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debian/changelog
View file @ 8254f008
libucsc (0.0+git20200121.ba14f430+dfsg-1) UNRELEASED; urgency=medium
libucsc (0.0+git20200125.51bc9725+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #xxxxxx)
......
debian/copyright
View file @ 8254f008
......@@ -19,8 +19,6 @@ Files-Excluded:
src/g*
src/hca
src/hg
src/htslib/config.log
src/htslib/config.status
src/idbQuery
src/index
src/intronerator
......@@ -37,6 +35,8 @@ Files-Excluded:
src/x*
src/README
*/.gitignore
*/mgSixhi6.c
src/htslib
Comment: The LICENSE file in the root dir says:
LICENSE files in subdirectories override the text of this LICENSE file.
......@@ -214,112 +214,6 @@ Comment: lib/font/README says:
http://www.fontsquirrel.com/fonts/sail
is most probably the source of the sail font
Files: src/lib/font/mgSixhi6.c
Copyright: unknown
License: unknown
lib/font/README says:
.
Two additional fonts - sail and sixhi - were from other sources now lost
in the midsts of time.
Comment: Websearch to find back what was lost was not successful. It
can be assumed thst this single file can be distributed and the package
is non-free anyway.
Files: src/htslib/*
Copyright: © 2012-2016 Genome Research Ltd.
© 2008-2013 Broad Institute / Massachusetts Institute of Technology
© The Wellcome Trust Sanger Institute
© 2008-2012 by Attractive Chaos <attractor@live.co.uk>
License: MIT
Comment: Asked upstream for compatibility to Debian packaged version
https://github.com/ucscGenomeBrowser/kent/issues/13
Files: src/htslib/cram/*
Copyright: © 2012-2014 Genome Research Ltd.
© 1995-2003 MEDICAL RESEARCH COUNCIL
License: Various_BSD-3-Clause
The files in the 'cram' directory are under one or both of the following
licenses.
.
---------------------------------------------------------------------------
.
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.
.
3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
Institute nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.
.
THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD 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 GENOME RESEARCH LTD 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.
.
---------------------------------------------------------------------------
.
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.
.
3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
promote products derived from this software without specific prior written
permission.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 COPYRIGHT OWNER 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.
Files: md5.c
Copyright: No copyright is claimed
License: solar-MD5
This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
MD5 Message-Digest Algorithm (RFC 1321).
.
Homepage:
http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
.
Author:
Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
.
This software was written by Alexander Peslyak in 2001. No copyright is
claimed, and the software is hereby placed in the public domain.
In case this attempt to disclaim copyright and place the software in the
public domain is deemed null and void, then the software is
Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
general public under the following terms:
.
Redistribution and use in source and binary forms, with or without
modification, are permitted.
.
There's ABSOLUTELY NO WARRANTY, express or implied.
License: MIT
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
......
debian/patches/remove_mgSixhi6.patch 0 → 100644
View file @ 8254f008
Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 27 Jan 2020 09:12:00 +0100
Description: Remove font with unknown license
Files: src/lib/font/mgSixhi6.c
Copyright: unknown
License: unknown
lib/font/README says:
.
Two additional fonts - sail and sixhi - were from other sources now lost
in the midsts of time.
Comment: Websearch to find back what was lost was not successful.
--- a/src/lib/makefile
+++ b/src/lib/makefile
@@ -20,7 +20,7 @@ O = aliType.o annoAssembly.o annoFilter.
font/mgHelvetica12.o font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o \
font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o font/mgHelveticaBold12.o \
font/mgHelveticaBold14.o font/mgHelveticaBold18.o font/mgHelveticaBold24.o \
- font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o font/mgSail8.o \
+ font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSail8.o \
font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o font/mgTimes18.o \
font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o font/mgMenlo12.o \
fq.o fuzzyShow.o \
debian/patches/series
View file @ 8254f008
# use_debian_packaged_htslib.patch
unbundle-htslib.patch
remove_mgSixhi6.patch
src/blat/version.doc
View file @ 8254f008
......@@ -4,6 +4,7 @@
o (in 36x2) Fixed problem with -maxIntron set to non-default value on protein query.
o (in 36x3) Added ipv6 support.
o (in 36x4) Added _alt support.
o (in 36x5) If ipv6 disabled, retries with ipv4-only socket.
36:
o (in 35x1) added repMatch default values for tileSizes 16 to 18 in genoFind.c
......
src/htslib/INSTALL deleted 100644 → 0
View file @ f6cc218e
Basic Installation
==================
To build and install HTSlib, 'cd' to the htslib-1.x directory containing
the package's source and type the following commands:
./configure
make
make install
The './configure' command checks your build environment and allows various
optional functionality to be enabled (see Configuration below). If you
don't want to select any optional functionality, you may wish to omit
configure and just type 'make; make install' as for previous versions
of HTSlib. However if the build fails you should run './configure' as
it can diagnose the common reasons for build failures.
The 'make' command builds the HTSlib library and and various useful
utilities: bgzip, htsfile, and tabix. If compilation fails you should
run './configure' as it can diagnose problems with your build environment
that cause build failures.
The 'make install' command installs the libraries, library header files,
utilities, several manual pages, and a pkgconfig file to /usr/local.
The installation location can be changed by configuring with --prefix=DIR
or via 'make prefix=DIR install' (see Installation Locations below).
Configuration
=============
By default, './configure' examines your build environment, checking for
requirements such as the zlib development files, and arranges for a plain
HTSlib build. The following configure options can be used to enable
various features and specify further optional external requirements:
--enable-plugins
Use plugins to implement exotic file access protocols and other
specialised facilities. This enables such facilities to be developed
and packaged outwith HTSlib, and somewhat isolates HTSlib-using programs
from their library dependencies. By default, any enabled pluggable
facilities (such as iRODS and libcurl file access) are built directly
within HTSlib.
--with-plugin-dir=DIR
Specifies the directory into which plugins built while building HTSlib
should be installed; by default, LIBEXECDIR/htslib.
--with-plugin-path=DIR:DIR:DIR...
Specifies the list of directories that HTSlib will search for plugins.
By default, only the directory specified via --with-plugin-dir will be
searched; you can use --with-plugin-path='DIR:$(plugindir):DIR' and so
on to cause additional directories to be searched.
--with-irods[=DIR]
Specifies the location of the iRODS client library to use to enable
access to data objects stored in iRODS (<http://irods.org/>) via file
paths like 'irods:DATAOBJ'. DIR is the base of an iRODS source tree
such that the library is present as DIR/lib/core/obj/libRodsAPI.* and
headers are present under DIR/lib/api/include and so on. If '=DIR' is
omitted, $IRODS_HOME will be used as a base directory.
--enable-libcurl
Use libcurl (<http://curl.haxx.se/>) to implement network access to
remote files via FTP, HTTP, HTTPS, S3, etc. By default, HTSlib uses
its own simple networking code to provide access via FTP and HTTP only.
The configure script also accepts the usual options and environment variables
for tuning installation locations and compilers: type './configure --help'
for details. For example,
./configure CC=icc --prefix=/opt/icc-compiled
would specify that HTSlib is to be built with icc and installed into bin,
lib, etc subdirectories under /opt/icc-compiled.
Installation Locations
======================
By default, 'make install' installs HTSlib libraries under /usr/local/lib,
HTSlib header files under /usr/local/include, utility programs under
/usr/local/bin, etc. (To be precise, the header files are installed within
a fixed 'htslib' subdirectory under the specified .../include location.)
You can specify a different location to install HTSlib by configuring
with --prefix=DIR or specify locations for particular parts of HTSlib by
configuring with --libdir=DIR and so on. Type './configure --help' for
the full list of such install directory options.
Alternatively you can specify different locations at install time by
typing 'make prefix=DIR install' or 'make libdir=DIR install' and so on.
Consult the list of prefix/exec_prefix/etc variables near the top of the
Makefile for the full list of such variables that can be overridden.
You can also specify a staging area by typing 'make DESTDIR=DIR install',
possibly in conjunction with other --prefix or prefix=DIR settings.
For example,
make DESTDIR=/tmp/staging prefix=/opt
would install into bin, lib, etc subdirectories under /tmp/staging/opt.
src/htslib/LICENSE deleted 100644 → 0
View file @ f6cc218e
[Files in this distribution outwith the cram/ subdirectory are distributed
according to the terms of the following MIT/Expat license.]
The MIT/Expat License
Copyright (C) 2012-2014 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.
[Files within the cram/ subdirectory in this distribution are distributed
according to the terms of the following Modified 3-Clause BSD license.]
The Modified-BSD License
Copyright (C) 2012-2014 Genome Research Ltd.
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.
3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute
nor the names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD 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 GENOME RESEARCH LTD OR ITS 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.
[The use of a range of years within a copyright notice in this distribution
should be interpreted as being equivalent to a list of years including the
first and last year specified and all consecutive years between them.
For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
2011-2012" should be interpreted as being identical to a notice that reads
"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
that reads "Copyright (C) 2005-2012" should be interpreted as being identical
to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
2011, 2012".]
src/htslib/Makefile deleted 100644 → 0
View file @ f6cc218e
# Makefile for htslib, a C library for high-throughput sequencing data formats.
#
# Copyright (C) 2013-2015 Genome Research Ltd.
#
# Author: John Marshall <jm18@sanger.ac.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.
kentSrc = ..
include ${kentSrc}/inc/common.mk
#CC = gcc -p
AR = ar
RANLIB = ranlib
CPPFLAGS =
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
CFLAGS += -DKNETFILE_HOOKS -DUCSC_CRAM
EXTRA_CFLAGS_PIC = -fpic
LDFLAGS =
LIBS =
# For now these don't work too well as samtools also needs to know to
# add -lbz2 and -llzma if linking against the static libhts.a library.
# TODO This needs configury and adding to htslib.pc.in.
#
# # Bzip2 support; optionally used by CRAM.
# HAVE_LIBBZ2 := $(shell echo -e "\#include <bzlib.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes)
# ifeq "$(HAVE_LIBBZ2)" "yes"
# CPPFLAGS += -DHAVE_LIBBZ2
# LIBS += -lbz2
# endif
#
# # Lzma support; optionally used by CRAM.
# HAVE_LIBLZMA := $(shell echo -e "\#include <lzma.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes)
# ifeq "$(HAVE_LIBLZMA)" "yes"
# CPPFLAGS += -DHAVE_LIBLZMA
# LIBS += -llzma
# endif
prefix = /usr/local
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
includedir = $(prefix)/include
libdir = $(exec_prefix)/lib
libexecdir = $(exec_prefix)/libexec
datarootdir = $(prefix)/share
mandir = $(datarootdir)/man
man1dir = $(mandir)/man1
man5dir = $(mandir)/man5
pkgconfigdir= $(libdir)/pkgconfig
MKDIR_P = mkdir -p
INSTALL = install -p
INSTALL_PROGRAM = $(INSTALL)
INSTALL_DATA = $(INSTALL) -m 644
INSTALL_DIR = $(MKDIR_P) -m 755
# Set by config.mk if plugins are enabled
plugindir =
BUILT_PROGRAMS = \
bgzip \
htsfile \
tabix
BUILT_TEST_PROGRAMS = \
test/fieldarith \
test/hfile \
test/sam \
test/test-regidx \
test/test_view \
test/test-vcf-api \
test/test-vcf-sweep
#all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
all: lib-static
HTSPREFIX =
include htslib_vars.mk
PACKAGE_VERSION = 1.3
LIBHTS_SOVERSION = 1
# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
# even if this is a dirty or untagged Git working tree.
NUMERIC_VERSION = $(PACKAGE_VERSION)
# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
# description of the working tree: either a release tag with the same value
# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag.
# Much of this is also GNU Make-specific. If you don't have GNU Make and/or
# are not building from a Git repository, comment out this conditional.
ifneq "$(wildcard .git)" ""
original_version := $(PACKAGE_VERSION)
PACKAGE_VERSION := $(shell git describe --always --dirty)
# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag
# with a numeric name, revert $(NUMERIC_VERSION) to the original version number
# written above, but with the patchlevel field bumped to 255.
ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "."
empty :=
NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255)
endif
# Force version.h to be remade if $(PACKAGE_VERSION) has changed.
version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
endif
version.h:
echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@
print-version:
@echo $(PACKAGE_VERSION)
.SUFFIXES: .bundle .c .o .pico .so
.c.o:
$(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $<
.c.pico:
$(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
LIBHTS_OBJS = \
kfunc.o \
knetfile.o \
kstring.o \
bgzf.o \
faidx.o \
hfile.o \
hfile_net.o \
hts.o \
md5.o \
regidx.o \
sam.o \
synced_bcf_reader.o \
vcf_sweep.o \
tbx.o \
vcf.o \
vcfutils.o \
cram/cram_codecs.o \
cram/cram_decode.o \
cram/cram_encode.o \
cram/cram_external.o \
cram/cram_index.o \
cram/cram_io.o \
cram/cram_samtools.o \
cram/cram_stats.o \
cram/files.o \
cram/mFILE.o \
cram/open_trace_file.o \
cram/pooled_alloc.o \
cram/rANS_static.o \
cram/sam_header.o \
cram/string_alloc.o \
cram/thread_pool.o \
cram/vlen.o \
cram/zfio.o
PLUGIN_OBJS =
cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h)
cram_io_h = cram/cram_io.h $(cram_misc_h)
cram_misc_h = cram/misc.h cram/os.h
cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h)
cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h)
cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
hfile_internal_h = hfile_internal.h $(htslib_hfile_h)
hts_internal_h = hts_internal.h $(htslib_hts_h)
# To be effective, config.mk needs to appear after most Makefile variables are
# set but before most rules appear, so that it can both use previously-set
# variables in its own rules' prerequisites and also update variables for use
# in later rules' prerequisites.
# If your make doesn't accept -include, change this to 'include' if you are
# using the configure script or just comment the line out if you are not.
-include config.mk
# Usually config.h is generated by running configure or config.status,
# but if those aren't used create a default config.h here.
config.h:
echo '/* Empty config.h generated by Makefile */' > $@
lib-static: libhts.a
# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have
# GNU Make, comment out the parts of this conditional that don't apply.
PLATFORM := $(shell uname -s)
ifeq "$(PLATFORM)" "Darwin"
SHLIB_FLAVOUR = dylib
lib-shared: libhts.dylib
BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle)
else
SHLIB_FLAVOUR = so
lib-shared: libhts.so
BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so)
endif
plugins: $(BUILT_PLUGINS)
libhts.a: $(LIBHTS_OBJS)
@-rm -f $@
$(AR) -rc $@ $(LIBHTS_OBJS)
-$(RANLIB) $@
# The target here is libhts.so, as that is the built file that other rules
# depend upon and that is used when -lhts appears in other program's recipes.
# As a byproduct invisible to make, libhts.so.NN is also created, as it is the
# file used at runtime (when $LD_LIBRARY_PATH includes the build directory).
libhts.so: $(LIBHTS_OBJS:.o=.pico)
$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS)
ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH
# includes this project's build directory).
libhts.dylib: $(LIBHTS_OBJS)
$(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS)
ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
.pico.so:
$(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS)
.o.bundle:
$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h)
kstring.o kstring.pico: kstring.c $(htslib_kstring_h)
knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h)
hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h)
hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h)
hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h)
vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h)
sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h)
tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h)
faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h)
synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h)
vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h)
kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h)
regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h)
md5.o md5.pico: md5.c config.h $(htslib_hts_h)
plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h)
cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h)
cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h)
cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h)
cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h
cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h
cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h)
cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h
cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h
cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h
cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h
cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h
cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h
bgzip: bgzip.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS)
htsfile: htsfile.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS)
tabix: tabix.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS)
bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h)
htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h)
# For tests that might use it, set $REF_PATH explicitly to use only reference
# areas within the test suite (or set it to ':' to use no reference areas).
check test: htsfile $(BUILT_TEST_PROGRAMS)
test/fieldarith test/fieldarith.sam
test/hfile
test/sam test/ce.fa test/faidx.fa
test/test-regidx
cd test && REF_PATH=: ./test_view.pl
cd test && REF_PATH=: ./test.pl
test/fieldarith: test/fieldarith.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS)
test/hfile: test/hfile.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS)
test/sam: test/sam.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS)
test/test-regidx: test/test-regidx.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS)
test/test_view: test/test_view.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS)
test/test-vcf-api: test/test-vcf-api.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS)
test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS)
test/fieldarith.o: test/fieldarith.c $(htslib_sam_h)
test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h)
test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h)
test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h)
test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h)
install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
$(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
$(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir)
$(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir)
installdirs:
$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir)
if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi
# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z,
# with symlinks libhts.so (used via -lhts during linking of client programs)
# and libhts.so.NN (used by client executables at runtime).
install-so: libhts.so installdirs
$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
install-dylib: libhts.dylib installdirs
$(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib
ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib
ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib
# Substitute these pseudo-autoconf variables only at install time
# so that "make install prefix=/prefix/path" etc continue to work.
install-pkgconfig: installdirs
sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc
chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc
# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides
# flags for building against the uninstalled library in this build directory.
htslib-uninstalled.pc: htslib.pc.in
sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@
testclean:
-rm -f test/*.tmp test/*.tmp.*
mostlyclean: testclean
-rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
clean: mostlyclean clean-$(SHLIB_FLAVOUR)
-rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS)
distclean maintainer-clean: clean
-rm -f config.cache config.h config.log config.mk config.status
-rm -f TAGS *-uninstalled.pc
clean-so:
-rm -f libhts.so libhts.so.*
clean-dylib:
-rm -f libhts.dylib libhts.*.dylib
tags TAGS:
ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h
# We recommend libhts-using programs be built against a separate htslib
# installation. However if you feel that you must bundle htslib source
# code with your program, this hook enables Automake-style "make dist"
# for this subdirectory. If you do bundle an htslib snapshot, please
# add identifying information to $(PACKAGE_VERSION) as appropriate.
# (The wildcards attempt to omit non-exported files (.git*, README.md,
# etc) and other detritus that might be in the top-level directory.)
distdir:
tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x)
+cd $(distdir) && $(MAKE) distclean
force:
.PHONY: all check clean distclean distdir force
.PHONY: install install-pkgconfig installdirs lib-shared lib-static
.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean
.PHONY: clean-so install-so
.PHONY: clean-dylib install-dylib
src/htslib/NEWS deleted 100644 → 0
View file @ f6cc218e
Noteworthy changes in release 1.3 (15 December 2015)
* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
and FTP, when HTSlib is configured to use libcurl for network file access
rather than the included basic knetfile networking.
* HTSlib can be built to use remote access hFILE backends (such as iRODS
and libcurl) via a plugin mechanism. This allows other backends to be
easily added and facilitates building tools that use HTSlib, as they
don't need to be linked with the backends' various required libraries.
* fai_build() and samtools faidx now accept initial whitespace in ">"
headers (e.g., "> chr1 description" is taken to refer to "chr1").
* tabix --only-header works again (was broken in 1.2.x; #249).
* HTSlib's configure script and Makefile now fully support the standard
convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
as needed. Previously the Makefile listened to $(LDLIBS) instead; if you
were overriding that, you should now override LIBS rather than LDLIBS.
* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296.
Noteworthy changes in release 1.2.1 (3 February 2015)
* Reinstated hts_file_type() and FT_* macros, which were available until 1.1
but briefly removed in 1.2. This function is deprecated and will be removed
in a future release -- you should use hts_detect_format() etc instead
Noteworthy changes in release 1.2 (2 February 2015)
* HTSlib now has a configure script which checks your build environment
and allows for selection of optional extras. See INSTALL for details
* By default, reference sequences are fetched from the EBI CRAM Reference
Registry and cached in your $HOME cache directory. This behaviour can
be controlled by setting REF_PATH and REF_CACHE enviroment variables
(see the samtools(1) man page for details)
* Numerous CRAM improvements:
- Support for CRAM v3.0, an upcoming revision to CRAM supporting
better compression and per-container checksums
- EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks)
- Non-standard values for PNEXT and TLEN fields are now preserved
- hts_set_fai_filename() now provides a reference file when encoding
- Generated read names are now numbered from 1, rather than being
labelled 'slice:record-in-slice'
- Multi-threading and speed improvements
* New htsfile command for identifying file formats, and corresponding
file format detection APIs
* New tabix --regions FILE, --targets FILE options for filtering via BED files
* Optional iRODS file access, disabled by default. Configure with --with-irods
to enable accessing iRODS data objects directly via 'irods:DATAOBJ'
* All occurences of 2^29 in the source have been eliminated, so indexing
and querying against reference sequences larger than 512Mbp works (when
using CSI indices)
* Support for plain GZIP compression in various places
* VCF header editing speed improvements
* Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table)
* Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1.
Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually
faidx_fetch_nseq() will be deprecated and removed [#156]
* Fixed bugs #141, #152, #155, #158, #159, and various memory leaks
src/htslib/README deleted 100644 → 0
View file @ f6cc218e
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.
See INSTALL for building and installation instructions.
src/htslib/bgzf.c deleted 100644 → 0
View file @ f6cc218e
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src/htslib/bgzip.c deleted 100644 → 0
View file @ f6cc218e
/* bgzip.c -- Block compression/decompression utility.
Copyright (C) 2008, 2009 Broad Institute / Massachusetts Institute of Technology
Copyright (C) 2010, 2013-2015 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 notices 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 <config.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <fcntl.h>
#include <unistd.h>
#include <errno.h>
#include <stdarg.h>
#include <getopt.h>
#include <sys/stat.h>
#include "htslib/bgzf.h"
#include "htslib/hts.h"
static const int WINDOW_SIZE = 64 * 1024;
static void error(const char *format, ...)
{
va_list ap;
va_start(ap, format);
vfprintf(stderr, format, ap);
va_end(ap);
exit(EXIT_FAILURE);
}
static int confirm_overwrite(const char *fn)
{
int save_errno = errno;
int ret = 0;
if (isatty(STDIN_FILENO)) {
char c;
fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
if (scanf("%c", &c) == 1 && (c == 'Y' || c == 'y')) ret = 1;
}
errno = save_errno;
return ret;
}
static int bgzip_main_usage(void)
{
fprintf(stderr, "\n");
fprintf(stderr, "Version: %s\n", hts_version());
fprintf(stderr, "Usage: bgzip [OPTIONS] [FILE] ...\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -b, --offset INT decompress at virtual file pointer (0-based uncompressed offset)\n");
fprintf(stderr, " -c, --stdout write on standard output, keep original files unchanged\n");
fprintf(stderr, " -d, --decompress decompress\n");
fprintf(stderr, " -f, --force overwrite files without asking\n");
fprintf(stderr, " -h, --help give this help\n");
fprintf(stderr, " -i, --index compress and create BGZF index\n");
fprintf(stderr, " -I, --index-name FILE name of BGZF index file [file.gz.gzi]\n");
fprintf(stderr, " -r, --reindex (re)index compressed file\n");
fprintf(stderr, " -s, --size INT decompress INT bytes (uncompressed size)\n");
fprintf(stderr, " -@, --threads INT number of compression threads to use [1]\n");
fprintf(stderr, "\n");
return 1;
}
int main(int argc, char **argv)
{
int c, compress, pstdout, is_forced, index = 0, reindex = 0;
BGZF *fp;
void *buffer;
long start, end, size;
char *index_fname = NULL;
int threads = 1;
static struct option loptions[] =
{
{"help",0,0,'h'},
{"offset",1,0,'b'},
{"stdout",0,0,'c'},
{"decompress",0,0,'d'},
{"force",0,0,'f'},
{"index",0,0,'i'},
{"index-name",1,0,'I'},
{"reindex",0,0,'r'},
{"size",1,0,'s'},
{"threads",1,0,'@'},
{0,0,0,0}
};
compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
while((c = getopt_long(argc, argv, "cdh?fb:@:s:iI:r",loptions,NULL)) >= 0){
switch(c){
case 'd': compress = 0; break;
case 'c': pstdout = 1; break;
case 'b': start = atol(optarg); compress = 0; pstdout = 1; break;
case 's': size = atol(optarg); pstdout = 1; break;
case 'f': is_forced = 1; break;
case 'i': index = 1; break;
case 'I': index_fname = optarg; break;
case 'r': reindex = 1; compress = 0; break;
case '@': threads = atoi(optarg); break;
case 'h':
case '?': return bgzip_main_usage();
}
}
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);
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)
fp = bgzf_open("-", "w");
else
{
char *name = malloc(strlen(argv[optind]) + 5);
strcpy(name, argv[optind]);
strcat(name, ".gz");
fp = bgzf_open(name, is_forced? "w" : "wx");
if (fp == NULL && errno == EEXIST && confirm_overwrite(name))
fp = bgzf_open(name, "w");
if (fp == NULL) {
fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno));
free(name);
return 1;
}
free(name);
}
}
else if (!pstdout && isatty(fileno((FILE *)stdout)) )
return bgzip_main_usage();
else if ( index && !index_fname )
{
fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n");
return 1;
}
else
fp = bgzf_open("-", "w");
if (threads > 1)
bgzf_mt(fp, threads, 256);
if ( index ) bgzf_index_build_init(fp);
buffer = malloc(WINDOW_SIZE);
while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
if (bgzf_write(fp, buffer, c) < 0) error("Could not write %d bytes: Error %d\n", c, fp->errcode);
if ( index )
{
if ( index_fname ) bgzf_index_dump(fp, index_fname, NULL);
else bgzf_index_dump(fp, argv[optind], ".gz.gzi");
}
if (bgzf_close(fp) < 0) error("Close failed: Error %d", fp->errcode);
if (argc > optind && !pstdout) unlink(argv[optind]);
free(buffer);
close(f_src);
return 0;
}
else if ( reindex )
{
if ( argc>optind )
{
fp = bgzf_open(argv[optind], "r");
if ( !fp ) error("[bgzip] Could not open file: %s\n", argv[optind]);
}
else
{
if ( !index_fname ) error("[bgzip] Index file name expected when reading from stdin\n");
fp = bgzf_open("-", "r");
if ( !fp ) error("[bgzip] Could not read from stdin: %s\n", strerror(errno));
}
buffer = malloc(BGZF_BLOCK_SIZE);
bgzf_index_build_init(fp);
int ret;
while ( (ret=bgzf_read(fp, buffer, BGZF_BLOCK_SIZE))>0 ) ;
free(buffer);
if ( ret<0 ) error("Is the file gzipped or bgzipped? The latter is required for indexing.\n");
if ( index_fname )
bgzf_index_dump(fp, index_fname, NULL);
else
bgzf_index_dump(fp, argv[optind], ".gzi");
if ( bgzf_close(fp)<0 ) error("Close failed: Error %d\n",fp->errcode);
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 {
const int wrflags = O_WRONLY | O_CREAT | O_TRUNC;
name = strdup(argv[optind]);
name[strlen(name) - 3] = '\0';
f_dst = open(name, is_forced? wrflags : wrflags|O_EXCL, 0666);
if (f_dst < 0 && errno == EEXIST && confirm_overwrite(name))
f_dst = open(name, wrflags, 0666);
if (f_dst < 0) {
fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno));
free(name);
return 1;
}
free(name);
}
}
else if (!pstdout && isatty(fileno((FILE *)stdin)) )
return bgzip_main_usage();
else
{
f_dst = fileno(stdout);
fp = bgzf_open("-", "r");
if (fp == NULL) {
fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
return 1;
}
}
buffer = malloc(WINDOW_SIZE);
if ( start>0 )
{
if ( bgzf_index_load(fp, argv[optind], ".gzi") < 0 ) error("Could not load index: %s.gzi\n", argv[optind]);
if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %d-th (uncompressd) byte\n", start);
}
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) error("Could not read %d bytes: Error %d\n", (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start), fp->errcode);
start += c;
if ( write(f_dst, buffer, c) != c ) error("Could not write %d bytes\n", c);
if (end >= 0 && start >= end) break;
}
free(buffer);
if (bgzf_close(fp) < 0) error("Close failed: Error %d\n",fp->errcode);
if (!pstdout) unlink(argv[optind]);
return 0;
}
return 0;
}
src/htslib/config.h deleted 100644 → 0
View file @ f6cc218e
/* config.h. Generated from config.h.in by configure. */
/* config.h.in -- template for config.h. If you use configure, this file
provides #defines reflecting your configuration choices. If you don't
run configure, suitable conservative defaults will be used.
This template file can be updated with autoheader, but do so carefully
as autoheader adds #defines such as PACKAGE_* that we don't want. */
/* Define if HTSlib should enable plugins. */
/* #undef ENABLE_PLUGINS */
/* Define if you have the Common Crypto library. */
/* #undef HAVE_COMMONCRYPTO */
/* Define to 1 if you have the `gmtime_r' function. */
#define HAVE_GMTIME_R 1
/* Define if you have libcrypto-style HMAC(). */
/* #undef HAVE_HMAC */
/* Define to 1 if iRODS file access is enabled. */
/* #undef HAVE_IRODS */
/* Define if libcurl file access is enabled. */
/* #undef HAVE_LIBCURL */
/* Define to 1 if you have a working `mmap' system call. */
#define HAVE_MMAP 1
src/htslib/config.h.in deleted 100644 → 0
View file @ f6cc218e
/* config.h.in -- template for config.h. If you use configure, this file
provides #defines reflecting your configuration choices. If you don't
run configure, suitable conservative defaults will be used.
This template file can be updated with autoheader, but do so carefully
as autoheader adds #defines such as PACKAGE_* that we don't want. */
/* Define if HTSlib should enable plugins. */
#undef ENABLE_PLUGINS
/* Define if you have the Common Crypto library. */
#undef HAVE_COMMONCRYPTO
/* Define to 1 if you have the `gmtime_r' function. */
#undef HAVE_GMTIME_R
/* Define if you have libcrypto-style HMAC(). */
#undef HAVE_HMAC
/* Define to 1 if iRODS file access is enabled. */
#undef HAVE_IRODS
/* Define if libcurl file access is enabled. */
#undef HAVE_LIBCURL
/* Define to 1 if you have a working `mmap' system call. */
#undef HAVE_MMAP
src/htslib/config.mk deleted 100644 → 0
View file @ f6cc218e
# Optional configure Makefile overrides for htslib.
#
# Copyright (C) 2015 Genome Research Ltd.
#
# Author: John Marshall <jm18@sanger.ac.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.
# This is config.mk. Generated from config.mk.in by configure.
#
# If you use configure, this file overrides variables and augments rules
# in the Makefile to reflect your configuration choices. If you don't run
# configure, the main Makefile contains suitable conservative defaults.
prefix = /usr/local
exec_prefix = ${prefix}
bindir = ${exec_prefix}/bin
includedir = ${prefix}/include
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
datarootdir = ${prefix}/share
mandir = ${datarootdir}/man
#CC = gcc34
RANLIB = ranlib
CPPFLAGS =
#CFLAGS = -g -O2
LDFLAGS =
LIBS =
# Lowercase here indicates these are "local" to config.mk
plugin_OBJS =
noplugin_LDFLAGS =
noplugin_LIBS =
# ifeq/.../endif, +=, and target-specific variables are GNU Make-specific.
# If you don't have GNU Make, comment out this conditional and note that
# to enable iRODS you will need to implement the following elsewhere.
ifeq "iRODS-disabled" "iRODS-enabled"
IRODS_HOME ?= /disabled
IRODS_CPPFLAGS = \
-I$(IRODS_HOME)/lib/api/include \
-I$(IRODS_HOME)/lib/core/include \
-I$(IRODS_HOME)/lib/md5/include \
-I$(IRODS_HOME)/lib/sha1/include \
-I$(IRODS_HOME)/server/core/include \
-I$(IRODS_HOME)/server/drivers/include \
-I$(IRODS_HOME)/server/icat/include
IRODS_LDFLAGS = -L$(IRODS_HOME)/lib/core/obj
IRODS_LIBS = -lRodsAPIs -lgssapi_krb5
plugin_OBJS += hfile_irods.o
hfile_irods.o hfile_irods.pico: CPPFLAGS += $(IRODS_CPPFLAGS)
hfile_irods.so hfile_irods.bundle: LDFLAGS += $(IRODS_LDFLAGS)
hfile_irods.so hfile_irods.bundle: LIBS += $(IRODS_LIBS)
noplugin_LDFLAGS += $(IRODS_LDFLAGS)
noplugin_LIBS += $(IRODS_LIBS)
endif
ifeq "libcurl-disabled" "libcurl-enabled"
LIBCURL_LIBS = -lcurl
plugin_OBJS += hfile_libcurl.o
hfile_libcurl.so hfile_libcurl.bundle: LIBS += $(LIBCURL_LIBS)
noplugin_LIBS += $(LIBCURL_LIBS)
endif
ifeq "plugins-no" "plugins-yes"
plugindir = $(libexecdir)/htslib
pluginpath = $(libexecdir)/htslib
LIBHTS_OBJS += plugin.o
PLUGIN_OBJS += $(plugin_OBJS)
plugin.o plugin.pico: CPPFLAGS += -DPLUGINPATH=\"$(pluginpath)\"
else
LIBHTS_OBJS += $(plugin_OBJS)
LDFLAGS += $(noplugin_LDFLAGS)
LIBS += $(noplugin_LIBS)
endif
src/htslib/config.mk.in deleted 100644 → 0
View file @ f6cc218e
# Optional configure Makefile overrides for htslib.
#
# Copyright (C) 2015 Genome Research Ltd.
#
# Author: John Marshall <jm18@sanger.ac.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.
# This is @configure_input@
#
# If you use configure, this file overrides variables and augments rules
# in the Makefile to reflect your configuration choices. If you don't run
# configure, the main Makefile contains suitable conservative defaults.
prefix = @prefix@
exec_prefix = @exec_prefix@
bindir = @bindir@
includedir = @includedir@
libdir = @libdir@
libexecdir = @libexecdir@
datarootdir = @datarootdir@
mandir = @mandir@
CC = @CC@
RANLIB = @RANLIB@
CPPFLAGS = @CPPFLAGS@
CFLAGS = @CFLAGS@
LDFLAGS = @LDFLAGS@
LIBS = @LIBS@
# Lowercase here indicates these are "local" to config.mk
plugin_OBJS =
noplugin_LDFLAGS =
noplugin_LIBS =
# ifeq/.../endif, +=, and target-specific variables are GNU Make-specific.
# If you don't have GNU Make, comment out this conditional and note that
# to enable iRODS you will need to implement the following elsewhere.
ifeq "iRODS-@irods@" "iRODS-enabled"
@define_IRODS_HOME@
IRODS_CPPFLAGS = \
-I$(IRODS_HOME)/lib/api/include \
-I$(IRODS_HOME)/lib/core/include \
-I$(IRODS_HOME)/lib/md5/include \
-I$(IRODS_HOME)/lib/sha1/include \
-I$(IRODS_HOME)/server/core/include \
-I$(IRODS_HOME)/server/drivers/include \
-I$(IRODS_HOME)/server/icat/include
IRODS_LDFLAGS = -L$(IRODS_HOME)/lib/core/obj
IRODS_LIBS = -lRodsAPIs -lgssapi_krb5
plugin_OBJS += hfile_irods.o
hfile_irods.o hfile_irods.pico: CPPFLAGS += $(IRODS_CPPFLAGS)
hfile_irods.so hfile_irods.bundle: LDFLAGS += $(IRODS_LDFLAGS)
hfile_irods.so hfile_irods.bundle: LIBS += $(IRODS_LIBS)
noplugin_LDFLAGS += $(IRODS_LDFLAGS)
noplugin_LIBS += $(IRODS_LIBS)
endif
ifeq "libcurl-@libcurl@" "libcurl-enabled"
LIBCURL_LIBS = -lcurl @CRYPTO_LIBS@
plugin_OBJS += hfile_libcurl.o
hfile_libcurl.so hfile_libcurl.bundle: LIBS += $(LIBCURL_LIBS)
noplugin_LIBS += $(LIBCURL_LIBS)
endif
ifeq "plugins-@enable_plugins@" "plugins-yes"
plugindir = @plugindir@
pluginpath = @pluginpath@
LIBHTS_OBJS += plugin.o
PLUGIN_OBJS += $(plugin_OBJS)
plugin.o plugin.pico: CPPFLAGS += -DPLUGINPATH=\"$(pluginpath)\"
else
LIBHTS_OBJS += $(plugin_OBJS)
LDFLAGS += $(noplugin_LDFLAGS)
LIBS += $(noplugin_LIBS)
endif
src/htslib/configure deleted 100755 → 0
View file @ f6cc218e
This diff is collapsed.
src/htslib/configure.ac deleted 100644 → 0
View file @ f6cc218e
# Configure script for htslib, a C library for high-throughput sequencing data.
#
# Copyright (C) 2015 Genome Research Ltd.
#
# Author: John Marshall <jm18@sanger.ac.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.
dnl Process this file with autoconf to produce a configure script
AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER
AC_CONFIG_SRCDIR(hts.c)
AC_CONFIG_HEADERS(config.h)
dnl Copyright notice to be copied into the generated configure script
AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
This configure script is free software: you are free to change and
redistribute it. There is NO WARRANTY, to the extent permitted by law.])
AC_PROG_CC
AC_PROG_RANLIB
need_crypto=no
AC_ARG_WITH([irods],
[AS_HELP_STRING([[--with-irods[=DIR]]],
[use RodsAPIs library (in DIR) to support iRODS URLs])],
[case $withval in
no) irods=disabled ;;
yes) irods=enabled ;;
*) irods=enabled; IRODS_HOME=$withval ;;
esac],
[irods=disabled])
AC_ARG_ENABLE([libcurl],
[AS_HELP_STRING([--enable-libcurl],
[enable libcurl-based support for http/https/etc URLs])],
[], [enable_libcurl=no])
AC_ARG_ENABLE([plugins],
[AS_HELP_STRING([--enable-plugins],
[enable separately-compiled plugins for file access])],
[], [enable_plugins=no])
AC_SUBST(enable_plugins)
AC_ARG_WITH([plugin-dir],
[AS_HELP_STRING([--with-plugin-dir=DIR],
[plugin installation location [LIBEXECDIR/htslib]])],
[case $withval in
yes|no) AC_MSG_ERROR([no directory specified for --with-plugin-dir]) ;;
esac],
[with_plugin_dir='$(libexecdir)/htslib'])
AC_SUBST([plugindir], $with_plugin_dir)
AC_ARG_WITH([plugin-path],
[AS_HELP_STRING([--with-plugin-path=PATH],
[default HTS_PATH plugin search path [PLUGINDIR]])],
[case $withval in
yes) AC_MSG_ERROR([no path specified for --with-plugin-path]) ;;
no) with_plugin_path= ;;
esac],
[with_plugin_path=$with_plugin_dir])
AC_SUBST([pluginpath], $with_plugin_path)
dnl FIXME This pulls in dozens of standard header checks
AC_FUNC_MMAP
AC_CHECK_FUNCS(gmtime_r)
if test $enable_plugins != no; then
AC_SEARCH_LIBS([dlopen], [dl], [],
[AC_MSG_ERROR([dlopen() not found
Plugin support requires dynamic linking facilities from the operating system.
Either configure with --disable-plugins or resolve this error to build HTSlib.])])
# TODO Test whether this is required and/or needs tweaking per-platform
LDFLAGS="$LDFLAGS -rdynamic"
AC_DEFINE([ENABLE_PLUGINS], 1, [Define if HTSlib should enable plugins.])
fi
save_LIBS=$LIBS
zlib_devel=ok
dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests
AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;])
AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing])
LIBS=$save_LIBS
if test $zlib_devel != ok; then
AC_MSG_ERROR([zlib development files not found
HTSlib uses compression routines from the zlib library <http://zlib.net>.
Building HTSlib requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed.
FAILED. This error must be resolved in order to build HTSlib successfully.])
fi
if test $irods = enabled; then
# TODO Also test whether we require libgssapi_krb5 and AC_CHECK_LIB it
save_LDFLAGS=$LDFLAGS
LDFLAGS="$LDFLAGS -L$IRODS_HOME/lib/core/obj"
AC_CHECK_LIB([RodsAPIs], [getRodsEnvFileName],
[case $with_irods in
yes) define_IRODS_HOME='# Uses $(IRODS_HOME) from the environment' ;;
*) define_IRODS_HOME="IRODS_HOME = $with_irods" ;;
esac],
[AC_MSG_ERROR([iRODS development files not found
Support for iRODS URLs requires the libRodsAPI client library and headers.
Configure with --with-irods=DIR (or just --with-irods if \$IRODS_HOME has
been exported with a suitable value), where DIR is the base of an iRODS tree
such that the library is present as DIR/lib/core/obj/libRodsAPI.* and headers
are present under DIR/lib/api/include and so on.])],
[-lgssapi_krb5 -lpthread])
LDFLAGS=$save_LDFLAGS
AC_DEFINE([HAVE_IRODS], 1, [Define to 1 if iRODS file access is enabled.])
else
define_IRODS_HOME='IRODS_HOME ?= /disabled'
fi
AC_SUBST([irods])
AC_SUBST([define_IRODS_HOME])
libcurl=disabled
if test "$enable_libcurl" != no; then
AC_CHECK_LIB([curl], [curl_easy_pause],
[AC_DEFINE([HAVE_LIBCURL], 1, [Define if libcurl file access is enabled.])
libcurl=enabled],
[AC_CHECK_LIB([curl], [curl_easy_init],
[message="library is too old (7.18+ required)"],
[message="library not found"])
case "$enable_libcurl" in
check) AC_MSG_WARN([libcurl not enabled: $message]) ;;
*) AC_MSG_ERROR([libcurl $message
Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.haxx.se/libcurl/>. Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions)
is installed.
Either configure with --disable-libcurl or resolve this error to build HTSlib.])
;;
esac])
need_crypto=yes
fi
AC_SUBST([libcurl])
CRYPTO_LIBS=
if test $need_crypto != no; then
AC_CHECK_FUNC([CCHmac],
[AC_DEFINE([HAVE_COMMONCRYPTO], 1,
[Define if you have the Common Crypto library.])],
[save_LIBS=$LIBS
AC_SEARCH_LIBS([HMAC], [crypto],
[AC_DEFINE([HAVE_HMAC], 1, [Define if you have libcrypto-style HMAC().])
case "$ac_cv_search_HMAC" in
-l*) CRYPTO_LIBS=$ac_cv_search_HMAC ;;
esac],
[AC_MSG_ERROR([SSL development files not found
Support for AWS S3 URLs requires routines from an SSL library. Building
HTSlib with libcurl enabled requires SSL development files to be installed
on the build machine; you may need to ensure a package such as libgnutls-dev,
libnss3-dev, or libssl-dev (on Debian or Ubuntu Linux, corresponding to the
libcurl4-*-dev package installed) or similar on RPM-based Linux distributions.
Either configure with --disable-libcurl or resolve this error to build HTSlib.])])
LIBS=$save_LIBS])
fi
AC_SUBST([CRYPTO_LIBS])
AC_CONFIG_FILES(config.mk)
AC_OUTPUT
src/htslib/cram/cram.h deleted 100644 → 0
View file @ f6cc218e
/*
Copyright (c) 2012-2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
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.
3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
Institute nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD 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 GENOME RESEARCH LTD 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.
*/
/*! \file
* CRAM interface.
*
* Consider using the higher level hts_*() API for programs that wish to
* be file format agnostic (see htslib/hts.h).
*
* This API should be used for CRAM specific code. The specifics of the
* public API are implemented in cram_io.h, cram_encode.h and cram_decode.h
* although these should not be included directly (use this file instead).
*/
#ifndef _CRAM_H_
#define _CRAM_H_
#include "cram/cram_samtools.h"
#include "cram/sam_header.h"
#include "cram_structs.h"
#include "cram_io.h"
#include "cram_encode.h"
#include "cram_decode.h"
#include "cram_stats.h"
#include "cram_codecs.h"
#include "cram_index.h"
// Validate against the external cram.h,
//
// This contains duplicated portions from cram_io.h and cram_structs.h,
// so we want to ensure that the prototypes match.
#include "htslib/cram.h"
#endif
src/htslib/cram/cram_codecs.c deleted 100644 → 0
View file @ f6cc218e
This diff is collapsed.