Release 1.0: first htslib-based samtools release

.gitignore

@@ -1,14 +1,19 @@
 *.o
-.*.swp
-*.a
 *.dSYM
-.DS_Store
-/bcftools/bcftools
+*~
+/version.h
+
+lib*.a
+
+/bgzip
 /misc/ace2sam
-/misc/bamcheck
 /misc/maq2sam-long
 /misc/maq2sam-short
 /misc/md5fa
 /misc/md5sum-lite
 /misc/wgsim
 /samtools
+
+/TAGS
+
+core

.travis.yml

@@ -5,4 +5,14 @@ compiler:
   - clang
   - gcc
 
-script: make CC=$CC
+matrix:
+  include:
+    # An unoptimised C99 build, for detecting non-static inline functions
+    - compiler: gcc
+      env: CFLAGS="-std=gnu99 -O0"
+
+before_script:
+  - git clone --depth=5 --branch=develop git://github.com/samtools/htslib.git
+  - export HTSDIR=./htslib
+
+script: make -e && make -e test

AUTHORS

@@ -7,14 +7,12 @@ underlying indexable compression format for the BAM format. BGZF does
 not support arithmetic between file offsets.
 
 Jue Ruan for the Beijing Genome Institute designed and implemented the
-RAZF format, an alternative indexable compression format. RAZF supports
-arithmetic between file offsets, at the cost of increased index file
-size and the full compatibility with gzip. RAZF is optional and only
-used in `faidx' for indexing RAZF compressed fasta files.
+RAZF format, an alternative indexable compression format. RAZF is no longer
+used by or provided with SAMtools. Source code remains available in older
+SAMtools 0.1.x releases and from the standalone branch in the repository.
 
 Colin Hercus updated novo2sam.pl to support gapped alignment by
 novoalign.
 
 Petr Danecek contributed the header parsing library sam_header.c and 
-sam2vcf.pl script and added knet support to the RAZF library.
-
+sam2vcf.pl script.

INSTALL

@@ -1,30 +1,49 @@
 System Requirements
 ===================
 
-SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
-preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
-file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
-diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.
+Samtools and HTSlib depend on the zlib library <http://zlib.net>.  Building
+them 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/yum-based distributions) is installed.
+
+SAMtools' faidx is able to index a bgzip-compressed FASTA file to save
+diskspace.
 
 The text-based viewer (tview) requires the GNU ncurses library
 <http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
 the modern Linux/Unix distributions. If you do not have this library installed,
 you can still compile the rest of SAMtools by manually changing:
 `-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
 comment out the line starting with `LIBCURSES='.
+Note that on some systems the library is available as -lcurses while on others
+as -lnurses. This can be set in Makefile by setting LIBCURSES= -lcurses vs
+-lncurses.
 
 
 Compilation
 ===========
 
-Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
-razip with `make razip'.
+'cd' to the samtools-1.x directory containing the package's source and type
+'make' to compile samtools.
+
+This samtools release contains a copy of HTSlib which will be used to build
+samtools.  If you already have a system-installed HTSlib or another HTSlib
+that you would prefer to build against, you can arrange this by overriding
+$(HTSDIR) by typing 'make HTSDIR=/path/to/htslib-source' -- see the makefile
+for details.
 
 
 Installation
 ============
 
-Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to
-a location you want (e.g. a directory in your $PATH). You may also copy
-`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
-that the `man' command may find the manual.
+Type 'make install' to install the samtools executable and various scripts
+and executables from misc/ and a manual page to /usr/local.
+
+Type 'make prefix=/path/to/dir install' to install everything under your
+choice of installation directory.  The install target also understands
+DESTDIR and the other usual installation directory variables.
+
+The bgzip and tabix utilities are provided by HTSlib.  If you have not also
+installed HTSlib separately, you may wish to install these utilities by hand
+by copying samtools-1.x/htslib-1.x/{bgzip,tabix} to the same bin directory
+to which you have installed samtools et al.

LICENSE

@@ -0,0 +1,33 @@
+The MIT/Expat License
+
+Copyright (C) 2008-2014 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.
+
+
+[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".]