New LD code reads directly from VCFs

Additional C code for calculating LD by reading directly from
bgzipped VCFs using htslib.

.gitignore

@@ -1,2 +1,3 @@
 /C_code/calc_genotypes
 /C_code/calc_genotypes.o
+/C_code/ld_vcf

.travis.yml

@@ -26,6 +26,7 @@ before_install:
     - cd htslib
     - make
     - cd ..
+    - export HTSLIB_DIR=$PWD/htslib
     - cd C_code/
     - make
     - cd ../
@@ -35,7 +36,6 @@ install:
     - cpanm -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
     - cpanm -v --installdeps --notest .
     - cpanm -n Devel::Cover::Report::Coveralls
-    - export HTSLIB_DIR=$PWD/htslib
     - export PERL5LIB=$PWD/bioperl-live-bioperl-release-1-2-3
     - cpanm Bio::DB::HTS
     - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf

C_code/Makefile

@@ -1,14 +1,21 @@
 CC = gcc
 
-all: calc_genotypes
+ifndef HTSLIB_DIR
+  $(error HTSLIB_DIR is undefined, see README for details)
+endif
+
+all: calc_genotypes ld_vcf
 
 install: calc_genotypes
 	mkdir -p ../bin
 	cp calc_genotypes ../bin/
+	cp ld_vcf ../bin/
 
 calc_genotypes: calc_genotypes.o
 	$(CC) -o calc_genotypes calc_genotypes.c
 calc_genotypes.o:
 	$(CC) -c calc_genotypes.c
+ld_vcf:
+	$(CC) -Wall ld_vcf.c -I $(HTSLIB_DIR)/htslib -o ld_vcf -L$(HTSLIB_DIR) -Wl,-rpath,$(HTSLIB_DIR) -lhts
 clean:
-	\rm -f *.o calc_genotypes
+	\rm -f *.o calc_genotypes ld_vcf