Merge branch 'release/v3.2.0'

Author: keiranmraine

.travis.yml

@@ -29,6 +29,12 @@ language: perl
 perl:
  - "5.22"
 
+before_script:
+ - git clone --depth 1 --single-branch --branch develop https://github.com/cancerit/cgpBigWig.git
+ - cd cgpBigWig
+ - ./setup.sh $HOME/wtsi-opt
+ - cd ../
+
 script:
  - ./setup.sh ~/wtsi-opt
  - ~/wtsi-opt/bin/samtools view # dump usage to show intact

CHANGES.md

@@ -1,3 +1,21 @@
+### 3.2.0
+* Move from legacy kent bigwig manipulation code and to [`cgpBigWig`](https://github.com/cancerit/cgpBigWig)
+  * Faster and handles the huge number of contigs in many new reference builds.
+  * Resulting changes to underlying installed tools is `bwcat` now `bwjoin` to be more descriptive of actual function.
+
+### 3.1.1
+Handle recent changes to BioPerl structure
+
+### 3.1.0
+* Use BWA default for `-T` previously hard coded to `-T 0`.
+  *  Can be passed through `bwa_mem.pl` other ags to bwa via the `-b` option.
+*  Fix `bam2bedgraph` compilation since changes to underlying libraries
+*  `bamToBw.pl` - expose read flag filters
+*  Drop dependancy on `Bio::DB::HTS INSTALL.pl` as can't fix to known good version.
+*  Added travis CI
+*  Add support for output directly to CRAM
+*  `bwa` version upgraded to [0.7.15](https://github.com/lh3/bwa/releases/tag/v0.7.15)
+
 ### 3.0.0
 * Threading module now converts currently running step to bash script for following reasons:
   * Changes logging to use file redirects instead of Capture::Tiny - prevent log bleed into wrong files

MANIFEST

@@ -10,15 +10,13 @@ bin/gnos_pull.pl
 bin/monitor.pl
 bin/xam_coverage_bins.pl
 bin/xml_to_bas.pl
-c/bam2bedgraph.c
 c/bam_access.c
 c/bam_access.h
 c/bam_stats.c
 c/bam_stats_calcs.c
 c/bam_stats_calcs.h
 c/bam_stats_output.c
 c/bam_stats_output.h
-c/bwcat.c
 c/c_tests/01_bam_stats_output_tests.c
 c/c_tests/02_bam_access_tests.c
 c/c_tests/03_bam_stats_calcs_tests.c

README.md

@@ -18,19 +18,22 @@ Please see the [wiki](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/wiki) for
 ---
 
 ###Dependencies/Install
-Some of the code included in this package has dependencies on external packages:
 
- * [biobambam](https://github.com/gt1/biobambam)
- * [bwa](https://github.com/lh3/bwa)
- * [samtools](https://github.com/samtools/samtools)
- * [kentUtils](https://github.com/ENCODE-DCC/kentUtils)
+Please install the following before running `setup.sh`:
+
+* [cgpBigWig](https://github.com/cancerit/cgpBigWig/releases)
+
+Dependancies installed by `setup.sh`:
+
+* [biobambam](https://github.com/gt1/biobambam)
+* [bwa](https://github.com/lh3/bwa)
+* [samtools](https://github.com/samtools/samtools)
 
 And various perl modules.
 
 Please see the respective licence for each before use.
 
-Please use `setup.sh` to install the dependencies.  Please be aware that this expects basic C
-compilation libraries and tools to be available, most are listed in `INSTALL`.
+Please be aware that this expects basic C compilation libraries and tools to be available, most are listed in `INSTALL`.
 
 ---
 

bin/bamToBw.pl

@@ -47,8 +47,10 @@
 {
   my $options = setup();
 
+  $options->{'ctg_lengths'} = PCAP::ref_lengths($options->{'reference'}.'.fai');
+
  	my $threads = PCAP::Threaded->new($options->{'threads'});
-	&PCAP::Threaded::disable_out_err if(exists $options->{'index'});
+	&PCAP::Threaded::disable_out_err unless(exists $options->{'index'});
 
   # register processes
 	$threads->add_function('bamToBw', \&PCAP::BigWig::bamToBw);

c/Makefile

@@ -14,23 +14,13 @@ CFLAGS = -Wall
 
 HTSLOC?=$(HTSLIB)
 
-#if test -z "$$LIBBIGWIG"
-#LIBBIGWIGLOC?=$(LIBBIGWIG)
-#echo "*******DEFINED"
-#endif
-
 HTSTMP?=./htslib_tmp
 prefix=?/usr/local/
 
 #Define locations of header files
 OPTINC?= -I$(HTSLOC)/
 INCLUDES= -I./ $(OPTINC) -rdynamic
 
-ifdef LIBBIGWIG
-CAT_INCLUDES= -I$(LIBBIGWIG)
-CAT_LFLAGS= -L$(LIBBIGWIG)
-endif
-
 CAT_INCLUDES+= -I$(prefix)/include
 CAT_LFLAGS+= -L$(prefix)/lib
 
@@ -64,9 +54,7 @@ MD := mkdir
 
 #Build target executable
 BAM_STATS_TARGET=../bin/bam_stats
-CAT_TARGET=../bin/bwcat
 SQ_TARGET=../bin/reheadSQ
-BAM2BG_TARGET=../bin/bam2bedgraph
 
 #
 # The following part of the makefile is generic; it can be used to
@@ -78,18 +66,12 @@ BAM2BG_TARGET=../bin/bam2bedgraph
 
 .NOTPARALLEL: test
 
-all: clean pre make_htslib_tmp $(BAM_STATS_TARGET) $(BAM2BG_TARGET) test remove_htslib_tmp $(CAT_TARGET) $(SQ_TARGET)
-	@echo  bam_stats, reheadSQ and bwcat compiled.
+all: clean pre make_htslib_tmp $(BAM_STATS_TARGET) $(BAM2BG_TARGET) $(BAM2BW_TARGET) test remove_htslib_tmp $(CAT_TARGET) $(SQ_TARGET)
+	@echo  bam_stats and reheadSQ compiled.
 
 $(BAM_STATS_TARGET): $(OBJS)
 	$(CC) $(CFLAGS) $(INCLUDES) -o $(BAM_STATS_TARGET) $(OBJS) $(LFLAGS) $(LIBS) ./bam_stats.c
 
-$(CAT_TARGET):
-	$(CC) $(CAT_INCLUDES) $(CFLAGS) ./bwcat.c $(CAT_LFLAGS) -lBigWig -lz -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit -o $(CAT_TARGET)
-
-$(BAM2BG_TARGET): $(OBJS)
-	$(CC) $(CFLAGS) $(INCLUDES) -o $(BAM2BG_TARGET) $(OBJS) $(LFLAGS) $(LIBS) ./bam2bedgraph.c
-
 $(SQ_TARGET):
 	$(CC) $(CFLAGS) ./reheadSQ.c -o $(SQ_TARGET)
 
@@ -104,9 +86,6 @@ test: $(TESTS)
 coverage: CFLAGS += --coverage
 coverage: test
 
-make_bigwigcat: $(CAT_TARGET)
-	@echo $(CAT_TARGET) done
-
 make_htslib_tmp:
 	$(MD) $(HTSTMP)
 	#Do some magic to ensure we compile BAM_STATS with the static libhts.a rather than libhts.so
@@ -118,7 +97,7 @@ remove_htslib_tmp:
 
 copyscript:
 	cp ./scripts/* ./bin/
-	chmod a+x $(BAM_STATS_TARGET) $(CAT_TARGET) $(SQ_TARGET)
+	chmod a+x $(BAM_STATS_TARGET) $(CAT_TARGET) $(SQ_TARGET) $(BAM2BW_TARGET) $(BAM2BG_TARGET)
 
 valgrind:
 	VALGRIND="valgrind --log-file=/tmp/valgrind-%p.log" $(MAKE)
@@ -133,7 +112,7 @@ valgrind:
 
 clean:
 	@echo clean
-	$(RM) ./*.o *~ $(BAM_STATS_TARGET) $(SQ_TARGET) $(CAT_TARGET) ./tests/tests_log $(TESTS) ./*.gcda ./*.gcov ./*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno
+	$(RM) ./*.o *~ $(BAM_STATS_TARGET) $(SQ_TARGET) ./tests/tests_log $(TESTS) ./*.gcda ./*.gcov ./*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno
 	-rm -rf $(HTSTMP)
 
 depend: $(SRCS)