debian/changelog

-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

@@ -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

+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

 # use_debian_packaged_htslib.patch
 unbundle-htslib.patch
+remove_mgSixhi6.patch

src/blat/version.doc

@@ -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

-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

-[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

-# 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

-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

-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/bgzip.c

-/* 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

-/* 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

-/* 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

-#  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

-#  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.ac

-# 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

-/*
-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