FLUSH);
+ rz->out += tout - rz->stream->avail_out;
+ if(rz->stream->avail_out) break;
+#ifdef _USE_KNETFILE
+ write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
+ write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
+ rz->stream->avail_out = RZ_BUFFER_SIZE;
+ rz->stream->next_out = rz->outbuf;
+ if(rz->stream->avail_in == 0) break;
+ };
+ rz->in += size - rz->stream->avail_in;
+ rz->block_off += size - rz->stream->avail_in;
+}
+
+static void razf_flush(RAZF *rz){
+ uint32_t tout;
+ if(rz->buf_len){
+ _razf_write(rz, rz->inbuf, rz->buf_len);
+ rz->buf_off = rz->buf_len = 0;
+ }
+ if(rz->stream->avail_out){
+#ifdef _USE_KNETFILE
+ write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
+ write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
+ rz->stream->avail_out = RZ_BUFFER_SIZE;
+ rz->stream->next_out = rz->outbuf;
+ }
+ while(1){
+ tout = rz->stream->avail_out;
+ deflate(rz->stream, Z_FULL_FLUSH);
+ rz->out += tout - rz->stream->avail_out;
+ if(rz->stream->avail_out == 0){
+#ifdef _USE_KNETFILE
+ write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
+ write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
+ rz->stream->avail_out = RZ_BUFFER_SIZE;
+ rz->stream->next_out = rz->outbuf;
+ } else break;
+ }
+ rz->block_pos = rz->out;
+ rz->block_off = 0;
+}
+
+static void razf_end_flush(RAZF *rz){
+ uint32_t tout;
+ if(rz->buf_len){
+ _razf_write(rz, rz->inbuf, rz->buf_len);
+ rz->buf_off = rz->buf_len = 0;
+ }
+ while(1){
+ tout = rz->stream->avail_out;
+ deflate(rz->stream, Z_FINISH);
+ rz->out += tout - rz->stream->avail_out;
+ if(rz->stream->avail_out < RZ_BUFFER_SIZE){
+#ifdef _USE_KNETFILE
+ write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
+ write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
+ rz->stream->avail_out = RZ_BUFFER_SIZE;
+ rz->stream->next_out = rz->outbuf;
+ } else break;
+ }
+}
+
+static void _razf_buffered_write(RAZF *rz, const void *data, int size){
+ int i, n;
+ while(1){
+ if(rz->buf_len == RZ_BUFFER_SIZE){
+ _razf_write(rz, rz->inbuf, rz->buf_len);
+ rz->buf_len = 0;
+ }
+ if(size + rz->buf_len < RZ_BUFFER_SIZE){
+ for(i=0;i<size;i++) ((char*)rz->inbuf + rz->buf_len)[i] = ((char*)data)[i];
+ rz->buf_len += size;
+ return;
+ } else {
+ n = RZ_BUFFER_SIZE - rz->buf_len;
+ for(i=0;i<n;i++) ((char*)rz->inbuf + rz->buf_len)[i] = ((char*)data)[i];
+ size -= n;
+ data += n;
+ rz->buf_len += n;
+ }
+ }
+}
+
+int razf_write(RAZF* rz, const void *data, int size){
+ int ori_size, n;
+ int64_t next_block;
+ ori_size = size;
+ next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
+ while(rz->in + rz->buf_len + size >= next_block){
+ n = next_block - rz->in - rz->buf_len;
+ _razf_buffered_write(rz, data, n);
+ data += n;
+ size -= n;
+ razf_flush(rz);
+ add_zindex(rz, rz->in, rz->out);
+ next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
+ }
+ _razf_buffered_write(rz, data, size);
+ return ori_size;
+}
+#endif
+
+/* gzip flag byte */
+#define ASCII_FLAG 0x01 /* bit 0 set: file probably ascii text */
+#define HEAD_CRC 0x02 /* bit 1 set: header CRC present */
+#define EXTRA_FIELD 0x04 /* bit 2 set: extra field present */
+#define ORIG_NAME 0x08 /* bit 3 set: original file name present */
+#define COMMENT 0x10 /* bit 4 set: file comment present */
+#define RESERVED 0xE0 /* bits 5..7: reserved */
+
+static int _read_gz_header(unsigned char *data, int size, int *extra_off, int *extra_len){
+ int method, flags, n, len;
+ if(size < 2) return 0;
+ if(data[0] != 0x1f || data[1] != 0x8b) return 0;
+ if(size < 4) return 0;
+ method = data[2];
+ flags = data[3];
+ if(method != Z_DEFLATED || (flags & RESERVED)) return 0;
+ n = 4 + 6; // Skip 6 bytes
+ *extra_off = n + 2;
+ *extra_len = 0;
+ if(flags & EXTRA_FIELD){
+ if(size < n + 2) return 0;
+ len = ((int)data[n + 1] << 8) | data[n];
+ n += 2;
+ *extra_off = n;
+ while(len){
+ if(n >= size) return 0;
+ n ++;
+ len --;
+ }
+ *extra_len = n - (*extra_off);
+ }
+ if(flags & ORIG_NAME) while(n < size && data[n++]);
+ if(flags & COMMENT) while(n < size && data[n++]);
+ if(flags & HEAD_CRC){
+ if(n + 2 > size) return 0;
+ n += 2;
+ }
+ return n;
+}
+
+#ifdef _USE_KNETFILE
+static RAZF* razf_open_r(knetFile *fp, int _load_index){
+#else
+static RAZF* razf_open_r(int fd, int _load_index){
+#endif
+ RAZF *rz;
+ int ext_off, ext_len;
+ int n, is_be, ret;
+ int64_t end;
+ unsigned char c[] = "RAZF";
+ rz = calloc(1, sizeof(RAZF));
+ rz->mode = 'r';
+#ifdef _USE_KNETFILE
+ rz->x.fpr = fp;
+#else
+#ifdef _WIN32
+ setmode(fd, O_BINARY);
+#endif
+ rz->filedes = fd;
+#endif
+ rz->stream = calloc(sizeof(z_stream), 1);
+ rz->inbuf = malloc(RZ_BUFFER_SIZE);
+ rz->outbuf = malloc(RZ_BUFFER_SIZE);
+ rz->end = rz->src_end = 0x7FFFFFFFFFFFFFFFLL;
+#ifdef _USE_KNETFILE
+ n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
+#else
+ n = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
+#endif
+ ret = _read_gz_header(rz->inbuf, n, &ext_off, &ext_len);
+ if(ret == 0){
+ PLAIN_FILE:
+ rz->in = n;
+ rz->file_type = FILE_TYPE_PLAIN;
+ memcpy(rz->outbuf, rz->inbuf, n);
+ rz->buf_len = n;
+ free(rz->stream);
+ rz->stream = NULL;
+ return rz;
+ }
+ rz->header_size = ret;
+ ret = inflateInit2(rz->stream, -WINDOW_BITS);
+ if(ret != Z_OK){ inflateEnd(rz->stream); goto PLAIN_FILE;}
+ rz->stream->avail_in = n - rz->header_size;
+ rz->stream->next_in = rz->inbuf + rz->header_size;
+ rz->stream->avail_out = RZ_BUFFER_SIZE;
+ rz->stream->next_out = rz->outbuf;
+ rz->file_type = FILE_TYPE_GZ;
+ rz->in = rz->header_size;
+ rz->block_pos = rz->header_size;
+ rz->next_block_pos = rz->header_size;
+ rz->block_off = 0;
+ if(ext_len < 7 || memcmp(rz->inbuf + ext_off, c, 4) != 0) return rz;
+ if(((((unsigned char*)rz->inbuf)[ext_off + 5] << 8) | ((unsigned char*)rz->inbuf)[ext_off + 6]) != RZ_BLOCK_SIZE){
+ fprintf(stderr, " -- WARNING: RZ_BLOCK_SIZE is not %d, treat source as gz file. in %s -- %s:%d --\n", RZ_BLOCK_SIZE, __FUNCTION__, __FILE__, __LINE__);
+ return rz;
+ }
+ rz->load_index = _load_index;
+ rz->file_type = FILE_TYPE_RZ;
+#ifdef _USE_KNETFILE
+ if(knet_seek(fp, -16, SEEK_END) == -1){
+#else
+ if(lseek(fd, -16, SEEK_END) == -1){
+#endif
+ UNSEEKABLE:
+ rz->seekable = 0;
+ rz->index = NULL;
+ rz->src_end = rz->end = 0x7FFFFFFFFFFFFFFFLL;
+ } else {
+ is_be = is_big_endian();
+ rz->seekable = 1;
+#ifdef _USE_KNETFILE
+ knet_read(fp, &end, sizeof(int64_t));
+#else
+ read(fd, &end, sizeof(int64_t));
+#endif
+ if(!is_be) rz->src_end = (int64_t)byte_swap_8((uint64_t)end);
+ else rz->src_end = end;
+
+#ifdef _USE_KNETFILE
+ knet_read(fp, &end, sizeof(int64_t));
+#else
+ read(fd, &end, sizeof(int64_t));
+#endif
+ if(!is_be) rz->end = (int64_t)byte_swap_8((uint64_t)end);
+ else rz->end = end;
+ if(n > rz->end){
+ rz->stream->avail_in -= n - rz->end;
+ n = rz->end;
+ }
+ if(rz->end > rz->src_end){
+#ifdef _USE_KNETFILE
+ knet_seek(fp, rz->in, SEEK_SET);
+#else
+ lseek(fd, rz->in, SEEK_SET);
+#endif
+ goto UNSEEKABLE;
+ }
+#ifdef _USE_KNETFILE
+ knet_seek(fp, rz->end, SEEK_SET);
+ if(knet_tell(fp) != rz->end){
+ knet_seek(fp, rz->in, SEEK_SET);
+#else
+ if(lseek(fd, rz->end, SEEK_SET) != rz->end){
+ lseek(fd, rz->in, SEEK_SET);
+#endif
+ goto UNSEEKABLE;
+ }
+#ifdef _USE_KNETFILE
+ load_zindex(rz, fp);
+ knet_seek(fp, n, SEEK_SET);
+#else
+ load_zindex(rz, fd);
+ lseek(fd, n, SEEK_SET);
+#endif
+ }
+ return rz;
+}
+
+#ifdef _USE_KNETFILE
+RAZF* razf_dopen(int fd, const char *mode){
+ if (strstr(mode, "r")) fprintf(stderr,"[razf_dopen] implement me\n");
+ else if(strstr(mode, "w")) return razf_open_w(fd);
+ return NULL;
+}
+
+RAZF* razf_dopen2(int fd, const char *mode)
+{
+ fprintf(stderr,"[razf_dopen2] implement me\n");
+ return NULL;
+}
+#else
+RAZF* razf_dopen(int fd, const char *mode){
+ if(strstr(mode, "r")) return razf_open_r(fd, 1);
+ else if(strstr(mode, "w")) return razf_open_w(fd);
+ else return NULL;
+}
+
+RAZF* razf_dopen2(int fd, const char *mode)
+{
+ if(strstr(mode, "r")) return razf_open_r(fd, 0);
+ else if(strstr(mode, "w")) return razf_open_w(fd);
+ else return NULL;
+}
+#endif
+
+static inline RAZF* _razf_open(const char *filename, const char *mode, int _load_index){
+ int fd;
+ RAZF *rz;
+ if(strstr(mode, "r")){
+#ifdef _USE_KNETFILE
+ knetFile *fd = knet_open(filename, "r");
+ if (fd == 0) {
+ fprintf(stderr, "[_razf_open] fail to open %s\n", filename);
+ return NULL;
+ }
+#else
+#ifdef _WIN32
+ fd = open(filename, O_RDONLY | O_BINARY);
+#else
+ fd = open(filename, O_RDONLY);
+#endif
+#endif
+ if(fd < 0) return NULL;
+ rz = razf_open_r(fd, _load_index);
+ } else if(strstr(mode, "w")){
+#ifdef _WIN32
+ fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666);
+#else
+ fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0666);
+#endif
+ if(fd < 0) return NULL;
+ rz = razf_open_w(fd);
+ } else return NULL;
+ return rz;
+}
+
+RAZF* razf_open(const char *filename, const char *mode){
+ return _razf_open(filename, mode, 1);
+}
+
+RAZF* razf_open2(const char *filename, const char *mode){
+ return _razf_open(filename, mode, 0);
+}
+
+int razf_get_data_size(RAZF *rz, int64_t *u_size, int64_t *c_size){
+ int64_t n;
+ if(rz->mode != 'r' && rz->mode != 'R') return 0;
+ switch(rz->file_type){
+ case FILE_TYPE_PLAIN:
+ if(rz->end == 0x7fffffffffffffffLL){
+#ifdef _USE_KNETFILE
+ if(knet_seek(rz->x.fpr, 0, SEEK_CUR) == -1) return 0;
+ n = knet_tell(rz->x.fpr);
+ knet_seek(rz->x.fpr, 0, SEEK_END);
+ rz->end = knet_tell(rz->x.fpr);
+ knet_seek(rz->x.fpr, n, SEEK_SET);
+#else
+ if((n = lseek(rz->filedes, 0, SEEK_CUR)) == -1) return 0;
+ rz->end = lseek(rz->filedes, 0, SEEK_END);
+ lseek(rz->filedes, n, SEEK_SET);
+#endif
+ }
+ *u_size = *c_size = rz->end;
+ return 1;
+ case FILE_TYPE_GZ:
+ return 0;
+ case FILE_TYPE_RZ:
+ if(rz->src_end == rz->end) return 0;
+ *u_size = rz->src_end;
+ *c_size = rz->end;
+ return 1;
+ default:
+ return 0;
+ }
+}
+
+static int _razf_read(RAZF* rz, void *data, int size){
+ int ret, tin;
+ if(rz->z_eof || rz->z_err) return 0;
+ if (rz->file_type == FILE_TYPE_PLAIN) {
+#ifdef _USE_KNETFILE
+ ret = knet_read(rz->x.fpr, data, size);
+#else
+ ret = read(rz->filedes, data, size);
+#endif
+ if (ret == 0) rz->z_eof = 1;
+ return ret;
+ }
+ rz->stream->avail_out = size;
+ rz->stream->next_out = data;
+ while(rz->stream->avail_out){
+ if(rz->stream->avail_in == 0){
+ if(rz->in >= rz->end){ rz->z_eof = 1; break; }
+ if(rz->end - rz->in < RZ_BUFFER_SIZE){
+#ifdef _USE_KNETFILE
+ rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, rz->end -rz->in);
+#else
+ rz->stream->avail_in = read(rz->filedes, rz->inbuf, rz->end -rz->in);
+#endif
+ } else {
+#ifdef _USE_KNETFILE
+ rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
+#else
+ rz->stream->avail_in = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
+#endif
+ }
+ if(rz->stream->avail_in == 0){
+ rz->z_eof = 1;
+ break;
+ }
+ rz->stream->next_in = rz->inbuf;
+ }
+ tin = rz->stream->avail_in;
+ ret = inflate(rz->stream, Z_BLOCK);
+ rz->in += tin - rz->stream->avail_in;
+ if(ret == Z_NEED_DICT || ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){
+ fprintf(stderr, "[_razf_read] inflate error: %d %s (at %s:%d)\n", ret, rz->stream->msg ? rz->stream->msg : "", __FILE__, __LINE__);
+ rz->z_err = 1;
+ break;
+ }
+ if(ret == Z_STREAM_END){
+ rz->z_eof = 1;
+ break;
+ }
+ if ((rz->stream->data_type&128) && !(rz->stream->data_type&64)){
+ rz->buf_flush = 1;
+ rz->next_block_pos = rz->in;
+ break;
+ }
+ }
+ return size - rz->stream->avail_out;
+}
+
+int razf_read(RAZF *rz, void *data, int size){
+ int ori_size, i;
+ ori_size = size;
+ while(size > 0){
+ if(rz->buf_len){
+ if(size < rz->buf_len){
+ for(i=0;i<size;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
+ rz->buf_off += size;
+ rz->buf_len -= size;
+ data += size;
+ rz->block_off += size;
+ size = 0;
+ break;
+ } else {
+ for(i=0;i<rz->buf_len;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
+ data += rz->buf_len;
+ size -= rz->buf_len;
+ rz->block_off += rz->buf_len;
+ rz->buf_off = 0;
+ rz->buf_len = 0;
+ if(rz->buf_flush){
+ rz->block_pos = rz->next_block_pos;
+ rz->block_off = 0;
+ rz->buf_flush = 0;
+ }
+ }
+ } else if(rz->buf_flush){
+ rz->block_pos = rz->next_block_pos;
+ rz->block_off = 0;
+ rz->buf_flush = 0;
+ }
+ if(rz->buf_flush) continue;
+ rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
+ if(rz->z_eof && rz->buf_len == 0) break;
+ }
+ rz->out += ori_size - size;
+ return ori_size - size;
+}
+
+int razf_skip(RAZF* rz, int size){
+ int ori_size;
+ ori_size = size;
+ while(size > 0){
+ if(rz->buf_len){
+ if(size < rz->buf_len){
+ rz->buf_off += size;
+ rz->buf_len -= size;
+ rz->block_off += size;
+ size = 0;
+ break;
+ } else {
+ size -= rz->buf_len;
+ rz->buf_off = 0;
+ rz->buf_len = 0;
+ rz->block_off += rz->buf_len;
+ if(rz->buf_flush){
+ rz->block_pos = rz->next_block_pos;
+ rz->block_off = 0;
+ rz->buf_flush = 0;
+ }
+ }
+ } else if(rz->buf_flush){
+ rz->block_pos = rz->next_block_pos;
+ rz->block_off = 0;
+ rz->buf_flush = 0;
+ }
+ if(rz->buf_flush) continue;
+ rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
+ if(rz->z_eof || rz->z_err) break;
+ }
+ rz->out += ori_size - size;
+ return ori_size - size;
+}
+
+static void _razf_reset_read(RAZF *rz, int64_t in, int64_t out){
+#ifdef _USE_KNETFILE
+ knet_seek(rz->x.fpr, in, SEEK_SET);
+#else
+ lseek(rz->filedes, in, SEEK_SET);
+#endif
+ rz->in = in;
+ rz->out = out;
+ rz->block_pos = in;
+ rz->next_block_pos = in;
+ rz->block_off = 0;
+ rz->buf_flush = 0;
+ rz->z_eof = rz->z_err = 0;
+ inflateReset(rz->stream);
+ rz->stream->avail_in = 0;
+ rz->buf_off = rz->buf_len = 0;
+}
+
+int64_t razf_jump(RAZF *rz, int64_t block_start, int block_offset){
+ int64_t pos;
+ rz->z_eof = 0;
+ if(rz->file_type == FILE_TYPE_PLAIN){
+ rz->buf_off = rz->buf_len = 0;
+ pos = block_start + block_offset;
+#ifdef _USE_KNETFILE
+ knet_seek(rz->x.fpr, pos, SEEK_SET);
+ pos = knet_tell(rz->x.fpr);
+#else
+ pos = lseek(rz->filedes, pos, SEEK_SET);
+#endif
+ rz->out = rz->in = pos;
+ return pos;
+ }
+ if(block_start == rz->block_pos && block_offset >= rz->block_off) {
+ block_offset -= rz->block_off;
+ goto SKIP; // Needn't reset inflate
+ }
+ if(block_start == 0) block_start = rz->header_size; // Automaticly revist wrong block_start
+ _razf_reset_read(rz, block_start, 0);
+ SKIP:
+ if(block_offset) razf_skip(rz, block_offset);
+ return rz->block_off;
+}
+
+int64_t razf_seek(RAZF* rz, int64_t pos, int where){
+ int64_t idx;
+ int64_t seek_pos, new_out;
+ rz->z_eof = 0;
+ if (where == SEEK_CUR) pos += rz->out;
+ else if (where == SEEK_END) pos += rz->src_end;
+ if(rz->file_type == FILE_TYPE_PLAIN){
+#ifdef _USE_KNETFILE
+ knet_seek(rz->x.fpr, pos, SEEK_SET);
+ seek_pos = knet_tell(rz->x.fpr);
+#else
+ seek_pos = lseek(rz->filedes, pos, SEEK_SET);
+#endif
+ rz->buf_off = rz->buf_len = 0;
+ rz->out = rz->in = seek_pos;
+ return seek_pos;
+ } else if(rz->file_type == FILE_TYPE_GZ){
+ if(pos >= rz->out) goto SKIP;
+ return rz->out;
+ }
+ if(pos == rz->out) return pos;
+ if(pos > rz->src_end) return rz->out;
+ if(!rz->seekable || !rz->load_index){
+ if(pos >= rz->out) goto SKIP;
+ }
+ idx = pos / RZ_BLOCK_SIZE - 1;
+ seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
+ new_out = (idx + 1) * RZ_BLOCK_SIZE;
+ if(pos > rz->out && new_out <= rz->out) goto SKIP;
+ _razf_reset_read(rz, seek_pos, new_out);
+ SKIP:
+ razf_skip(rz, (int)(pos - rz->out));
+ return rz->out;
+}
+
+uint64_t razf_tell2(RAZF *rz)
+{
+ /*
+ if (rz->load_index) {
+ int64_t idx, seek_pos;
+ idx = rz->out / RZ_BLOCK_SIZE - 1;
+ seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
+ if (seek_pos != rz->block_pos || rz->out%RZ_BLOCK_SIZE != rz->block_off)
+ fprintf(stderr, "[razf_tell2] inconsistent block offset: (%lld, %lld) != (%lld, %lld)\n",
+ (long long)seek_pos, (long long)rz->out%RZ_BLOCK_SIZE, (long long)rz->block_pos, (long long) rz->block_off);
+ }
+ */
+ return (uint64_t)rz->block_pos<<16 | (rz->block_off&0xffff);
+}
+
+int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where)
+{
+ if (where != SEEK_SET) return -1;
+ return razf_jump(rz, voffset>>16, voffset&0xffff);
+}
+
+void razf_close(RAZF *rz){
+ if(rz->mode == 'w'){
+#ifndef _RZ_READONLY
+ razf_end_flush(rz);
+ deflateEnd(rz->stream);
+#ifdef _USE_KNETFILE
+ save_zindex(rz, rz->x.fpw);
+ if(is_big_endian()){
+ write(rz->x.fpw, &rz->in, sizeof(int64_t));
+ write(rz->x.fpw, &rz->out, sizeof(int64_t));
+ } else {
+ uint64_t v64 = byte_swap_8((uint64_t)rz->in);
+ write(rz->x.fpw, &v64, sizeof(int64_t));
+ v64 = byte_swap_8((uint64_t)rz->out);
+ write(rz->x.fpw, &v64, sizeof(int64_t));
+ }
+#else
+ save_zindex(rz, rz->filedes);
+ if(is_big_endian()){
+ write(rz->filedes, &rz->in, sizeof(int64_t));
+ write(rz->filedes, &rz->out, sizeof(int64_t));
+ } else {
+ uint64_t v64 = byte_swap_8((uint64_t)rz->in);
+ write(rz->filedes, &v64, sizeof(int64_t));
+ v64 = byte_swap_8((uint64_t)rz->out);
+ write(rz->filedes, &v64, sizeof(int64_t));
+ }
+#endif
+#endif
+ } else if(rz->mode == 'r'){
+ if(rz->stream) inflateEnd(rz->stream);
+ }
+ if(rz->inbuf) free(rz->inbuf);
+ if(rz->outbuf) free(rz->outbuf);
+ if(rz->header){
+ free(rz->header->extra);
+ free(rz->header->name);
+ free(rz->header->comment);
+ free(rz->header);
+ }
+ if(rz->index){
+ free(rz->index->bin_offsets);
+ free(rz->index->cell_offsets);
+ free(rz->index);
+ }
+ free(rz->stream);
+#ifdef _USE_KNETFILE
+ if (rz->mode == 'r')
+ knet_close(rz->x.fpr);
+ if (rz->mode == 'w')
+ close(rz->x.fpw);
+#else
+ close(rz->filedes);
+#endif
+ free(rz);
+}
+
+#endif
diff --git a/src/samtools-0.1.18/razf.h b/src/samtools-0.1.18/razf.h
new file mode 100644
index 0000000..60a0c96
--- /dev/null
+++ b/src/samtools-0.1.18/razf.h
@@ -0,0 +1,134 @@
+ /*-
+ * RAZF : Random Access compressed(Z) File
+ * Version: 1.0
+ * Release Date: 2008-10-27
+ *
+ * Copyright 2008, Jue Ruan <ruanjue at gmail.com>, Heng Li <lh3 at sanger.ac.uk>
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+
+
+#ifndef __RAZF_RJ_H
+#define __RAZF_RJ_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include "zlib.h"
+
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+#if ZLIB_VERNUM < 0x1221
+#define _RZ_READONLY
+struct _gz_header_s;
+typedef struct _gz_header_s _gz_header;
+#define gz_header _gz_header
+#endif
+
+#define WINDOW_BITS 15
+
+#ifndef RZ_BLOCK_SIZE
+#define RZ_BLOCK_SIZE (1<<WINDOW_BITS)
+#endif
+
+#ifndef RZ_BUFFER_SIZE
+#define RZ_BUFFER_SIZE 4096
+#endif
+
+#ifndef RZ_COMPRESS_LEVEL
+#define RZ_COMPRESS_LEVEL 6
+#endif
+
+#define RZ_BIN_SIZE ((1LLU << 32) / RZ_BLOCK_SIZE)
+
+typedef struct {
+ uint32_t *cell_offsets; // i
+ int64_t *bin_offsets; // i / BIN_SIZE
+ int size;
+ int cap;
+} ZBlockIndex;
+/* When storing index, output bytes in Big-Endian everywhere */
+
+#define FILE_TYPE_RZ 1
+#define FILE_TYPE_PLAIN 2
+#define FILE_TYPE_GZ 3
+
+typedef struct RandomAccessZFile {
+ char mode; /* 'w' : write mode; 'r' : read mode */
+ int file_type;
+ /* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */
+#ifdef _USE_KNETFILE
+ union {
+ knetFile *fpr;
+ int fpw;
+ } x;
+#else
+ int filedes; /* the file descriptor */
+#endif
+ z_stream *stream;
+ ZBlockIndex *index;
+ int64_t in, out, end, src_end;
+ /* in: n bytes total in; out: n bytes total out; */
+ /* end: the end of all data blocks, while the start of index; src_end: the true end position in uncompressed file */
+ int buf_flush; // buffer should be flush, suspend inflate util buffer is empty
+ int64_t block_pos, block_off, next_block_pos;
+ /* block_pos: the start postiion of current block in compressed file */
+ /* block_off: tell how many bytes have been read from current block */
+ void *inbuf, *outbuf;
+ int header_size;
+ gz_header *header;
+ /* header is used to transfer inflate_state->mode from HEAD to TYPE after call inflateReset */
+ int buf_off, buf_len;
+ int z_err, z_eof;
+ int seekable;
+ /* Indice where the source is seekable */
+ int load_index;
+ /* set has_index to 0 in mode 'w', then index will be discarded */
+} RAZF;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ RAZF* razf_dopen(int data_fd, const char *mode);
+ RAZF *razf_open(const char *fn, const char *mode);
+ int razf_write(RAZF* rz, const void *data, int size);
+ int razf_read(RAZF* rz, void *data, int size);
+ int64_t razf_seek(RAZF* rz, int64_t pos, int where);
+ void razf_close(RAZF* rz);
+
+#define razf_tell(rz) ((rz)->out)
+
+ RAZF* razf_open2(const char *filename, const char *mode);
+ RAZF* razf_dopen2(int fd, const char *mode);
+ uint64_t razf_tell2(RAZF *rz);
+ int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/samtools-0.1.18/razip.c b/src/samtools-0.1.18/razip.c
new file mode 100644
index 0000000..825e732
--- /dev/null
+++ b/src/samtools-0.1.18/razip.c
@@ -0,0 +1,141 @@
+#include <stdio.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <string.h>
+#include "razf.h"
+
+#define WINDOW_SIZE 4096
+
+static int razf_main_usage()
+{
+ printf("\n");
+ printf("Usage: razip [options] [file] ...\n\n");
+ printf("Options: -c write on standard output, keep original files unchanged\n");
+ printf(" -d decompress\n");
+ printf(" -l list compressed file contents\n");
+ printf(" -b INT decompress at INT position in the uncompressed file\n");
+ printf(" -s INT decompress INT bytes in the uncompressed file\n");
+ printf(" -h give this help\n");
+ printf("\n");
+ return 0;
+}
+
+static int write_open(const char *fn, int is_forced)
+{
+ int fd = -1;
+ char c;
+ if (!is_forced) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
+ printf("razip: %s already exists; do you wish to overwrite (y or n)? ", fn);
+ scanf("%c", &c);
+ if (c != 'Y' && c != 'y') {
+ printf("razip: not overwritten\n");
+ exit(1);
+ }
+ }
+ }
+ if (fd < 0) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
+ fprintf(stderr, "razip: %s: Fail to write\n", fn);
+ exit(1);
+ }
+ }
+ return fd;
+}
+
+int main(int argc, char **argv)
+{
+ int c, compress, pstdout, is_forced;
+ RAZF *rz;
+ void *buffer;
+ long start, end, size;
+
+ compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
+ while((c = getopt(argc, argv, "cdlhfb:s:")) >= 0){
+ switch(c){
+ case 'h': return razf_main_usage();
+ case 'd': compress = 0; break;
+ case 'c': pstdout = 1; break;
+ case 'l': compress = 2; break;
+ case 'b': start = atol(optarg); break;
+ case 's': size = atol(optarg); break;
+ case 'f': is_forced = 1; break;
+ }
+ }
+ if (size >= 0) end = start + size;
+ if(end >= 0 && end < start){
+ fprintf(stderr, " -- Illegal region: [%ld, %ld] --\n", start, end);
+ return 1;
+ }
+ if(compress == 1){
+ int f_src, f_dst = -1;
+ if(argc > optind){
+ if((f_src = open(argv[optind], O_RDONLY)) < 0){
+ fprintf(stderr, " -- Cannot open file: %s --\n", argv[optind]);
+ return 1;
+ }
+ if(pstdout){
+ f_dst = fileno(stdout);
+ } else {
+ char *name = malloc(sizeof(strlen(argv[optind]) + 5));
+ strcpy(name, argv[optind]);
+ strcat(name, ".rz");
+ f_dst = write_open(name, is_forced);
+ if (f_dst < 0) return 1;
+ free(name);
+ }
+ } else if(pstdout){
+ f_src = fileno(stdin);
+ f_dst = fileno(stdout);
+ } else return razf_main_usage();
+ rz = razf_dopen(f_dst, "w");
+ buffer = malloc(WINDOW_SIZE);
+ while((c = read(f_src, buffer, WINDOW_SIZE)) > 0) razf_write(rz, buffer, c);
+ razf_close(rz); // f_dst will be closed here
+ if (argc > optind && !pstdout) unlink(argv[optind]);
+ free(buffer);
+ close(f_src);
+ return 0;
+ } else {
+ if(argc <= optind) return razf_main_usage();
+ if(compress == 2){
+ rz = razf_open(argv[optind], "r");
+ if(rz->file_type == FILE_TYPE_RZ) {
+ printf("%20s%20s%7s %s\n", "compressed", "uncompressed", "ratio", "name");
+ printf("%20lld%20lld%6.1f%% %s\n", (long long)rz->end, (long long)rz->src_end, rz->end * 100.0f / rz->src_end,
+ argv[optind]);
+ } else fprintf(stdout, "%s is not a regular rz file\n", argv[optind]);
+ } else {
+ int f_dst;
+ if (argc > optind && !pstdout) {
+ char *name;
+ if (strstr(argv[optind], ".rz") - argv[optind] != strlen(argv[optind]) - 3) {
+ printf("razip: %s: unknown suffix -- ignored\n", argv[optind]);
+ return 1;
+ }
+ name = strdup(argv[optind]);
+ name[strlen(name) - 3] = '\0';
+ f_dst = write_open(name, is_forced);
+ free(name);
+ } else f_dst = fileno(stdout);
+ rz = razf_open(argv[optind], "r");
+ buffer = malloc(WINDOW_SIZE);
+ razf_seek(rz, start, SEEK_SET);
+ while(1){
+ if(end < 0) c = razf_read(rz, buffer, WINDOW_SIZE);
+ else c = razf_read(rz, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
+ if(c <= 0) break;
+ start += c;
+ write(f_dst, buffer, c);
+ if(end >= 0 && start >= end) break;
+ }
+ free(buffer);
+ if (!pstdout) unlink(argv[optind]);
+ }
+ razf_close(rz);
+ return 0;
+ }
+}
+
diff --git a/src/samtools-0.1.18/sam.c b/src/samtools-0.1.18/sam.c
new file mode 100644
index 0000000..f026bc8
--- /dev/null
+++ b/src/samtools-0.1.18/sam.c
@@ -0,0 +1,179 @@
+#include <string.h>
+#include <unistd.h>
+#include "faidx.h"
+#include "sam.h"
+
+#define TYPE_BAM 1
+#define TYPE_READ 2
+
+bam_header_t *bam_header_dup(const bam_header_t *h0)
+{
+ bam_header_t *h;
+ int i;
+ h = bam_header_init();
+ *h = *h0;
+ h->hash = h->dict = h->rg2lib = 0;
+ h->text = (char*)calloc(h->l_text + 1, 1);
+ memcpy(h->text, h0->text, h->l_text);
+ h->target_len = (uint32_t*)calloc(h->n_targets, 4);
+ h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
+ for (i = 0; i < h->n_targets; ++i) {
+ h->target_len[i] = h0->target_len[i];
+ h->target_name[i] = strdup(h0->target_name[i]);
+ }
+ return h;
+}
+static void append_header_text(bam_header_t *header, char* text, int len)
+{
+ int x = header->l_text + 1;
+ int y = header->l_text + len + 1; // 1 byte null
+ if (text == 0) return;
+ kroundup32(x);
+ kroundup32(y);
+ if (x < y) header->text = (char*)realloc(header->text, y);
+ strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
+ header->l_text += len;
+ header->text[header->l_text] = 0;
+}
+
+samfile_t *samopen(const char *fn, const char *mode, const void *aux)
+{
+ samfile_t *fp;
+ fp = (samfile_t*)calloc(1, sizeof(samfile_t));
+ if (strchr(mode, 'r')) { // read
+ fp->type |= TYPE_READ;
+ if (strchr(mode, 'b')) { // binary
+ fp->type |= TYPE_BAM;
+ fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
+ if (fp->x.bam == 0) goto open_err_ret;
+ fp->header = bam_header_read(fp->x.bam);
+ } else { // text
+ fp->x.tamr = sam_open(fn);
+ if (fp->x.tamr == 0) goto open_err_ret;
+ fp->header = sam_header_read(fp->x.tamr);
+ if (fp->header->n_targets == 0) { // no @SQ fields
+ if (aux) { // check if aux is present
+ bam_header_t *textheader = fp->header;
+ fp->header = sam_header_read2((const char*)aux);
+ if (fp->header == 0) goto open_err_ret;
+ append_header_text(fp->header, textheader->text, textheader->l_text);
+ bam_header_destroy(textheader);
+ }
+ if (fp->header->n_targets == 0 && bam_verbose >= 1)
+ fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
+ } else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
+ }
+ } else if (strchr(mode, 'w')) { // write
+ fp->header = bam_header_dup((const bam_header_t*)aux);
+ if (strchr(mode, 'b')) { // binary
+ char bmode[3];
+ int i, compress_level = -1;
+ for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break;
+ if (mode[i]) compress_level = mode[i] - '0';
+ if (strchr(mode, 'u')) compress_level = 0;
+ bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0;
+ fp->type |= TYPE_BAM;
+ fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
+ if (fp->x.bam == 0) goto open_err_ret;
+ bam_header_write(fp->x.bam, fp->header);
+ } else { // text
+ // open file
+ fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
+ if (fp->x.tamr == 0) goto open_err_ret;
+ if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
+ else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
+ else fp->type |= BAM_OFDEC<<2;
+ // write header
+ if (strchr(mode, 'h')) {
+ int i;
+ bam_header_t *alt;
+ // parse the header text
+ alt = bam_header_init();
+ alt->l_text = fp->header->l_text; alt->text = fp->header->text;
+ sam_header_parse(alt);
+ alt->l_text = 0; alt->text = 0;
+ // check if there are @SQ lines in the header
+ fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL
+ if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
+ if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1)
+ fprintf(stderr, "[samopen] inconsistent number of target sequences. Output the text header.\n");
+ } else { // then dump ->target_{name,len}
+ for (i = 0; i < fp->header->n_targets; ++i)
+ fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
+ }
+ bam_header_destroy(alt);
+ }
+ }
+ }
+ return fp;
+
+open_err_ret:
+ free(fp);
+ return 0;
+}
+
+void samclose(samfile_t *fp)
+{
+ if (fp == 0) return;
+ if (fp->header) bam_header_destroy(fp->header);
+ if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
+ else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
+ else fclose(fp->x.tamw);
+ free(fp);
+}
+
+int samread(samfile_t *fp, bam1_t *b)
+{
+ if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
+ if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
+ else return sam_read1(fp->x.tamr, fp->header, b);
+}
+
+int samwrite(samfile_t *fp, const bam1_t *b)
+{
+ if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
+ if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
+ else {
+ char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
+ int l = strlen(s);
+ fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
+ free(s);
+ return l + 1;
+ }
+}
+
+int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
+{
+ bam_plbuf_t *buf;
+ int ret;
+ bam1_t *b;
+ b = bam_init1();
+ buf = bam_plbuf_init(func, func_data);
+ bam_plbuf_set_mask(buf, mask);
+ while ((ret = samread(fp, b)) >= 0)
+ bam_plbuf_push(b, buf);
+ bam_plbuf_push(0, buf);
+ bam_plbuf_destroy(buf);
+ bam_destroy1(b);
+ return 0;
+}
+
+char *samfaipath(const char *fn_ref)
+{
+ char *fn_list = 0;
+ if (fn_ref == 0) return 0;
+ fn_list = calloc(strlen(fn_ref) + 5, 1);
+ strcat(strcpy(fn_list, fn_ref), ".fai");
+ if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
+ if (access(fn_ref, R_OK) == -1) {
+ fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
+ } else {
+ if (bam_verbose >= 3) fprintf(stderr, "[samfaipath] build FASTA index...\n");
+ if (fai_build(fn_ref) == -1) {
+ fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
+ free(fn_list); fn_list = 0;
+ }
+ }
+ }
+ return fn_list;
+}
diff --git a/src/samtools-0.1.18/sam.h b/src/samtools-0.1.18/sam.h
new file mode 100644
index 0000000..0b87194
--- /dev/null
+++ b/src/samtools-0.1.18/sam.h
@@ -0,0 +1,98 @@
+#ifndef BAM_SAM_H
+#define BAM_SAM_H
+
+#include "bam.h"
+
+/*!
+ @header
+
+ This file provides higher level of I/O routines and unifies the APIs
+ for SAM and BAM formats. These APIs are more convenient and
+ recommended.
+
+ @copyright Genome Research Ltd.
+ */
+
+/*! @typedef
+ @abstract SAM/BAM file handler
+ @field type type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format
+ @field bam BAM file handler; valid if (type&1) == 1
+ @field tamr SAM file handler for reading; valid if type == 2
+ @field tamw SAM file handler for writing; valid if type == 0
+ @field header header struct
+ */
+typedef struct {
+ int type;
+ union {
+ tamFile tamr;
+ bamFile bam;
+ FILE *tamw;
+ } x;
+ bam_header_t *header;
+} samfile_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ /*!
+ @abstract Open a SAM/BAM file
+
+ @param fn SAM/BAM file name; "-" is recognized as stdin (for
+ reading) or stdout (for writing).
+
+ @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading,
+ 'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output,
+ 'h' for outputing header in SAM, 'x' for HEX flag and 'X' for
+ string flag. If 'b' present, it must immediately follow 'r' or
+ 'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX",
+ "rb", "wb" and "wbu" exclusively.
+
+ @param aux auxiliary data; if mode[0]=='w', aux points to
+ bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM
+ are absent, aux points the file name of the list of the reference;
+ aux is not used otherwise. If @SQ header lines are present in SAM,
+ aux is not used, either.
+
+ @return SAM/BAM file handler
+ */
+ samfile_t *samopen(const char *fn, const char *mode, const void *aux);
+
+ /*!
+ @abstract Close a SAM/BAM handler
+ @param fp file handler to be closed
+ */
+ void samclose(samfile_t *fp);
+
+ /*!
+ @abstract Read one alignment
+ @param fp file handler
+ @param b alignment
+ @return bytes read
+ */
+ int samread(samfile_t *fp, bam1_t *b);
+
+ /*!
+ @abstract Write one alignment
+ @param fp file handler
+ @param b alignment
+ @return bytes written
+ */
+ int samwrite(samfile_t *fp, const bam1_t *b);
+
+ /*!
+ @abstract Get the pileup for a whole alignment file
+ @param fp file handler
+ @param mask mask transferred to bam_plbuf_set_mask()
+ @param func user defined function called in the pileup process
+ #param data user provided data for func()
+ */
+ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data);
+
+ char *samfaipath(const char *fn_ref);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/samtools-0.1.18/sam_header.c b/src/samtools-0.1.18/sam_header.c
new file mode 100644
index 0000000..f4c8a3b
--- /dev/null
+++ b/src/samtools-0.1.18/sam_header.c
@@ -0,0 +1,736 @@
+#include "sam_header.h"
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <stdarg.h>
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(str, const char *)
+
+struct _HeaderList
+{
+ struct _HeaderList *last; // Hack: Used and maintained only by list_append_to_end. Maintained in the root node only.
+ struct _HeaderList *next;
+ void *data;
+};
+typedef struct _HeaderList list_t;
+typedef list_t HeaderDict;
+
+typedef struct
+{
+ char key[2];
+ char *value;
+}
+HeaderTag;
+
+typedef struct
+{
+ char type[2];
+ list_t *tags;
+}
+HeaderLine;
+
+const char *o_hd_tags[] = {"SO","GO",NULL};
+const char *r_hd_tags[] = {"VN",NULL};
+
+const char *o_sq_tags[] = {"AS","M5","UR","SP",NULL};
+const char *r_sq_tags[] = {"SN","LN",NULL};
+const char *u_sq_tags[] = {"SN",NULL};
+
+const char *o_rg_tags[] = {"CN","DS","DT","FO","KS","LB","PG","PI","PL","PU","SM",NULL};
+const char *r_rg_tags[] = {"ID",NULL};
+const char *u_rg_tags[] = {"ID",NULL};
+
+const char *o_pg_tags[] = {"VN","CL",NULL};
+const char *r_pg_tags[] = {"ID",NULL};
+
+const char *types[] = {"HD","SQ","RG","PG","CO",NULL};
+const char **optional_tags[] = {o_hd_tags,o_sq_tags,o_rg_tags,o_pg_tags,NULL,NULL};
+const char **required_tags[] = {r_hd_tags,r_sq_tags,r_rg_tags,r_pg_tags,NULL,NULL};
+const char **unique_tags[] = {NULL, u_sq_tags,u_rg_tags,NULL,NULL,NULL};
+
+
+static void debug(const char *format, ...)
+{
+ va_list ap;
+ va_start(ap, format);
+ vfprintf(stderr, format, ap);
+ va_end(ap);
+}
+
+#if 0
+// Replaced by list_append_to_end
+static list_t *list_prepend(list_t *root, void *data)
+{
+ list_t *l = malloc(sizeof(list_t));
+ l->next = root;
+ l->data = data;
+ return l;
+}
+#endif
+
+// Relies on the root->last being correct. Do not use with the other list_*
+// routines unless they are fixed to modify root->last as well.
+static list_t *list_append_to_end(list_t *root, void *data)
+{
+ list_t *l = malloc(sizeof(list_t));
+ l->last = l;
+ l->next = NULL;
+ l->data = data;
+
+ if ( !root )
+ return l;
+
+ root->last->next = l;
+ root->last = l;
+ return root;
+}
+
+static list_t *list_append(list_t *root, void *data)
+{
+ list_t *l = root;
+ while (l && l->next)
+ l = l->next;
+ if ( l )
+ {
+ l->next = malloc(sizeof(list_t));
+ l = l->next;
+ }
+ else
+ {
+ l = malloc(sizeof(list_t));
+ root = l;
+ }
+ l->data = data;
+ l->next = NULL;
+ return root;
+}
+
+static void list_free(list_t *root)
+{
+ list_t *l = root;
+ while (root)
+ {
+ l = root;
+ root = root->next;
+ free(l);
+ }
+}
+
+
+
+// Look for a tag "XY" in a predefined const char *[] array.
+static int tag_exists(const char *tag, const char **tags)
+{
+ int itag=0;
+ if ( !tags ) return -1;
+ while ( tags[itag] )
+ {
+ if ( tags[itag][0]==tag[0] && tags[itag][1]==tag[1] ) return itag;
+ itag++;
+ }
+ return -1;
+}
+
+
+
+// Mimics the behaviour of getline, except it returns pointer to the next chunk of the text
+// or NULL if everything has been read. The lineptr should be freed by the caller. The
+// newline character is stripped.
+static const char *nextline(char **lineptr, size_t *n, const char *text)
+{
+ int len;
+ const char *to = text;
+
+ if ( !*to ) return NULL;
+
+ while ( *to && *to!='\n' && *to!='\r' ) to++;
+ len = to - text + 1;
+
+ if ( *to )
+ {
+ // Advance the pointer for the next call
+ if ( *to=='\n' ) to++;
+ else if ( *to=='\r' && *(to+1)=='\n' ) to+=2;
+ }
+ if ( !len )
+ return to;
+
+ if ( !*lineptr )
+ {
+ *lineptr = malloc(len);
+ *n = len;
+ }
+ else if ( *n<len )
+ {
+ *lineptr = realloc(*lineptr, len);
+ *n = len;
+ }
+ if ( !*lineptr ) {
+ debug("[nextline] Insufficient memory!\n");
+ return 0;
+ }
+
+ memcpy(*lineptr,text,len);
+ (*lineptr)[len-1] = 0;
+
+ return to;
+}
+
+// name points to "XY", value_from points to the first character of the value string and
+// value_to points to the last character of the value string.
+static HeaderTag *new_tag(const char *name, const char *value_from, const char *value_to)
+{
+ HeaderTag *tag = malloc(sizeof(HeaderTag));
+ int len = value_to-value_from+1;
+
+ tag->key[0] = name[0];
+ tag->key[1] = name[1];
+ tag->value = malloc(len+1);
+ memcpy(tag->value,value_from,len+1);
+ tag->value[len] = 0;
+ return tag;
+}
+
+static HeaderTag *header_line_has_tag(HeaderLine *hline, const char *key)
+{
+ list_t *tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *tag = tags->data;
+ if ( tag->key[0]==key[0] && tag->key[1]==key[1] ) return tag;
+ tags = tags->next;
+ }
+ return NULL;
+}
+
+
+// Return codes:
+// 0 .. different types or unique tags differ or conflicting tags, cannot be merged
+// 1 .. all tags identical -> no need to merge, drop one
+// 2 .. the unique tags match and there are some conflicting tags (same tag, different value) -> error, cannot be merged nor duplicated
+// 3 .. there are some missing complementary tags and no unique conflict -> can be merged into a single line
+static int sam_header_compare_lines(HeaderLine *hline1, HeaderLine *hline2)
+{
+ HeaderTag *t1, *t2;
+
+ if ( hline1->type[0]!=hline2->type[0] || hline1->type[1]!=hline2->type[1] )
+ return 0;
+
+ int itype = tag_exists(hline1->type,types);
+ if ( itype==-1 ) {
+ debug("[sam_header_compare_lines] Unknown type [%c%c]\n", hline1->type[0],hline1->type[1]);
+ return -1; // FIXME (lh3): error; I do not know how this will be handled in Petr's code
+ }
+
+ if ( unique_tags[itype] )
+ {
+ t1 = header_line_has_tag(hline1,unique_tags[itype][0]);
+ t2 = header_line_has_tag(hline2,unique_tags[itype][0]);
+ if ( !t1 || !t2 ) // this should never happen, the unique tags are required
+ return 2;
+
+ if ( strcmp(t1->value,t2->value) )
+ return 0; // the unique tags differ, cannot be merged
+ }
+ if ( !required_tags[itype] && !optional_tags[itype] )
+ {
+ t1 = hline1->tags->data;
+ t2 = hline2->tags->data;
+ if ( !strcmp(t1->value,t2->value) ) return 1; // identical comments
+ return 0;
+ }
+
+ int missing=0, itag=0;
+ while ( required_tags[itype] && required_tags[itype][itag] )
+ {
+ t1 = header_line_has_tag(hline1,required_tags[itype][itag]);
+ t2 = header_line_has_tag(hline2,required_tags[itype][itag]);
+ if ( !t1 && !t2 )
+ return 2; // this should never happen
+ else if ( !t1 || !t2 )
+ missing = 1; // there is some tag missing in one of the hlines
+ else if ( strcmp(t1->value,t2->value) )
+ {
+ if ( unique_tags[itype] )
+ return 2; // the lines have a matching unique tag but have a conflicting tag
+
+ return 0; // the lines contain conflicting tags, cannot be merged
+ }
+ itag++;
+ }
+ itag = 0;
+ while ( optional_tags[itype] && optional_tags[itype][itag] )
+ {
+ t1 = header_line_has_tag(hline1,optional_tags[itype][itag]);
+ t2 = header_line_has_tag(hline2,optional_tags[itype][itag]);
+ if ( !t1 && !t2 )
+ {
+ itag++;
+ continue;
+ }
+ if ( !t1 || !t2 )
+ missing = 1; // there is some tag missing in one of the hlines
+ else if ( strcmp(t1->value,t2->value) )
+ {
+ if ( unique_tags[itype] )
+ return 2; // the lines have a matching unique tag but have a conflicting tag
+
+ return 0; // the lines contain conflicting tags, cannot be merged
+ }
+ itag++;
+ }
+ if ( missing ) return 3; // there are some missing complementary tags with no conflicts, can be merged
+ return 1;
+}
+
+
+static HeaderLine *sam_header_line_clone(const HeaderLine *hline)
+{
+ list_t *tags;
+ HeaderLine *out = malloc(sizeof(HeaderLine));
+ out->type[0] = hline->type[0];
+ out->type[1] = hline->type[1];
+ out->tags = NULL;
+
+ tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *old = tags->data;
+
+ HeaderTag *new = malloc(sizeof(HeaderTag));
+ new->key[0] = old->key[0];
+ new->key[1] = old->key[1];
+ new->value = strdup(old->value);
+ out->tags = list_append(out->tags, new);
+
+ tags = tags->next;
+ }
+ return out;
+}
+
+static int sam_header_line_merge_with(HeaderLine *out_hline, const HeaderLine *tmpl_hline)
+{
+ list_t *tmpl_tags;
+
+ if ( out_hline->type[0]!=tmpl_hline->type[0] || out_hline->type[1]!=tmpl_hline->type[1] )
+ return 0;
+
+ tmpl_tags = tmpl_hline->tags;
+ while (tmpl_tags)
+ {
+ HeaderTag *tmpl_tag = tmpl_tags->data;
+ HeaderTag *out_tag = header_line_has_tag(out_hline, tmpl_tag->key);
+ if ( !out_tag )
+ {
+ HeaderTag *tag = malloc(sizeof(HeaderTag));
+ tag->key[0] = tmpl_tag->key[0];
+ tag->key[1] = tmpl_tag->key[1];
+ tag->value = strdup(tmpl_tag->value);
+ out_hline->tags = list_append(out_hline->tags,tag);
+ }
+ tmpl_tags = tmpl_tags->next;
+ }
+ return 1;
+}
+
+
+static HeaderLine *sam_header_line_parse(const char *headerLine)
+{
+ HeaderLine *hline;
+ HeaderTag *tag;
+ const char *from, *to;
+ from = headerLine;
+
+ if ( *from != '@' ) {
+ debug("[sam_header_line_parse] expected '@', got [%s]\n", headerLine);
+ return 0;
+ }
+ to = ++from;
+
+ while (*to && *to!='\t') to++;
+ if ( to-from != 2 ) {
+ debug("[sam_header_line_parse] expected '@XY', got [%s]\nHint: The header tags must be tab-separated.\n", headerLine);
+ return 0;
+ }
+
+ hline = malloc(sizeof(HeaderLine));
+ hline->type[0] = from[0];
+ hline->type[1] = from[1];
+ hline->tags = NULL;
+
+ int itype = tag_exists(hline->type, types);
+
+ from = to;
+ while (*to && *to=='\t') to++;
+ if ( to-from != 1 ) {
+ debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+ return 0;
+ }
+ from = to;
+ while (*from)
+ {
+ while (*to && *to!='\t') to++;
+
+ if ( !required_tags[itype] && !optional_tags[itype] )
+ {
+ // CO is a special case, it can contain anything, including tabs
+ if ( *to ) { to++; continue; }
+ tag = new_tag(" ",from,to-1);
+ }
+ else
+ tag = new_tag(from,from+3,to-1);
+
+ if ( header_line_has_tag(hline,tag->key) )
+ debug("The tag '%c%c' present (at least) twice on line [%s]\n", tag->key[0],tag->key[1], headerLine);
+ hline->tags = list_append(hline->tags, tag);
+
+ from = to;
+ while (*to && *to=='\t') to++;
+ if ( *to && to-from != 1 ) {
+ debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+ return 0;
+ }
+
+ from = to;
+ }
+ return hline;
+}
+
+
+// Must be of an existing type, all tags must be recognised and all required tags must be present
+static int sam_header_line_validate(HeaderLine *hline)
+{
+ list_t *tags;
+ HeaderTag *tag;
+ int itype, itag;
+
+ // Is the type correct?
+ itype = tag_exists(hline->type, types);
+ if ( itype==-1 )
+ {
+ debug("The type [%c%c] not recognised.\n", hline->type[0],hline->type[1]);
+ return 0;
+ }
+
+ // Has all required tags?
+ itag = 0;
+ while ( required_tags[itype] && required_tags[itype][itag] )
+ {
+ if ( !header_line_has_tag(hline,required_tags[itype][itag]) )
+ {
+ debug("The tag [%c%c] required for [%c%c] not present.\n", required_tags[itype][itag][0],required_tags[itype][itag][1],
+ hline->type[0],hline->type[1]);
+ return 0;
+ }
+ itag++;
+ }
+
+ // Are all tags recognised?
+ tags = hline->tags;
+ while ( tags )
+ {
+ tag = tags->data;
+ if ( !tag_exists(tag->key,required_tags[itype]) && !tag_exists(tag->key,optional_tags[itype]) )
+ {
+ debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
+ return 0;
+ }
+ tags = tags->next;
+ }
+
+ return 1;
+}
+
+
+static void print_header_line(FILE *fp, HeaderLine *hline)
+{
+ list_t *tags = hline->tags;
+ HeaderTag *tag;
+
+ fprintf(fp, "@%c%c", hline->type[0],hline->type[1]);
+ while (tags)
+ {
+ tag = tags->data;
+
+ fprintf(fp, "\t");
+ if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
+ fprintf(fp, "%c%c:", tag->key[0],tag->key[1]);
+ fprintf(fp, "%s", tag->value);
+
+ tags = tags->next;
+ }
+ fprintf(fp,"\n");
+}
+
+
+static void sam_header_line_free(HeaderLine *hline)
+{
+ list_t *tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *tag = tags->data;
+ free(tag->value);
+ free(tag);
+ tags = tags->next;
+ }
+ list_free(hline->tags);
+ free(hline);
+}
+
+void sam_header_free(void *_header)
+{
+ HeaderDict *header = (HeaderDict*)_header;
+ list_t *hlines = header;
+ while (hlines)
+ {
+ sam_header_line_free(hlines->data);
+ hlines = hlines->next;
+ }
+ list_free(header);
+}
+
+HeaderDict *sam_header_clone(const HeaderDict *dict)
+{
+ HeaderDict *out = NULL;
+ while (dict)
+ {
+ HeaderLine *hline = dict->data;
+ out = list_append(out, sam_header_line_clone(hline));
+ dict = dict->next;
+ }
+ return out;
+}
+
+// Returns a newly allocated string
+char *sam_header_write(const void *_header)
+{
+ const HeaderDict *header = (const HeaderDict*)_header;
+ char *out = NULL;
+ int len=0, nout=0;
+ const list_t *hlines;
+
+ // Calculate the length of the string to allocate
+ hlines = header;
+ while (hlines)
+ {
+ len += 4; // @XY and \n
+
+ HeaderLine *hline = hlines->data;
+ list_t *tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *tag = tags->data;
+ len += strlen(tag->value) + 1; // \t
+ if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
+ len += strlen(tag->value) + 3; // XY:
+ tags = tags->next;
+ }
+ hlines = hlines->next;
+ }
+
+ nout = 0;
+ out = malloc(len+1);
+ hlines = header;
+ while (hlines)
+ {
+ HeaderLine *hline = hlines->data;
+
+ nout += sprintf(out+nout,"@%c%c",hline->type[0],hline->type[1]);
+
+ list_t *tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *tag = tags->data;
+ nout += sprintf(out+nout,"\t");
+ if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
+ nout += sprintf(out+nout,"%c%c:", tag->key[0],tag->key[1]);
+ nout += sprintf(out+nout,"%s", tag->value);
+ tags = tags->next;
+ }
+ hlines = hlines->next;
+ nout += sprintf(out+nout,"\n");
+ }
+ out[len] = 0;
+ return out;
+}
+
+void *sam_header_parse2(const char *headerText)
+{
+ list_t *hlines = NULL;
+ HeaderLine *hline;
+ const char *text;
+ char *buf=NULL;
+ size_t nbuf = 0;
+ int tovalidate = 0;
+
+ if ( !headerText )
+ return 0;
+
+ text = headerText;
+ while ( (text=nextline(&buf, &nbuf, text)) )
+ {
+ hline = sam_header_line_parse(buf);
+ if ( hline && (!tovalidate || sam_header_line_validate(hline)) )
+ // With too many (~250,000) reference sequences the header parsing was too slow with list_append.
+ hlines = list_append_to_end(hlines, hline);
+ else
+ {
+ if (hline) sam_header_line_free(hline);
+ sam_header_free(hlines);
+ if ( buf ) free(buf);
+ return NULL;
+ }
+ }
+ if ( buf ) free(buf);
+
+ return hlines;
+}
+
+void *sam_header2tbl(const void *_dict, char type[2], char key_tag[2], char value_tag[2])
+{
+ const HeaderDict *dict = (const HeaderDict*)_dict;
+ const list_t *l = dict;
+ khash_t(str) *tbl = kh_init(str);
+ khiter_t k;
+ int ret;
+
+ if (_dict == 0) return tbl; // return an empty (not null) hash table
+ while (l)
+ {
+ HeaderLine *hline = l->data;
+ if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
+ {
+ l = l->next;
+ continue;
+ }
+
+ HeaderTag *key, *value;
+ key = header_line_has_tag(hline,key_tag);
+ value = header_line_has_tag(hline,value_tag);
+ if ( !key || !value )
+ {
+ l = l->next;
+ continue;
+ }
+
+ k = kh_get(str, tbl, key->value);
+ if ( k != kh_end(tbl) )
+ debug("[sam_header_lookup_table] They key %s not unique.\n", key->value);
+ k = kh_put(str, tbl, key->value, &ret);
+ kh_value(tbl, k) = value->value;
+
+ l = l->next;
+ }
+ return tbl;
+}
+
+char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n)
+{
+ const HeaderDict *dict = (const HeaderDict*)_dict;
+ const list_t *l = dict;
+ int max, n;
+ char **ret;
+
+ ret = 0; *_n = max = n = 0;
+ while (l)
+ {
+ HeaderLine *hline = l->data;
+ if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
+ {
+ l = l->next;
+ continue;
+ }
+
+ HeaderTag *key;
+ key = header_line_has_tag(hline,key_tag);
+ if ( !key )
+ {
+ l = l->next;
+ continue;
+ }
+
+ if (n == max) {
+ max = max? max<<1 : 4;
+ ret = realloc(ret, max * sizeof(void*));
+ }
+ ret[n++] = key->value;
+
+ l = l->next;
+ }
+ *_n = n;
+ return ret;
+}
+
+const char *sam_tbl_get(void *h, const char *key)
+{
+ khash_t(str) *tbl = (khash_t(str)*)h;
+ khint_t k;
+ k = kh_get(str, tbl, key);
+ return k == kh_end(tbl)? 0 : kh_val(tbl, k);
+}
+
+int sam_tbl_size(void *h)
+{
+ khash_t(str) *tbl = (khash_t(str)*)h;
+ return h? kh_size(tbl) : 0;
+}
+
+void sam_tbl_destroy(void *h)
+{
+ khash_t(str) *tbl = (khash_t(str)*)h;
+ kh_destroy(str, tbl);
+}
+
+void *sam_header_merge(int n, const void **_dicts)
+{
+ const HeaderDict **dicts = (const HeaderDict**)_dicts;
+ HeaderDict *out_dict;
+ int idict, status;
+
+ if ( n<2 ) return NULL;
+
+ out_dict = sam_header_clone(dicts[0]);
+
+ for (idict=1; idict<n; idict++)
+ {
+ const list_t *tmpl_hlines = dicts[idict];
+
+ while ( tmpl_hlines )
+ {
+ list_t *out_hlines = out_dict;
+ int inserted = 0;
+ while ( out_hlines )
+ {
+ status = sam_header_compare_lines(tmpl_hlines->data, out_hlines->data);
+ if ( status==0 )
+ {
+ out_hlines = out_hlines->next;
+ continue;
+ }
+
+ if ( status==2 )
+ {
+ print_header_line(stderr,tmpl_hlines->data);
+ print_header_line(stderr,out_hlines->data);
+ debug("Conflicting lines, cannot merge the headers.\n");
+ return 0;
+ }
+ if ( status==3 )
+ sam_header_line_merge_with(out_hlines->data, tmpl_hlines->data);
+
+ inserted = 1;
+ break;
+ }
+ if ( !inserted )
+ out_dict = list_append(out_dict, sam_header_line_clone(tmpl_hlines->data));
+
+ tmpl_hlines = tmpl_hlines->next;
+ }
+ }
+
+ return out_dict;
+}
+
+
diff --git a/src/samtools-0.1.18/sam_header.h b/src/samtools-0.1.18/sam_header.h
new file mode 100644
index 0000000..e5c754f
--- /dev/null
+++ b/src/samtools-0.1.18/sam_header.h
@@ -0,0 +1,24 @@
+#ifndef __SAM_HEADER_H__
+#define __SAM_HEADER_H__
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ void *sam_header_parse2(const char *headerText);
+ void *sam_header_merge(int n, const void **dicts);
+ void sam_header_free(void *header);
+ char *sam_header_write(const void *headerDict); // returns a newly allocated string
+
+ char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n);
+
+ void *sam_header2tbl(const void *dict, char type[2], char key_tag[2], char value_tag[2]);
+ const char *sam_tbl_get(void *h, const char *key);
+ int sam_tbl_size(void *h);
+ void sam_tbl_destroy(void *h);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/samtools-0.1.18/sam_view.c b/src/samtools-0.1.18/sam_view.c
new file mode 100644
index 0000000..efda4e8
--- /dev/null
+++ b/src/samtools-0.1.18/sam_view.c
@@ -0,0 +1,406 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <math.h>
+#include "sam_header.h"
+#include "sam.h"
+#include "faidx.h"
+#include "kstring.h"
+#include "khash.h"
+KHASH_SET_INIT_STR(rg)
+
+// When counting records instead of printing them,
+// data passed to the bam_fetch callback is encapsulated in this struct.
+typedef struct {
+ bam_header_t *header;
+ int *count;
+} count_func_data_t;
+
+typedef khash_t(rg) *rghash_t;
+
+// FIXME: we'd better use no global variables...
+static rghash_t g_rghash = 0;
+static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+static float g_subsam = -1;
+static char *g_library, *g_rg;
+static void *g_bed;
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
+
+static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
+{
+ if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
+ return 1;
+ if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
+ return 1;
+ if (g_subsam > 0.) {
+ int x = (int)(g_subsam + .499);
+ uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + x;
+ if (k%1024 / 1024.0 >= g_subsam - x) return 1;
+ }
+ if (g_rg || g_rghash) {
+ uint8_t *s = bam_aux_get(b, "RG");
+ if (s) {
+ if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1;
+ if (g_rghash) {
+ khint_t k = kh_get(rg, g_rghash, (char*)(s + 1));
+ return (k != kh_end(g_rghash))? 0 : 1;
+ }
+ }
+ }
+ if (g_library) {
+ const char *p = bam_get_library((bam_header_t*)h, b);
+ return (p && strcmp(p, g_library) == 0)? 0 : 1;
+ }
+ return 0;
+}
+
+static char *drop_rg(char *hdtxt, rghash_t h, int *len)
+{
+ char *p = hdtxt, *q, *r, *s;
+ kstring_t str;
+ memset(&str, 0, sizeof(kstring_t));
+ while (1) {
+ int toprint = 0;
+ q = strchr(p, '\n');
+ if (q == 0) q = p + strlen(p);
+ if (q - p < 3) break; // the line is too short; then stop
+ if (strncmp(p, "@RG\t", 4) == 0) {
+ int c;
+ khint_t k;
+ if ((r = strstr(p, "\tID:")) != 0) {
+ r += 4;
+ for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
+ c = *s; *s = '\0';
+ k = kh_get(rg, h, r);
+ *s = c;
+ if (k != kh_end(h)) toprint = 1;
+ }
+ } else toprint = 1;
+ if (toprint) {
+ kputsn(p, q - p, &str); kputc('\n', &str);
+ }
+ p = q + 1;
+ }
+ *len = str.l;
+ return str.s;
+}
+
+// callback function for bam_fetch() that prints nonskipped records
+static int view_func(const bam1_t *b, void *data)
+{
+ if (!__g_skip_aln(((samfile_t*)data)->header, b))
+ samwrite((samfile_t*)data, b);
+ return 0;
+}
+
+// callback function for bam_fetch() that counts nonskipped records
+static int count_func(const bam1_t *b, void *data)
+{
+ if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
+ (*((count_func_data_t*)data)->count)++;
+ }
+ return 0;
+}
+
+static int usage(int is_long_help);
+
+int main_samview(int argc, char *argv[])
+{
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
+ int of_type = BAM_OFDEC, is_long_help = 0;
+ int count = 0;
+ samfile_t *in = 0, *out = 0;
+ char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;
+
+ /* parse command-line options */
+ strcpy(in_mode, "r"); strcpy(out_mode, "w");
+ while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:")) >= 0) {
+ switch (c) {
+ case 's': g_subsam = atof(optarg); break;
+ case 'c': is_count = 1; break;
+ case 'S': is_bamin = 0; break;
+ case 'b': is_bamout = 1; break;
+ case 't': fn_list = strdup(optarg); is_bamin = 0; break;
+ case 'h': is_header = 1; break;
+ case 'H': is_header_only = 1; break;
+ case 'o': fn_out = strdup(optarg); break;
+ case 'f': g_flag_on = strtol(optarg, 0, 0); break;
+ case 'F': g_flag_off = strtol(optarg, 0, 0); break;
+ case 'q': g_min_mapQ = atoi(optarg); break;
+ case 'u': compress_level = 0; break;
+ case '1': compress_level = 1; break;
+ case 'l': g_library = strdup(optarg); break;
+ case 'L': g_bed = bed_read(optarg); break;
+ case 'r': g_rg = strdup(optarg); break;
+ case 'R': fn_rg = strdup(optarg); break;
+ case 'x': of_type = BAM_OFHEX; break;
+ case 'X': of_type = BAM_OFSTR; break;
+ case '?': is_long_help = 1; break;
+ case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
+ default: return usage(is_long_help);
+ }
+ }
+ if (compress_level >= 0) is_bamout = 1;
+ if (is_header_only) is_header = 1;
+ if (is_bamout) strcat(out_mode, "b");
+ else {
+ if (of_type == BAM_OFHEX) strcat(out_mode, "x");
+ else if (of_type == BAM_OFSTR) strcat(out_mode, "X");
+ }
+ if (is_bamin) strcat(in_mode, "b");
+ if (is_header) strcat(out_mode, "h");
+ if (compress_level >= 0) {
+ char tmp[2];
+ tmp[0] = compress_level + '0'; tmp[1] = '\0';
+ strcat(out_mode, tmp);
+ }
+ if (argc == optind) return usage(is_long_help); // potential memory leak...
+
+ // read the list of read groups
+ if (fn_rg) {
+ FILE *fp_rg;
+ char buf[1024];
+ int ret;
+ g_rghash = kh_init(rg);
+ fp_rg = fopen(fn_rg, "r");
+ while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but bear me...
+ kh_put(rg, g_rghash, strdup(buf), &ret); // we'd better check duplicates...
+ fclose(fp_rg);
+ }
+
+ // generate the fn_list if necessary
+ if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
+ // open file handlers
+ if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
+ fprintf(stderr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]);
+ ret = 1;
+ goto view_end;
+ }
+ if (in->header == 0) {
+ fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]);
+ ret = 1;
+ goto view_end;
+ }
+ if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
+ char *tmp;
+ int l;
+ tmp = drop_rg(in->header->text, g_rghash, &l);
+ free(in->header->text);
+ in->header->text = tmp;
+ in->header->l_text = l;
+ }
+ if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
+ fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+ ret = 1;
+ goto view_end;
+ }
+ if (is_header_only) goto view_end; // no need to print alignments
+
+ if (argc == optind + 1) { // convert/print the entire file
+ bam1_t *b = bam_init1();
+ int r;
+ while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
+ if (!__g_skip_aln(in->header, b)) {
+ if (!is_count) samwrite(out, b); // write the alignment to `out'
+ count++;
+ }
+ }
+ if (r < -1) {
+ fprintf(stderr, "[main_samview] truncated file.\n");
+ ret = 1;
+ }
+ bam_destroy1(b);
+ } else { // retrieve alignments in specified regions
+ int i;
+ bam_index_t *idx = 0;
+ if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index
+ if (idx == 0) { // index is unavailable
+ fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n");
+ ret = 1;
+ goto view_end;
+ }
+ for (i = optind + 1; i < argc; ++i) {
+ int tid, beg, end, result;
+ bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
+ if (tid < 0) { // reference name is not found
+ fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
+ continue;
+ }
+ // fetch alignments
+ if (is_count) {
+ count_func_data_t count_data = { in->header, &count };
+ result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func);
+ } else
+ result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func);
+ if (result < 0) {
+ fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
+ ret = 1;
+ break;
+ }
+ }
+ bam_index_destroy(idx); // destroy the BAM index
+ }
+
+view_end:
+ if (is_count && ret == 0) {
+ printf("%d\n", count);
+ }
+ // close files, free and return
+ free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
+ if (g_bed) bed_destroy(g_bed);
+ if (g_rghash) {
+ khint_t k;
+ for (k = 0; k < kh_end(g_rghash); ++k)
+ if (kh_exist(g_rghash, k)) free((char*)kh_key(g_rghash, k));
+ kh_destroy(rg, g_rghash);
+ }
+ samclose(in);
+ if (!is_count)
+ samclose(out);
+ return ret;
+}
+
+static int usage(int is_long_help)
+{
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\n");
+ fprintf(stderr, "Options: -b output BAM\n");
+ fprintf(stderr, " -h print header for the SAM output\n");
+ fprintf(stderr, " -H print header only (no alignments)\n");
+ fprintf(stderr, " -S input is SAM\n");
+ fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
+ fprintf(stderr, " -1 fast compression (force -b)\n");
+ fprintf(stderr, " -x output FLAG in HEX (samtools-C specific)\n");
+ fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n");
+ fprintf(stderr, " -c print only the count of matching records\n");
+ fprintf(stderr, " -L FILE output alignments overlapping the input BED FILE [null]\n");
+ fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
+ fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");
+ fprintf(stderr, " -o FILE output file name [stdout]\n");
+ fprintf(stderr, " -R FILE list of read groups to be outputted [null]\n");
+ fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");
+ fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n");
+ fprintf(stderr, " -q INT minimum mapping quality [0]\n");
+ fprintf(stderr, " -l STR only output reads in library STR [null]\n");
+ fprintf(stderr, " -r STR only output reads in read group STR [null]\n");
+ fprintf(stderr, " -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n");
+ fprintf(stderr, " -? longer help\n");
+ fprintf(stderr, "\n");
+ if (is_long_help)
+ fprintf(stderr, "Notes:\n\
+\n\
+ 1. By default, this command assumes the file on the command line is in\n\
+ the BAM format and it prints the alignments in SAM. If `-t' is\n\
+ applied, the input file is assumed to be in the SAM format. The\n\
+ file supplied with `-t' is SPACE/TAB delimited with the first two\n\
+ fields of each line consisting of the reference name and the\n\
+ corresponding sequence length. The `.fai' file generated by `faidx'\n\
+ can be used here. This file may be empty if reads are unaligned.\n\
+\n\
+ 2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\
+\n\
+ 3. BAM->SAM conversion: `samtools view in.bam'.\n\
+\n\
+ 4. A region should be presented in one of the following formats:\n\
+ `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
+ specified, the input alignment file must be an indexed BAM file.\n\
+\n\
+ 5. Option `-u' is preferred over `-b' when the output is piped to\n\
+ another samtools command.\n\
+\n\
+ 6. In a string FLAG, each character represents one bit with\n\
+ p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped),\n\
+ U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse)\n\
+ 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), \n\
+ f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and\n\
+ `-X' are samtools-C specific. Picard and older samtools do not\n\
+ support HEX or string flags.\n\
+\n");
+ return 1;
+}
+
+int main_import(int argc, char *argv[])
+{
+ int argc2, ret;
+ char **argv2;
+ if (argc != 4) {
+ fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
+ return 1;
+ }
+ argc2 = 6;
+ argv2 = calloc(6, sizeof(char*));
+ argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
+ ret = main_samview(argc2, argv2);
+ free(argv2);
+ return ret;
+}
+
+int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 };
+
+int main_bam2fq(int argc, char *argv[])
+{
+ bamFile fp;
+ bam_header_t *h;
+ bam1_t *b;
+ int8_t *buf;
+ int max_buf;
+ if (argc == 1) {
+ fprintf(stderr, "Usage: samtools bam2fq <in.bam>\n");
+ return 1;
+ }
+ fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
+ if (fp == 0) return 1;
+ h = bam_header_read(fp);
+ b = bam_init1();
+ buf = 0;
+ max_buf = 0;
+ while (bam_read1(fp, b) >= 0) {
+ int i, qlen = b->core.l_qseq;
+ uint8_t *seq;
+ putchar('@'); fputs(bam1_qname(b), stdout);
+ if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
+ else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
+ else putchar('\n');
+ if (max_buf < qlen + 1) {
+ max_buf = qlen + 1;
+ kroundup32(max_buf);
+ buf = realloc(buf, max_buf);
+ }
+ buf[qlen] = 0;
+ seq = bam1_seq(b);
+ for (i = 0; i < qlen; ++i)
+ buf[i] = bam1_seqi(seq, i);
+ if (b->core.flag & 16) { // reverse complement
+ for (i = 0; i < qlen>>1; ++i) {
+ int8_t t = seq_comp_table[buf[qlen - 1 - i]];
+ buf[qlen - 1 - i] = seq_comp_table[buf[i]];
+ buf[i] = t;
+ }
+ if (qlen&1) buf[i] = seq_comp_table[buf[i]];
+ }
+ for (i = 0; i < qlen; ++i)
+ buf[i] = bam_nt16_rev_table[buf[i]];
+ puts((char*)buf);
+ puts("+");
+ seq = bam1_qual(b);
+ for (i = 0; i < qlen; ++i)
+ buf[i] = 33 + seq[i];
+ if (b->core.flag & 16) { // reverse
+ for (i = 0; i < qlen>>1; ++i) {
+ int8_t t = buf[qlen - 1 - i];
+ buf[qlen - 1 - i] = buf[i];
+ buf[i] = t;
+ }
+ }
+ puts((char*)buf);
+ }
+ free(buf);
+ bam_destroy1(b);
+ bam_header_destroy(h);
+ bam_close(fp);
+ return 0;
+}
diff --git a/src/samtools-0.1.18/sample.c b/src/samtools-0.1.18/sample.c
new file mode 100644
index 0000000..830b9d1
--- /dev/null
+++ b/src/samtools-0.1.18/sample.c
@@ -0,0 +1,107 @@
+#include <stdlib.h>
+#include <string.h>
+#include "sample.h"
+#include "khash.h"
+KHASH_MAP_INIT_STR(sm, int)
+
+bam_sample_t *bam_smpl_init(void)
+{
+ bam_sample_t *s;
+ s = calloc(1, sizeof(bam_sample_t));
+ s->rg2smid = kh_init(sm);
+ s->sm2id = kh_init(sm);
+ return s;
+}
+
+void bam_smpl_destroy(bam_sample_t *sm)
+{
+ int i;
+ khint_t k;
+ khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+ if (sm == 0) return;
+ for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
+ free(sm->smpl);
+ for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
+ if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
+ kh_destroy(sm, sm->rg2smid);
+ kh_destroy(sm, sm->sm2id);
+ free(sm);
+}
+
+static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
+{
+ khint_t k_rg, k_sm;
+ int ret;
+ khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+ k_rg = kh_get(sm, rg2smid, key);
+ if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
+ k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
+ k_sm = kh_get(sm, sm2id, val);
+ if (k_sm == kh_end(sm2id)) { // absent
+ if (sm->n == sm->m) {
+ sm->m = sm->m? sm->m<<1 : 1;
+ sm->smpl = realloc(sm->smpl, sizeof(void*) * sm->m);
+ }
+ sm->smpl[sm->n] = strdup(val);
+ k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
+ kh_val(sm2id, k_sm) = sm->n++;
+ }
+ kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
+}
+
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
+{
+ const char *p = txt, *q, *r;
+ kstring_t buf, first_sm;
+ int n = 0;
+ khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
+ if (txt == 0) {
+ add_pair(sm, sm2id, fn, fn);
+ return 0;
+ }
+ memset(&buf, 0, sizeof(kstring_t));
+ memset(&first_sm, 0, sizeof(kstring_t));
+ while ((q = strstr(p, "@RG")) != 0) {
+ p = q + 3;
+ r = q = 0;
+ if ((q = strstr(p, "\tID:")) != 0) q += 4;
+ if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+ if (r && q) {
+ char *u, *v;
+ int oq, or;
+ for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+ for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+ oq = *u; or = *v; *u = *v = '\0';
+ buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
+ add_pair(sm, sm2id, buf.s, r);
+ if ( !first_sm.s )
+ kputs(r,&first_sm);
+ *u = oq; *v = or;
+ } else break;
+ p = q > r? q : r;
+ ++n;
+ }
+ if (n == 0) add_pair(sm, sm2id, fn, fn);
+ // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
+ // use the tag instead.
+ else if ( n==1 && first_sm.s )
+ add_pair(sm,sm2id,fn,first_sm.s);
+ if ( first_sm.s )
+ free(first_sm.s);
+
+// add_pair(sm, sm2id, fn, fn);
+ free(buf.s);
+ return 0;
+}
+
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
+{
+ khint_t k;
+ khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+ if (rg) {
+ str->l = 0;
+ kputs(fn, str); kputc('/', str); kputs(rg, str);
+ k = kh_get(sm, rg2smid, str->s);
+ } else k = kh_get(sm, rg2smid, fn);
+ return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
+}
diff --git a/src/samtools-0.1.18/sample.h b/src/samtools-0.1.18/sample.h
new file mode 100644
index 0000000..85fe499
--- /dev/null
+++ b/src/samtools-0.1.18/sample.h
@@ -0,0 +1,17 @@
+#ifndef BAM_SAMPLE_H
+#define BAM_SAMPLE_H
+
+#include "kstring.h"
+
+typedef struct {
+ int n, m;
+ char **smpl;
+ void *rg2smid, *sm2id;
+} bam_sample_t;
+
+bam_sample_t *bam_smpl_init(void);
+int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt);
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str);
+void bam_smpl_destroy(bam_sample_t *sm);
+
+#endif
diff --git a/src/samtools-0.1.18/samtools.1 b/src/samtools-0.1.18/samtools.1
new file mode 100644
index 0000000..98ce9d0
--- /dev/null
+++ b/src/samtools-0.1.18/samtools.1
@@ -0,0 +1,994 @@
+.TH samtools 1 "05 July 2011" "samtools-0.1.17" "Bioinformatics tools"
+.SH NAME
+.PP
+samtools - Utilities for the Sequence Alignment/Map (SAM) format
+
+bcftools - Utilities for the Binary Call Format (BCF) and VCF
+.SH SYNOPSIS
+.PP
+samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
+.PP
+samtools sort aln.bam aln.sorted
+.PP
+samtools index aln.sorted.bam
+.PP
+samtools idxstats aln.sorted.bam
+.PP
+samtools view aln.sorted.bam chr2:20,100,000-20,200,000
+.PP
+samtools merge out.bam in1.bam in2.bam in3.bam
+.PP
+samtools faidx ref.fasta
+.PP
+samtools pileup -vcf ref.fasta aln.sorted.bam
+.PP
+samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
+.PP
+samtools tview aln.sorted.bam ref.fasta
+.PP
+bcftools index in.bcf
+.PP
+bcftools view in.bcf chr2:100-200 > out.vcf
+.PP
+bcftools view -vc in.bcf > out.vcf 2> out.afs
+
+.SH DESCRIPTION
+.PP
+Samtools is a set of utilities that manipulate alignments in the BAM
+format. It imports from and exports to the SAM (Sequence Alignment/Map)
+format, does sorting, merging and indexing, and allows to retrieve reads
+in any regions swiftly.
+
+Samtools is designed to work on a stream. It regards an input file `-'
+as the standard input (stdin) and an output file `-' as the standard
+output (stdout). Several commands can thus be combined with Unix
+pipes. Samtools always output warning and error messages to the standard
+error output (stderr).
+
+Samtools is also able to open a BAM (not SAM) file on a remote FTP or
+HTTP server if the BAM file name starts with `ftp://' or `http://'.
+Samtools checks the current working directory for the index file and
+will download the index upon absence. Samtools does not retrieve the
+entire alignment file unless it is asked to do so.
+
+.SH SAMTOOLS COMMANDS AND OPTIONS
+
+.TP 10
+.B view
+samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]]
+
+Extract/print all or sub alignments in SAM or BAM format. If no region
+is specified, all the alignments will be printed; otherwise only
+alignments overlapping the specified regions will be output. An
+alignment may be given multiple times if it is overlapping several
+regions. A region can be presented, for example, in the following
+format: `chr2' (the whole chr2), `chr2:1000000' (region starting from
+1,000,000bp) or `chr2:1,000,000-2,000,000' (region between 1,000,000 and
+2,000,000bp including the end points). The coordinate is 1-based.
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -b
+Output in the BAM format.
+.TP
+.BI -f \ INT
+Only output alignments with all bits in INT present in the FLAG
+field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]
+.TP
+.BI -F \ INT
+Skip alignments with bits present in INT [0]
+.TP
+.B -h
+Include the header in the output.
+.TP
+.B -H
+Output the header only.
+.TP
+.BI -l \ STR
+Only output reads in library STR [null]
+.TP
+.BI -o \ FILE
+Output file [stdout]
+.TP
+.BI -q \ INT
+Skip alignments with MAPQ smaller than INT [0]
+.TP
+.BI -r \ STR
+Only output reads in read group STR [null]
+.TP
+.BI -R \ FILE
+Output reads in read groups listed in
+.I FILE
+[null]
+.TP
+.B -S
+Input is in SAM. If @SQ header lines are absent, the
+.B `-t'
+option is required.
+.TP
+.B -c
+Instead of printing the alignments, only count them and print the
+total number. All filter options, such as
+.B `-f',
+.B `-F'
+and
+.B `-q'
+, are taken into account.
+.TP
+.BI -t \ FILE
+This file is TAB-delimited. Each line must contain the reference name
+and the length of the reference, one line for each distinct reference;
+additional fields are ignored. This file also defines the order of the
+reference sequences in sorting. If you run `samtools faidx <ref.fa>',
+the resultant index file
+.I <ref.fa>.fai
+can be used as this
+.I <in.ref_list>
+file.
+.TP
+.B -u
+Output uncompressed BAM. This option saves time spent on
+compression/decomprssion and is thus preferred when the output is piped
+to another samtools command.
+.RE
+
+.TP
+.B tview
+samtools tview <in.sorted.bam> [ref.fasta]
+
+Text alignment viewer (based on the ncurses library). In the viewer,
+press `?' for help and press `g' to check the alignment start from a
+region in the format like `chr10:10,000,000' or `=10,000,000' when
+viewing the same reference sequence.
+
+.TP
+.B mpileup
+.B samtools mpileup
+.RB [ \-EBug ]
+.RB [ \-C
+.IR capQcoef ]
+.RB [ \-r
+.IR reg ]
+.RB [ \-f
+.IR in.fa ]
+.RB [ \-l
+.IR list ]
+.RB [ \-M
+.IR capMapQ ]
+.RB [ \-Q
+.IR minBaseQ ]
+.RB [ \-q
+.IR minMapQ ]
+.I in.bam
+.RI [ in2.bam
+.RI [ ... ]]
+
+Generate BCF or pileup for one or multiple BAM files. Alignment records
+are grouped by sample identifiers in @RG header lines. If sample
+identifiers are absent, each input file is regarded as one sample.
+
+In the pileup format (without
+.BR -u or -g ),
+each
+line represents a genomic position, consisting of chromosome name,
+coordinate, reference base, read bases, read qualities and alignment
+mapping qualities. Information on match, mismatch, indel, strand,
+mapping quality and start and end of a read are all encoded at the read
+base column. At this column, a dot stands for a match to the reference
+base on the forward strand, a comma for a match on the reverse strand,
+a '>' or '<' for a reference skip, `ACGTN' for a mismatch on the forward
+strand and `acgtn' for a mismatch on the reverse strand. A pattern
+`\\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this
+reference position and the next reference position. The length of the
+insertion is given by the integer in the pattern, followed by the
+inserted sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+'
+represents a deletion from the reference. The deleted bases will be
+presented as `*' in the following lines. Also at the read base column, a
+symbol `^' marks the start of a read. The ASCII of the character
+following `^' minus 33 gives the mapping quality. A symbol `$' marks the
+end of a read segment.
+
+.B Input Options:
+.RS
+.TP 10
+.B -6
+Assume the quality is in the Illumina 1.3+ encoding.
+.B -A
+Do not skip anomalous read pairs in variant calling.
+.TP
+.B -B
+Disable probabilistic realignment for the computation of base alignment
+quality (BAQ). BAQ is the Phred-scaled probability of a read base being
+misaligned. Applying this option greatly helps to reduce false SNPs
+caused by misalignments.
+.TP
+.BI -b \ FILE
+List of input BAM files, one file per line [null]
+.TP
+.BI -C \ INT
+Coefficient for downgrading mapping quality for reads containing
+excessive mismatches. Given a read with a phred-scaled probability q of
+being generated from the mapped position, the new mapping quality is
+about sqrt((INT-q)/INT)*INT. A zero value disables this
+functionality; if enabled, the recommended value for BWA is 50. [0]
+.TP
+.BI -d \ INT
+At a position, read maximally
+.I INT
+reads per input BAM. [250]
+.TP
+.B -E
+Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt
+specificity a little bit.
+.TP
+.BI -f \ FILE
+The
+.BR faidx -indexed
+reference file in the FASTA format. The file can be optionally compressed by
+.BR razip .
+[null]
+.TP
+.BI -l \ FILE
+BED or position list file containing a list of regions or sites where pileup or BCF should be generated [null]
+.TP
+.BI -q \ INT
+Minimum mapping quality for an alignment to be used [0]
+.TP
+.BI -Q \ INT
+Minimum base quality for a base to be considered [13]
+.TP
+.BI -r \ STR
+Only generate pileup in region
+.I STR
+[all sites]
+.TP
+.B Output Options:
+
+.TP
+.B -D
+Output per-sample read depth
+.TP
+.B -g
+Compute genotype likelihoods and output them in the binary call format (BCF).
+.TP
+.B -S
+Output per-sample Phred-scaled strand bias P-value
+.TP
+.B -u
+Similar to
+.B -g
+except that the output is uncompressed BCF, which is preferred for piping.
+
+.TP
+.B Options for Genotype Likelihood Computation (for -g or -u):
+
+.TP
+.BI -e \ INT
+Phred-scaled gap extension sequencing error probability. Reducing
+.I INT
+leads to longer indels. [20]
+.TP
+.BI -h \ INT
+Coefficient for modeling homopolymer errors. Given an
+.IR l -long
+homopolymer
+run, the sequencing error of an indel of size
+.I s
+is modeled as
+.IR INT * s / l .
+[100]
+.TP
+.B -I
+Do not perform INDEL calling
+.TP
+.BI -L \ INT
+Skip INDEL calling if the average per-sample depth is above
+.IR INT .
+[250]
+.TP
+.BI -o \ INT
+Phred-scaled gap open sequencing error probability. Reducing
+.I INT
+leads to more indel calls. [40]
+.TP
+.BI -P \ STR
+Comma dilimited list of platforms (determined by
+.BR @RG-PL )
+from which indel candidates are obtained. It is recommended to collect
+indel candidates from sequencing technologies that have low indel error
+rate such as ILLUMINA. [all]
+.RE
+
+.TP
+.B reheader
+samtools reheader <in.header.sam> <in.bam>
+
+Replace the header in
+.I in.bam
+with the header in
+.I in.header.sam.
+This command is much faster than replacing the header with a
+BAM->SAM->BAM conversion.
+
+.TP
+.B cat
+samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ]
+
+Concatenate BAMs. The sequence dictionary of each input BAM must be identical,
+although this command does not check this. This command uses a similar trick
+to
+.B reheader
+which enables fast BAM concatenation.
+
+.TP
+.B sort
+samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
+
+Sort alignments by leftmost coordinates. File
+.I <out.prefix>.bam
+will be created. This command may also create temporary files
+.I <out.prefix>.%d.bam
+when the whole alignment cannot be fitted into memory (controlled by
+option -m).
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -o
+Output the final alignment to the standard output.
+.TP
+.B -n
+Sort by read names rather than by chromosomal coordinates
+.TP
+.BI -m \ INT
+Approximately the maximum required memory. [500000000]
+.RE
+
+.TP
+.B merge
+samtools merge [-nur1f] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...]
+
+Merge multiple sorted alignments.
+The header reference lists of all the input BAM files, and the @SQ headers of
+.IR inh.sam ,
+if any, must all refer to the same set of reference sequences.
+The header reference list and (unless overridden by
+.BR -h )
+`@' headers of
+.I in1.bam
+will be copied to
+.IR out.bam ,
+and the headers of other files will be ignored.
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -1
+Use zlib compression level 1 to comrpess the output
+.TP
+.B -f
+Force to overwrite the output file if present.
+.TP 8
+.BI -h \ FILE
+Use the lines of
+.I FILE
+as `@' headers to be copied to
+.IR out.bam ,
+replacing any header lines that would otherwise be copied from
+.IR in1.bam .
+.RI ( FILE
+is actually in SAM format, though any alignment records it may contain
+are ignored.)
+.TP
+.B -n
+The input alignments are sorted by read names rather than by chromosomal
+coordinates
+.TP
+.BI -R \ STR
+Merge files in the specified region indicated by
+.I STR
+[null]
+.TP
+.B -r
+Attach an RG tag to each alignment. The tag value is inferred from file names.
+.TP
+.B -u
+Uncompressed BAM output
+.RE
+
+.TP
+.B index
+samtools index <aln.bam>
+
+Index sorted alignment for fast random access. Index file
+.I <aln.bam>.bai
+will be created.
+
+.TP
+.B idxstats
+samtools idxstats <aln.bam>
+
+Retrieve and print stats in the index file. The output is TAB delimited
+with each line consisting of reference sequence name, sequence length, #
+mapped reads and # unmapped reads.
+
+.TP
+.B faidx
+samtools faidx <ref.fasta> [region1 [...]]
+
+Index reference sequence in the FASTA format or extract subsequence from
+indexed reference sequence. If no region is specified,
+.B faidx
+will index the file and create
+.I <ref.fasta>.fai
+on the disk. If regions are speficified, the subsequences will be
+retrieved and printed to stdout in the FASTA format. The input file can
+be compressed in the
+.B RAZF
+format.
+
+.TP
+.B fixmate
+samtools fixmate <in.nameSrt.bam> <out.bam>
+
+Fill in mate coordinates, ISIZE and mate related flags from a
+name-sorted alignment.
+
+.TP
+.B rmdup
+samtools rmdup [-sS] <input.srt.bam> <out.bam>
+
+Remove potential PCR duplicates: if multiple read pairs have identical
+external coordinates, only retain the pair with highest mapping quality.
+In the paired-end mode, this command
+.B ONLY
+works with FR orientation and requires ISIZE is correctly set. It does
+not work for unpaired reads (e.g. two ends mapped to different
+chromosomes or orphan reads).
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -s
+Remove duplicate for single-end reads. By default, the command works for
+paired-end reads only.
+.TP 8
+.B -S
+Treat paired-end reads and single-end reads.
+.RE
+
+.TP
+.B calmd
+samtools calmd [-EeubSr] [-C capQcoef] <aln.bam> <ref.fasta>
+
+Generate the MD tag. If the MD tag is already present, this command will
+give a warning if the MD tag generated is different from the existing
+tag. Output SAM by default.
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -A
+When used jointly with
+.B -r
+this option overwrites the original base quality.
+.TP 8
+.B -e
+Convert a the read base to = if it is identical to the aligned reference
+base. Indel caller does not support the = bases at the moment.
+.TP
+.B -u
+Output uncompressed BAM
+.TP
+.B -b
+Output compressed BAM
+.TP
+.B -S
+The input is SAM with header lines
+.TP
+.BI -C \ INT
+Coefficient to cap mapping quality of poorly mapped reads. See the
+.B pileup
+command for details. [0]
+.TP
+.B -r
+Compute the BQ tag (without -A) or cap base quality by BAQ (with -A).
+.TP
+.B -E
+Extended BAQ calculation. This option trades specificity for sensitivity, though the
+effect is minor.
+.RE
+
+.TP
+.B targetcut
+samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>
+
+This command identifies target regions by examining the continuity of read depth, computes
+haploid consensus sequences of targets and outputs a SAM with each sequence corresponding
+to a target. When option
+.B -f
+is in use, BAQ will be applied. This command is
+.B only
+designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et al. (2010)].
+.RE
+
+.TP
+.B phase
+samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>
+
+Call and phase heterozygous SNPs.
+.B OPTIONS:
+.RS
+.TP 8
+.B -A
+Drop reads with ambiguous phase.
+.TP 8
+.BI -b \ STR
+Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file
+.BR STR .0.bam
+and phase-1 reads in
+.BR STR .1.bam.
+Phase unknown reads will be randomly allocated to one of the two files. Chimeric reads
+with switch errors will be saved in
+.BR STR .chimeric.bam.
+[null]
+.TP
+.B -F
+Do not attempt to fix chimeric reads.
+.TP
+.BI -k \ INT
+Maximum length for local phasing. [13]
+.TP
+.BI -q \ INT
+Minimum Phred-scaled LOD to call a heterozygote. [40]
+.TP
+.BI -Q \ INT
+Minimum base quality to be used in het calling. [13]
+.RE
+
+.SH BCFTOOLS COMMANDS AND OPTIONS
+
+.TP 10
+.B view
+.B bcftools view
+.RB [ \-AbFGNQSucgv ]
+.RB [ \-D
+.IR seqDict ]
+.RB [ \-l
+.IR listLoci ]
+.RB [ \-s
+.IR listSample ]
+.RB [ \-i
+.IR gapSNPratio ]
+.RB [ \-t
+.IR mutRate ]
+.RB [ \-p
+.IR varThres ]
+.RB [ \-P
+.IR prior ]
+.RB [ \-1
+.IR nGroup1 ]
+.RB [ \-d
+.IR minFrac ]
+.RB [ \-U
+.IR nPerm ]
+.RB [ \-X
+.IR permThres ]
+.RB [ \-T
+.IR trioType ]
+.I in.bcf
+.RI [ region ]
+
+Convert between BCF and VCF, call variant candidates and estimate allele
+frequencies.
+
+.RS
+.TP
+.B Input/Output Options:
+.TP 10
+.B -A
+Retain all possible alternate alleles at variant sites. By default, the view
+command discards unlikely alleles.
+.TP 10
+.B -b
+Output in the BCF format. The default is VCF.
+.TP
+.BI -D \ FILE
+Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]
+.TP
+.B -F
+Indicate PL is generated by r921 or before (ordering is different).
+.TP
+.B -G
+Suppress all individual genotype information.
+.TP
+.BI -l \ FILE
+List of sites at which information are outputted [all sites]
+.TP
+.B -N
+Skip sites where the REF field is not A/C/G/T
+.TP
+.B -Q
+Output the QCALL likelihood format
+.TP
+.BI -s \ FILE
+List of samples to use. The first column in the input gives the sample names
+and the second gives the ploidy, which can only be 1 or 2. When the 2nd column
+is absent, the sample ploidy is assumed to be 2. In the output, the ordering of
+samples will be identical to the one in
+.IR FILE .
+[null]
+.TP
+.B -S
+The input is VCF instead of BCF.
+.TP
+.B -u
+Uncompressed BCF output (force -b).
+.TP
+.B Consensus/Variant Calling Options:
+.TP 10
+.B -c
+Call variants using Bayesian inference. This option automatically invokes option
+.BR -e .
+.TP
+.BI -d \ FLOAT
+When
+.B -v
+is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0]
+.TP
+.B -e
+Perform max-likelihood inference only, including estimating the site allele frequency,
+testing Hardy-Weinberg equlibrium and testing associations with LRT.
+.TP
+.B -g
+Call per-sample genotypes at variant sites (force -c)
+.TP
+.BI -i \ FLOAT
+Ratio of INDEL-to-SNP mutation rate [0.15]
+.TP
+.BI -p \ FLOAT
+A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
+.TP
+.BI -P \ STR
+Prior or initial allele frequency spectrum. If STR can be
+.IR full ,
+.IR cond2 ,
+.I flat
+or the file consisting of error output from a previous variant calling
+run.
+.TP
+.BI -t \ FLOAT
+Scaled muttion rate for variant calling [0.001]
+.TP
+.BI -T \ STR
+Enable pair/trio calling. For trio calling, option
+.B -s
+is usually needed to be applied to configure the trio members and their ordering.
+In the file supplied to the option
+.BR -s ,
+the first sample must be the child, the second the father and the third the mother.
+The valid values of
+.I STR
+are `pair', `trioauto', `trioxd' and `trioxs', where `pair' calls differences between two input samples, and `trioxd' (`trioxs') specifies that the input
+is from the X chromosome non-PAR regions and the child is a female (male). [null]
+.TP
+.B -v
+Output variant sites only (force -c)
+.TP
+.B Contrast Calling and Association Test Options:
+.TP
+.BI -1 \ INT
+Number of group-1 samples. This option is used for dividing the samples into
+two groups for contrast SNP calling or association test.
+When this option is in use, the following VCF INFO will be outputted:
+PC2, PCHI2 and QCHI2. [0]
+.TP
+.BI -U \ INT
+Number of permutations for association test (effective only with
+.BR -1 )
+[0]
+.TP
+.BI -X \ FLOAT
+Only perform permutations for P(chi^2)<FLOAT (effective only with
+.BR -U )
+[0.01]
+.RE
+
+.TP
+.B index
+.B bcftools index
+.I in.bcf
+
+Index sorted BCF for random access.
+.RE
+
+.TP
+.B cat
+.B bcftools cat
+.I in1.bcf
+.RI [ "in2.bcf " [ ... "]]]"
+
+Concatenate BCF files. The input files are required to be sorted and
+have identical samples appearing in the same order.
+.RE
+.SH SAM FORMAT
+
+Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started
+with the `@' symbol, each alignment line consists of:
+
+.TS
+center box;
+cb | cb | cb
+n | l | l .
+Col Field Description
+_
+1 QNAME Query template/pair NAME
+2 FLAG bitwise FLAG
+3 RNAME Reference sequence NAME
+4 POS 1-based leftmost POSition/coordinate of clipped sequence
+5 MAPQ MAPping Quality (Phred-scaled)
+6 CIAGR extended CIGAR string
+7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
+8 MPOS 1-based Mate POSistion
+9 TLEN inferred Template LENgth (insert size)
+10 SEQ query SEQuence on the same strand as the reference
+11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
+12+ OPT variable OPTional fields in the format TAG:VTYPE:VALUE
+.TE
+
+.PP
+Each bit in the FLAG field is defined as:
+
+.TS
+center box;
+cb | cb | cb
+l | c | l .
+Flag Chr Description
+_
+0x0001 p the read is paired in sequencing
+0x0002 P the read is mapped in a proper pair
+0x0004 u the query sequence itself is unmapped
+0x0008 U the mate is unmapped
+0x0010 r strand of the query (1 for reverse)
+0x0020 R strand of the mate
+0x0040 1 the read is the first read in a pair
+0x0080 2 the read is the second read in a pair
+0x0100 s the alignment is not primary
+0x0200 f the read fails platform/vendor quality checks
+0x0400 d the read is either a PCR or an optical duplicate
+.TE
+
+where the second column gives the string representation of the FLAG field.
+
+.SH VCF FORMAT
+
+The Variant Call Format (VCF) is a TAB-delimited format with each data line consists of the following fields:
+.TS
+center box;
+cb | cb | cb
+n | l | l .
+Col Field Description
+_
+1 CHROM CHROMosome name
+2 POS the left-most POSition of the variant
+3 ID unique variant IDentifier
+4 REF the REFerence allele
+5 ALT the ALTernate allele(s), separated by comma
+6 QUAL variant/reference QUALity
+7 FILTER FILTers applied
+8 INFO INFOrmation related to the variant, separated by semi-colon
+9 FORMAT FORMAT of the genotype fields, separated by colon (optional)
+10+ SAMPLE SAMPLE genotypes and per-sample information (optional)
+.TE
+
+.PP
+The following table gives the
+.B INFO
+tags used by samtools and bcftools.
+
+.TS
+center box;
+cb | cb | cb
+l | l | l .
+Tag Format Description
+_
+AF1 double Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
+DP int Raw read depth (without quality filtering)
+DP4 int[4] # high-quality reference forward bases, ref reverse, alternate for and alt rev bases
+FQ int Consensus quality. Positive: sample genotypes different; negative: otherwise
+MQ int Root-Mean-Square mapping quality of covering reads
+PC2 int[2] Phred probability of AF in group1 samples being larger (,smaller) than in group2
+PCHI2 double Posterior weighted chi^2 P-value between group1 and group2 samples
+PV4 double[4] P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
+QCHI2 int Phred-scaled PCHI2
+RP int # permutations yielding a smaller PCHI2
+CLR int Phred log ratio of genotype likelihoods with and without the trio/pair constraint
+UGT string Most probable genotype configuration without the trio constraint
+CGT string Most probable configuration with the trio constraint
+.TE
+
+.SH EXAMPLES
+.IP o 2
+Import SAM to BAM when
+.B @SQ
+lines are present in the header:
+
+ samtools view -bS aln.sam > aln.bam
+
+If
+.B @SQ
+lines are absent:
+
+ samtools faidx ref.fa
+ samtools view -bt ref.fa.fai aln.sam > aln.bam
+
+where
+.I ref.fa.fai
+is generated automatically by the
+.B faidx
+command.
+
+.IP o 2
+Attach the
+.B RG
+tag while merging sorted alignments:
+
+ perl -e 'print "@RG\\tID:ga\\tSM:hs\\tLB:ga\\tPL:Illumina\\n at RG\\tID:454\\tSM:hs\\tLB:454\\tPL:454\\n"' > rg.txt
+ samtools merge -rh rg.txt merged.bam ga.bam 454.bam
+
+The value in a
+.B RG
+tag is determined by the file name the read is coming from. In this
+example, in the
+.IR merged.bam ,
+reads from
+.I ga.bam
+will be attached
+.IR RG:Z:ga ,
+while reads from
+.I 454.bam
+will be attached
+.IR RG:Z:454 .
+
+.IP o 2
+Call SNPs and short INDELs for one diploid individual:
+
+ samtools mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcf
+ bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf
+
+The
+.B -D
+option of varFilter controls the maximum read depth, which should be
+adjusted to about twice the average read depth. One may consider to add
+.B -C50
+to
+.B mpileup
+if mapping quality is overestimated for reads containing excessive
+mismatches. Applying this option usually helps
+.B BWA-short
+but may not other mappers.
+
+.IP o 2
+Generate the consensus sequence for one diploid individual:
+
+ samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
+
+.IP o 2
+Call somatic mutations from a pair of samples:
+
+ samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf
+
+In the output INFO field,
+.I CLR
+gives the Phred-log ratio between the likelihood by treating the
+two samples independently, and the likelihood by requiring the genotype to be identical.
+This
+.I CLR
+is effectively a score measuring the confidence of somatic calls. The higher the better.
+
+.IP o 2
+Call de novo and somatic mutations from a family trio:
+
+ samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair -s samples.txt - > var.bcf
+
+File
+.I samples.txt
+should consist of three lines specifying the member and order of samples (in the order of child-father-mother).
+Similarly,
+.I CLR
+gives the Phred-log likelihood ratio with and without the trio constraint.
+.I UGT
+shows the most likely genotype configuration without the trio constraint, and
+.I CGT
+gives the most likely genotype configuration satisfying the trio constraint.
+
+.IP o 2
+Phase one individual:
+
+ samtools calmd -AEur aln.bam ref.fa | samtools phase -b prefix - > phase.out
+
+The
+.B calmd
+command is used to reduce false heterozygotes around INDELs.
+
+.IP o 2
+Call SNPs and short indels for multiple diploid individuals:
+
+ samtools mpileup -P ILLUMINA -ugf ref.fa *.bam | bcftools view -bcvg - > var.raw.bcf
+ bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > var.flt.vcf
+
+Individuals are identified from the
+.B SM
+tags in the
+.B @RG
+header lines. Individuals can be pooled in one alignment file; one
+individual can also be separated into multiple files. The
+.B -P
+option specifies that indel candidates should be collected only from
+read groups with the
+.B @RG-PL
+tag set to
+.IR ILLUMINA .
+Collecting indel candidates from reads sequenced by an indel-prone
+technology may affect the performance of indel calling.
+
+.IP o 2
+Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals:
+
+ samtools mpileup -Igf ref.fa *.bam > all.bcf
+ bcftools view -bl sites.list all.bcf > sites.bcf
+ bcftools view -cGP cond2 sites.bcf > /dev/null 2> sites.1.afs
+ bcftools view -cGP sites.1.afs sites.bcf > /dev/null 2> sites.2.afs
+ bcftools view -cGP sites.2.afs sites.bcf > /dev/null 2> sites.3.afs
+ ......
+
+where
+.I sites.list
+contains the list of sites with each line consisting of the reference
+sequence name and position. The following
+.B bcftools
+commands estimate AFS by EM.
+
+.IP o 2
+Dump BAQ applied alignment for other SNP callers:
+
+ samtools calmd -bAr aln.bam > aln.baq.bam
+
+It adds and corrects the
+.B NM
+and
+.B MD
+tags at the same time. The
+.B calmd
+command also comes with the
+.B -C
+option, the same as the one in
+.B pileup
+and
+.BR mpileup .
+Apply if it helps.
+
+.SH LIMITATIONS
+.PP
+.IP o 2
+Unaligned words used in bam_import.c, bam_endian.h, bam.c and bam_aux.c.
+.IP o 2
+Samtools paired-end rmdup does not work for unpaired reads (e.g. orphan
+reads or ends mapped to different chromosomes). If this is a concern,
+please use Picard's MarkDuplicate which correctly handles these cases,
+although a little slower.
+
+.SH AUTHOR
+.PP
+Heng Li from the Sanger Institute wrote the C version of samtools. Bob
+Handsaker from the Broad Institute implemented the BGZF library and Jue
+Ruan from Beijing Genomics Institute wrote the RAZF library. John
+Marshall and Petr Danecek contribute to the source code and various
+people from the 1000 Genomes Project have contributed to the SAM format
+specification.
+
+.SH SEE ALSO
+.PP
+Samtools website: <http://samtools.sourceforge.net>
diff --git a/src/segment_juncs.cpp b/src/segment_juncs.cpp
index 8941043..2405c05 100644
--- a/src/segment_juncs.cpp
+++ b/src/segment_juncs.cpp
@@ -26,10 +26,6 @@
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/file.h>
-#include <seqan/find.h>
-#include <seqan/modifier.h>
-#include <seqan/align.h>
-#include <seqan/graph_align.h>
#include <getopt.h>
#include <boost/thread.hpp>
@@ -47,7 +43,6 @@
using namespace seqan;
using namespace std;
-using namespace __gnu_cxx;
// daehwan //geo
//#define B_DEBUG 1
@@ -2593,100 +2588,6 @@ void detect_small_deletion(RefSequenceTable& rt,
return;
}
-void gappedAlignment(const seqan::String<char>& read,
- const seqan::String<char>& leftReference,
- const seqan::String<char>& rightReference,
- vector<int>& insertLeftPositions,
- vector<int>& insertRightPositions,
- int& mismatchCount)
-{
- const Score<int> globalScore(0, -5, -1, -10); // (match, mismatch, gapextend, gapopen)
- Align<String<char> > align;
- appendValue(rows(align), read);
-
- String<char> genomicSequence;
- assign(genomicSequence, leftReference);
- append(genomicSequence, rightReference);
- appendValue(rows(align), genomicSequence);
- // int score = globalAlignment(align, globalScore);
-
- Row<Align<String<char> > >::Type& row0 = row(align, 0);
- Row<Align<String<char> > >::Type& row1 = row(align, 1);
-
- // find gap whose length >= read_len - 10
- int start_in_align = -1, end_in_align = -1;
- int start_in_ref = -1, end_in_ref = -1;
-
- int temp_start = -1;
- int ref_pos = 0;
-
- int gap = 0;
- mismatchCount = 0;
-
- int len = length(row0);
- for (int i = 0; i < len; ++i)
- {
- if (row0[i] == '-')
- {
- if (temp_start < 0)
- temp_start = i;
- }
- else if (row1[i] != '-')
- {
- if (temp_start >= 0)
- {
- if (i - temp_start > end_in_align - start_in_align)
- {
- end_in_align = i;
- start_in_align = temp_start;
-
- end_in_ref = ref_pos;
- start_in_ref = ref_pos - (i - temp_start);
- temp_start = -1;
- }
- }
-
- if (row0[i] != row1[i])
- ++mismatchCount;
- }
-
- if (row0[i] == '-' || row1[i] == '-')
- ++gap;
- if (row1[i] != '-')
- ++ref_pos;
- }
-
- // assume the lengths of read, leftReference, and rightReference are all equal.
- const int max_gap = end_in_align - start_in_align;
- if (max_gap < (int)length(read) - 10)
- return;
-
- if (start_in_ref < 0)
- return;
-
- insertLeftPositions.push_back(start_in_ref);
- insertRightPositions.push_back(end_in_ref - length(leftReference));
-
-#if B_DEBUG
- if (gap - max_gap >= 0)
- {
- cerr << "Score = " << score << endl;
- cerr << row(align, 0) << endl
- << row(align, 1) << endl;
-
- cerr << "len: " << len
- << ", gap: " << gap
- << ", max_gap: " << max_gap
- << "(" << start_in_align << ", " << end_in_align
- << "), ref (" << start_in_ref << ", " << end_in_ref
- << "), mismatch: " << mismatchCount << endl;
-
- if (gap - max_gap > 0)
- cerr << "daehwan" << endl;
- }
-#endif
-}
-
void detect_fusion(RefSequenceTable& rt,
seqan::String<char>& read_sequence,
BowtieHit& leftHit,
@@ -2744,28 +2645,16 @@ void detect_fusion(RefSequenceTable& rt,
vector<int> bestRightInsertPositions;
int minErrors = -1;
- // todo - we need to do (efficient) Smith-Waterman Alignment using SIMD like the way Bowtie2 does!
- // too slow and too many false positives
- // daehwan - turn off this for now.
- if (bowtie2 && false)
- gappedAlignment(read_sequence,
- leftGenomicSequence,
- rightGenomicSequence,
- bestLeftInsertPositions,
- bestRightInsertPositions,
- minErrors);
- else
- simpleSplitAlignment(read_sequence,
- leftGenomicSequence,
- rightGenomicSequence,
- bestLeftInsertPositions,
- minErrors);
+ simpleSplitAlignment(read_sequence,
+ leftGenomicSequence,
+ rightGenomicSequence,
+ bestLeftInsertPositions,
+ minErrors);
uint32_t total_edit_dist = leftHit.edit_dist() + rightHit.edit_dist();
if (minErrors > (int)total_edit_dist)
return;
-#if 1
if (minErrors > 2)
return;
@@ -2780,28 +2669,6 @@ void detect_fusion(RefSequenceTable& rt,
return;
}
- // daehwan - this is very slow - the older version of "difference" is way faster
-#else
- if (read_length <= 60)
- {
- /*
- * check if the two contig from two different chromosome are different enough
- */
- const Score<int> globalScore(0, -1, -2, -2);
- Align<String<char> > align;
- appendValue(rows(align), read_sequence);
- appendValue(rows(align), leftGenomicSequence);
-
- int score = globalAlignment(align, globalScore);
- assignSource(row(align, 0), read_sequence);
- assignSource(row(align, 1), rightGenomicSequence);
-
- score = max(score, globalAlignment(align, globalScore));
- if (abs(score) < read_length / 6)
- return;
- }
-#endif
-
for (size_t i = 0; i < bestLeftInsertPositions.size(); ++i)
{
int bestLeftInsertPosition = bestLeftInsertPositions[i];
diff --git a/src/tophat-fusion-post b/src/tophat-fusion-post
index c946699..f704ff3 100755
--- a/src/tophat-fusion-post
+++ b/src/tophat-fusion-post
@@ -2588,7 +2588,7 @@ def prog_path(program):
def get_version():
- return "2.0.12"
+ return "2.0.13"
def main(argv=None):
diff --git a/src/tophat.py b/src/tophat.py
index 34729ed..2310a49 100755
--- a/src/tophat.py
+++ b/src/tophat.py
@@ -182,7 +182,7 @@ use_BWT_FIFO = False # can only be set to True if use_zpacker is True and only w
unmapped_reads_fifo = None # if use_BWT_FIFO is True, this tricks bowtie into writing the
# unmapped reads into a compressed file
-samtools_path = None
+samtools_path = "samtools_0.1.18"
bowtie_path = None
fail_str = "\t[FAILED]\n"
gtf_juncs = None #file name with junctions extracted from given GFF file
@@ -1155,7 +1155,7 @@ def nonzeroFile(filepath):
fpath, fname=os.path.split(filepath)
fbase, fext =os.path.splitext(fname)
if fext.lower() == ".bam":
- samtools_view_cmd = ["samtools", "view", filepath]
+ samtools_view_cmd = [samtools_path, "view", filepath]
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
head_cmd = ["head", "-1"]
head = subprocess.Popen(head_cmd, stdin=samtools_view.stdout, stdout=subprocess.PIPE)
@@ -1553,15 +1553,16 @@ def get_samtools_version():
# Make sure the SAM tools are installed and are recent enough to be useful
def check_samtools():
- th_log("Checking for Samtools")
+ #th_log("Checking for Samtools")
global samtools_path
- samtools_path=prog_path("samtools")
- samtools_version_str, samtools_version_arr = get_samtools_version()
- if samtools_version_str == None:
- die("Error: Samtools not found on this system")
- elif samtools_version_arr[1] < 1 or samtools_version_arr[2] < 7:
- die("Error: TopHat requires Samtools 0.1.7 or later")
- th_logp("\t\tSamtools version:\t %s" % ".".join([str(x) for x in samtools_version_arr]))
+ samtools_path=prog_path("samtools_0.1.18")
+ #samtools_version_str, samtools_version_arr = get_samtools_version()
+ #if samtools_version_str == None:
+ if not samtools_path:
+ die("Error: Required samtools version not found on this system")
+ #elif samtools_version_arr[1] < 1 or samtools_version_arr[2] < 7:
+ # die("Error: TopHat2 requires Samtools 0.1.19")
+ #th_logp("\t\tSamtools version:\t %s" % ".".join([str(x) for x in samtools_version_arr]))
diff --git a/src/tophat_reports.cpp b/src/tophat_reports.cpp
index 91e39df..43d1a2e 100644
--- a/src/tophat_reports.cpp
+++ b/src/tophat_reports.cpp
@@ -2854,10 +2854,10 @@ for (; deletion_iter != deletions.end(); ++deletion_iter)
fprintf(stderr, "Warning: %lu small overhang junctions!\n", (long unsigned int)small_overhangs);
*/
- JunctionSet vfinal_junctions[num_threads];
- InsertionSet vfinal_insertions[num_threads];
- DeletionSet vfinal_deletions[num_threads];
- FusionSet vfinal_fusions[num_threads];
+ vector<JunctionSet> vfinal_junctions(num_threads);
+ vector<InsertionSet> vfinal_insertions(num_threads);
+ vector<DeletionSet> vfinal_deletions(num_threads);
+ vector<FusionSet> vfinal_fusions(num_threads);
vector<SAlignStats> alnStats(num_threads);
--
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