Merge pull request #22 from wtsi-npg/devel

devel to master merge

.travis.yml

@@ -1,5 +1,3 @@
-# Control file for continuous integration testing at http://travis-ci.org/
-
 language: c
 
 addons:
@@ -9,30 +7,49 @@ addons:
 
 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
+  - os: linux
+    compiler: clang
+  - os: linux
+    compiler: gcc
+  - 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:$PATH
+  - HTSLIB=`pwd`/htslib
+  - HTSDIR=$HTSLIB/b
+  - SAMTOOLSDIR=`pwd`/samtools
+  - PATH=$SAMTOOLSDIR:$PATH
+  - DISTCHECK_CONFIGURE_FLAGS=--with-htslib=$HTSDIR
 
 install:
-  - .travis/clone ${HTSREPO:-git://github.com/samtools/htslib.git} $HTSLIB master
-  - .travis/clone ${HTSREPO:-git://github.com/samtools/samtools.git} $SAMTOOLSDIR master
+- .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)
+- (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 distcheck
+
+after_success:
+  - make dist
+  - export DIST_FILE=$(ls bambi-*.tar.gz)
+  - export SHA256_FILE=$DIST_FILE.sha256
+  - shasum -a 256 $DIST_FILE > $SHA256_FILE
 
-script: autoreconf -i && ./configure -V && ./configure --with-htslib=$HTSDIR && make -e && make -e check
+deploy:
+  provider: releases
+  api_key:
+    secure: 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
+  file:
+    - $DIST_FILE
+    - $SHA256_FILE
+  skip_cleanup: true
+  on:
+    tags: true
+    repo: jenniferliddle/bambi
+    branch: master

Makefile.am

@@ -1,5 +1,6 @@
 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_SUBDIRS = test/decode/data test/decode/out test/i2b/data test/i2b/out
 dist_doc_DATA = README.md LICENSE
 AM_COLOR_TESTS=always

configure.ac

@@ -1,6 +1,6 @@
 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])
+AM_INIT_AUTOMAKE([-Wall -Werror foreign subdir-objects tar-pax no-dependencies])
 AC_PROG_CC
 
 LT_INIT
@@ -17,6 +17,7 @@ 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()?])])
+AC_CHECK_LIB([hts], [sam_hdr_del], [AC_DEFINE([HAVE_SAM_HDR_DEL],[1],[Does htslib contain sam_hdr_del()?])])
 CPPFLAGS="$saved_CPPFLAGS"
 LDFLAGS="$saved_LDFLAGS"
 

src/Makefile.am

@@ -2,6 +2,8 @@ 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_SOURCES = bambi.c bclfile.c  decode.c  filterfile.c  hts_addendum.c  i2b.c  posfile.c array.c \
+                bambi.h bclfile.h            filterfile.h  hts_addendum.h         posfile.h array.h
+nobase_include_HEADERS = cram/cram_samtools.h cram/pooled_alloc.h cram/sam_header.h cram/string_alloc.h
 bambi_CFLAGS = -I/usr/include/libxml2
 bambi_LDADD = $(HTSLIB_HOME)/lib/libhts.a -ldl -lxml2 -lz -llzma -lbz2 -lpthread

src/array.c

@@ -0,0 +1,97 @@
+/*  array.c -- simple array handling functions.
+
+    Copyright (C) 2016 Genome Research Ltd.
+
+    Author: Jennifer Liddle <[email protected]>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as published
+by the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include "array.h"
+
+/*
+ * integer array functions
+ */
+
+int ia_compare(const void *ia1, const void *ia2)
+{
+    return *(int *)ia1 - *(int *)ia2;
+}
+
+void ia_sort(ia_t *ia)
+{
+    qsort(ia->entries, ia->end, sizeof(int), ia_compare);
+}
+
+void ia_push(ia_t *ia, int i)
+{
+    if (ia->end == ia->max) {
+        // expand the array
+        ia->max *= 2;
+        ia->entries = realloc(ia->entries, ia->max * sizeof(int));
+    }
+    ia->entries[ia->end] = i;
+    ia->end++;
+}
+
+void ia_free(ia_t *ia)
+{
+    free(ia->entries);
+    free(ia);
+}
+
+ia_t *ia_init(int max)
+{
+    ia_t *ia = calloc(1, sizeof(ia_t));
+    ia->end = 0;
+    ia->max = max;
+    ia->entries = calloc(ia->max, sizeof(int));
+    return ia;
+}
+
+
+/*
+ * generic arrays
+ */
+
+va_t *va_init(int max, void(*free_entry)(void*))
+{
+    va_t *va = calloc(1,sizeof(va_t));
+    va->end = 0;
+    va->max = max;
+    va->free_entry = free_entry;
+    va->entries = calloc(va->max, sizeof(void *));
+    return va;
+}
+
+void va_push(va_t *va, void *ent)
+{
+    if (va->end == va->max) {
+        // expand the array
+        va->max *= 2;
+        va->entries = realloc(va->entries, va->max * sizeof(void *));
+    }
+    va->entries[va->end] = ent;
+    va->end++;
+}
+
+void va_free(va_t *va)
+{
+    int n;
+    if (!va) return;
+    for (n=0; n < va->end; n++) {
+        va->free_entry(va->entries[n]);
+    }
+    free(va->entries);
+    free(va);
+}
+

src/array.h

@@ -0,0 +1,60 @@
+/*  array.h -- simple array handling functions.
+
+    Copyright (C) 2016 Genome Research Ltd.
+
+    Author: Jennifer Liddle <[email protected]>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as published
+by the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef __ARRAY_H__
+#define __ARRAY_H__
+
+#include <stdbool.h>
+#include <stdlib.h>
+
+/*
+ * integer array functions
+ */
+
+typedef struct {
+    int end;
+    int max;
+    int *entries;
+} ia_t;
+
+ia_t *ia_init(int max);
+int ia_compare(const void *ia1, const void *ia2);
+void ia_sort(ia_t *ia);
+void ia_push(ia_t *ia, int i);
+void ia_free(ia_t *ia);
+static inline bool ia_isEmpty(ia_t *ia) { return (ia->end == 0); }
+
+
+/*
+ * generic arrays
+ */
+
+typedef struct {
+    int end;
+    int max;
+    void (*free_entry)(void *);
+    void **entries;
+} va_t;
+
+va_t *va_init(int max, void(*free_entry)(void*));
+void va_push(va_t *va, void *ent);
+void va_free(va_t *va);
+static inline bool va_isEmpty(va_t *va) { return va->end == 0; }
+
+#endif
+

src/bambi.h

@@ -21,8 +21,8 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #ifndef __BAMBI_H__
 #define __BAMBI_H__
 
-#include "hts_addendum.h"
 #include "config.h"
+#include "hts_addendum.h"
 const char *bambi_version(void);
 
 #endif

src/hts_addendum.c

@@ -57,6 +57,7 @@ int bam_aux_update_str(bam1_t *b, const char tag[2], int len, const char *data)
 }
 #endif
 
+#ifndef HAVE_SAM_HDR_DEL
 SAM_hdr *sam_hdr_del(SAM_hdr *hdr, char *type, char *ID_key, char *ID_value) {
     int i,n;
     int *lines;
@@ -81,4 +82,5 @@ SAM_hdr *sam_hdr_del(SAM_hdr *hdr, char *type, char *ID_key, char *ID_value) {
     free(newtext);
     return hdr;
 }
+#endif
 

src/hts_addendum.h

@@ -27,8 +27,13 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "cram/sam_header.h"
 #include "cram/cram_samtools.h"
 
+#ifndef HAVE_BAM_AUX_UPDATE_STR
 int bam_aux_update_str(bam1_t *b, const char tag[2], int len, const char *data);
+#endif
+
+#ifndef HAVE_SAM_HDR_DEL
 SAM_hdr * sam_hdr_del(SAM_hdr *hdr, char *type, char *ID_key, char *ID_value);
+#endif
 
 #endif