Merge pull request #14 from wtsi-npg/devel

sync master with develop (release 0.9 prep)

.travis.yml

@@ -0,0 +1,38 @@
+# Control file for continuous integration testing at http://travis-ci.org/
+
+language: c
+
+addons:
+  apt:
+    packages:
+    - liblzma-dev
+
+matrix:
+  include:
+    - os: linux
+      compiler: clang
+    - os: linux
+      compiler: gcc
+    # An unoptimised C99 build, for detecting non-static inline functions
+    - os: linux
+      compiler: gcc
+      env: CFLAGS="-std=gnu99 -O0"
+    - os: osx
+      compiler: gcc
+
+env:
+  global:
+    - HTSLIB=`pwd`/htslib
+    - HTSDIR=$HTSLIB/b
+    - SAMTOOLSDIR=samtools
+    - PATH=$SAMTOOLSDIR:$PATH
+
+install:
+  - .travis/clone ${HTSREPO:-git://github.com/samtools/htslib.git} $HTSLIB master
+  - .travis/clone ${HTSREPO:-git://github.com/samtools/samtools.git} $SAMTOOLSDIR master
+
+before_script:
+  - (cd $HTSLIB && autoreconf && mkdir b && ./configure --prefix=$HTSDIR && make && make install)
+  - (cd $SAMTOOLSDIR && autoconf && make)
+
+script: autoreconf -i && ./configure -V && ./configure --with-htslib=$HTSDIR && make -e && make -e check

.travis/clone

@@ -0,0 +1,14 @@
+#!/bin/sh
+# Usage: .travis/clone REPOSITORY [DIR] [BRANCH]
+#
+# Creates a shallow clone, checking out the specified branch.  If BRANCH is
+# omitted or if there is no branch with that name, checks out origin/HEAD.
+
+repository=$1
+localdir=$2
+branch=$3
+
+[ -n "$branch" ] && ref=$(git ls-remote --heads $repository $branch)
+
+set -x
+git clone --depth=1 ${ref:+--branch=$branch} $repository $localdir

Makefile.am

@@ -0,0 +1,5 @@
+ACLOCAL_AMFLAGS= -I m4
+TESTS = test/posfile/t_posfile test/filterfile/t_filterfile test/bclfile/t_bclfile test/decode/t_decode test/i2b/t_i2b
+SUBDIRS = src test/posfile test/bclfile test/filterfile test/decode test/i2b
+dist_doc_DATA = README.md LICENSE
+AM_COLOR_TESTS=always

README.md

@@ -1,2 +1,20 @@
 # bambi
 A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB
+
+to install:
+
+
+clone into a local directory (eg 'bambi')
+
+cd bambi
+autoreconf -i
+configure --prefix=<place to install> --with-htslib=<directory containing a htslib release>
+
+(eg configure --prefix=/usr/local/bambi --with-htslib=/usr/local/htslib/1.3)
+
+make
+
+make check (to run tests)
+
+
+

config.mk

@@ -24,8 +24,8 @@
 # configure, the main Makefile contains suitable conservative defaults.
 
 
-HTSDIR = /software/solexa/pkg/htslib/htslib-1.3
-### include $(HTSDIR)/src/htslib.mk
+HTSDIR = ../htslib
+include $(HTSDIR)/htslib.mk
 HTSLIB = $(HTSDIR)/libhts.a
 HTSLIB_LIB = $(HTSLIB)
 BGZIP = $(HTSDIR)/bin/bgzip

configure.ac

@@ -0,0 +1,33 @@
+AC_INIT([bambi], m4_esyscmd_s([git describe --dirty --always --tags]), [[email protected]])
+AC_ARG_VAR(HTSDIR,Directory to look for hts)
+AM_INIT_AUTOMAKE([-Wall -Werror foreign subdir-objects])
+AC_PROG_CC
+
+LT_INIT
+
+AC_CONFIG_MACRO_DIR([m4])
+
+AX_WITH_HTSLIB
+
+AC_CONFIG_HEADERS([config.h])
+
+saved_CPPFLAGS="$CPPFLAGS"
+saved_LDFLAGS="$LDFLAGS"
+CPPFLAGS="$HTSLIB_CPPFLAGS"
+LDFLAGS="$HTSLIB_LDFLAGS"
+AC_CHECK_HEADERS([cram/sam_header.h])
+AC_CHECK_LIB([hts], [bam_aux_update_str], [AC_DEFINE([HAVE_BAM_AUX_UPDATE_STR],[1],[Does htslib contain bam_aux_update_str()?])])
+CPPFLAGS="$saved_CPPFLAGS"
+LDFLAGS="$saved_LDFLAGS"
+
+AC_CONFIG_FILES([
+ Makefile
+ src/Makefile
+ test/posfile/Makefile
+ test/bclfile/Makefile
+ test/filterfile/Makefile
+ test/decode/Makefile
+ test/i2b/Makefile
+])
+AC_OUTPUT
+

m4/ax_with_htslib.m4

@@ -0,0 +1,117 @@
+#
+# SYNOPSIS
+#
+#   AX_WITH_HTSLIB()
+#
+# DESCRIPTION
+#
+#   This macro searches for the header files and libraries of a htslib
+#   (https://github.com/samtools/htslib) installation.  If --with-htslib is specified
+#   without argument, or as --with-htslib=yes, a packaged (.deb or
+#   .rpm) installation is assumed and the default system paths will be
+#   searched.  If --with-htslib=DIR is specified, a run-in-place htslib
+#   installation will be searched for in DIR.
+#
+#   The system header and library paths will be used for run-in-place
+#   iRODS installation dependencies, in preference to the those
+#   dependencies provided by iRODS in its 'externals' directory
+#   because the latter cannot be determined reliably.
+#
+#   The macro defines the symbol HAVE_HTSLIB if the library is found
+#   and the following output variables are set with AC_SUBST:
+#
+#     HTSLIB_CPPFLAGS
+#     HTSLIB_LDFLAGS
+#     HTSLIB_LIBS
+#
+#   You can use them like this in Makefile.am:
+#
+#      AM_CPPFLAGS       = $(HTSLIB_CPPFLAGS)
+#      AM_LDFLAGS        = $(HTSLIB_LDFLAGS)
+#      library_la_LIBADD = $(HTSLIB_LIBS)
+#      program_LDADD     = $(HTSLIB_LIBS)
+#
+# LICENSE
+#
+# Copyright (C) 2016, Genome Research Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+AC_DEFUN([AX_WITH_HTSLIB], [
+   HTSLIB_HOME=
+   HTSLIB_CPPFLAGS=
+   HTSLIB_LDFLAGS=
+   HTSLIB_LIBS=
+
+   saved_CPPFLAGS="$CPPFLAGS"
+   saved_LDFLAGS="$LDFLAGS"
+   saved_LIBS="$LIBS"
+
+   AC_ARG_WITH([htslib],
+       [AS_HELP_STRING([--with-htslib[[=DIR]]], [select htslib directory])], [
+           AS_IF([test "x$with_htslib" != "xno"], [
+
+               AS_IF([test "x$with_htslib" = "xyes"], [
+                   AC_MSG_CHECKING([for packaged htslib])
+                   CPPFLAGS="-I/usr/include/htslib $CPPFLAGS"
+                   LDFLAGS="-L/usr/lib/htslib/externals $LDFLAGS"
+               ], [
+                   HTSLIB_HOME="$with_htslib"
+                   CPPFLAGS="-I$HTSLIB_HOME/include $CPPFLAGS"
+                   LDFLAGS="-L$HTSLIB_HOME/lib $LDFLAGS"
+               ])
+
+               LIBS="$HTSLIB_HOME/lib/libhts.a -lz -ldl -lbz2 -llzma -lpthread"
+
+               AC_MSG_CHECKING([checking htslib version])
+               AC_RUN_IFELSE([AC_LANG_PROGRAM([
+                #include "htslib/hts.h"
+                #include <stdlib.h>
+                #include <string.h>
+#include <stdio.h>
+               ], [
+                char *v=strdup(hts_version());
+                char *s = strtok(v,".-");
+                int n = atoi(s) * 100000;
+                s = strtok(NULL,".-");
+                if (s) n += atoi(s) * 1000;
+                s = strtok(NULL,".-");
+                if (s) n += atoi(s) * 10;
+printf("  n=%d   ",n);
+                if(n>=103010) return 0;
+                else exit(-1);
+               ])
+               ], [AC_MSG_RESULT([Ok])],
+                  [AC_MSG_ERROR([htslib version must be 1.3.1 or greater])]
+               )
+
+               HTSLIB_CPPFLAGS="$CPPFLAGS"
+               HTSLIB_LDFLAGS="$LDFLAGS"
+               HTSLIB_LIBS="$LIBS"
+
+               CPPFLAGS="$saved_CPPFLAGS"
+               LDFLAGS="$saved_LDFLAGS"
+               LIBS="$saved_LIBS"
+
+               unset saved_CPPFLAGS
+               unset saved_LDFLAGS
+               unset saved_LIBS
+
+               AC_SUBST([HTSLIB_HOME])
+               AC_SUBST([HTSLIB_CPPFLAGS])
+               AC_SUBST([HTSLIB_LDFLAGS])
+               AC_SUBST([HTSLIB_LIBS])
+
+           ])
+   ])
+])

src/Makefile.am

@@ -0,0 +1,7 @@
+AM_CPPFLAGS = $(HTSLIB_CPPFLAGS)
+AM_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS)
+
+bin_PROGRAMS = bambi 
+bambi_SOURCES = bambi.c bclfile.c  decode.c  filterfile.c  hts_addendum.c  i2b.c  posfile.c
+bambi_CFLAGS = -I/usr/include/libxml2
+bambi_LDADD = $(HTSLIB_HOME)/lib/libhts.a -ldl -lxml2 -lz -llzma -lbz2 -lpthread