Merge pull request #72 from Bioinformatics/HAP-317

HAP-317 always check for BCF errors + htslib version bump

RELEASES.md

@@ -1,5 +1,11 @@
 # Hap.py Release Notes / Change Log
 
+## v0.3.9
+
+| Ticket  | Description                                                                        |
+|---------|------------------------------------------------------------------------------------|
+| HAP-317 | Update htslib to 1.4.1 and always check for BCF conversion errors                  |
+
 ## v0.3.8
 
 | Ticket  | Description                                                                        |

example/haploid/query.vcf

@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##contig=<ID=chrX>
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 chrX	5	tp	A	T	.	PASS	.	GT	1/1

example/homref/homref.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##FILTER=<ID=PASS,Description="All	filters	passed">
 ##INFO=<ID=END,Number=.,Type=Integer,Description="SV end position">
-##contig=<ID=21,length=48129895>
+##contig=<ID=chr21,length=48129895>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 chr21	20001394	.	C	.	.	PASS	END=20001396	GT	0/0
 chr21	20001450	.	C	.	.	PASS	END=20001480	GT	0/0

example/homref/homref2.vcf

@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##FILTER=<ID=PASS,Description="All	filters	passed">
 ##INFO=<ID=END,Number=.,Type=Integer,Description="SV end position">
-##contig=<ID=21,length=48129895>
+##contig=<ID=chr21,length=48129895>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12877
 chr21	20001394	.	C	.	.	PASS	END=20001397	GT	0/0
 chr21	20001400	.	C	.	.	PASS	END=20001500	GT	0/0

example/integration/integrationtest_lhs.vcf

@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.1
 ##FILTER=<ID=PASS,Description="All	filters	passed">
 ##reference=hg19
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>

example/integration/integrationtest_rhs.vcf

@@ -2,6 +2,7 @@
 ##FILTER=<ID=PASS,Description="All	filters	passed">
 ##FILTER=<ID=LowGQX,Description="Low GQX">
 ##FILTER=<ID=HighDPFRatio,Description="DPF Ratio high">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##reference=hg19
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>

external/make_dependencies.sh

@@ -34,7 +34,7 @@ fi
 
 if [ -z "$BOOST_ROOT" ];
 then
-    if [ ! -d ${ISD}/include/boost ]; 
+    if [ ! -d ${ISD}/include/boost ];
     then
         cd ${TLD}
         rm -rf ${TLD}/boost_subset_1_58_0
@@ -57,11 +57,13 @@ then
     tar xzf ${DIR}/htslib.tar.gz
     cd htslib
     ./configure --prefix=${ISD} \
-        CFLAGS=-I${ISD}/include \
-        CXXFLAGS=-I${ISD}/include \
+        CFLAGS=-I${ISD}/include\ -g \
+        CXXFLAGS=-I${ISD}/include\ -g \
         LDFLAGS=-L${ISD}/lib \
         --disable-plugins \
-        --disable-libcurl
+        --disable-libcurl \
+        --disable-lzma \
+        --disable-bz2
     make -j4
     make -j4 install
 
@@ -92,13 +94,14 @@ then
     rm -rf ${TLD}/samtools
     tar xzf ${DIR}/samtools.tar.gz
     cd samtools
+    autoconf -Wno-syntax || autoconf -Wno-syntax
     ./configure --prefix=${ISD} \
         --with-htslib=${TLD}/htslib \
         --without-curses \
         CFLAGS=-I${ISD}/include \
         CPPFLAGS=-I${ISD}/include \
-        LDFLAGS=-L${ISD}/lib 
-    make -j4 
+        LDFLAGS=-L${ISD}/lib
+    make -j4
     make -j4 install
 else
     echo "samtools already built. To rebuild, delete ${ISD}/bin/samtools"
@@ -135,6 +138,6 @@ if [[ ! -z $BUILD_VCFEVAL ]]; then
     if [[ -f ${VCFEVAL_WRAPPER} ]]; then
         echo "using wrapper for rtg-tools: ${VCFEVAL_WRAPPER}"
         cp ${VCFEVAL_WRAPPER} ${ISD}/libexec/rtg-tools-install/rtg-wrapper.sh
-        chmod +x ${ISD}/libexec/rtg-tools-install/rtg-wrapper.sh 
+        chmod +x ${ISD}/libexec/rtg-tools-install/rtg-wrapper.sh
     fi
 fi