1. Moved computeLikelihoods from PairHMM to native implementation

2. Disabled debug - debug code still left (hopefully, not part of
bytecode)
3. Added directory PairHMM_JNI in the root which holds the C++ library
that contains the PairHMM AVX implementation. See PairHMM_JNI/JNI_README
first

PairHMM_JNI/JNI_README

@@ -0,0 +1 @@
+TEST

PairHMM_JNI/run.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+rm -f *.txt
+export GSA_ROOT_DIR=/home/karthikg/broad/gsa-unstable
+#-Djava.library.path is needed if you are using JNI_LOGLESS_CACHING, else not needed
+java  -Djava.library.path=${GSA_ROOT_DIR}/PairHMM_JNI -jar ${GSA_ROOT_DIR}/dist/GenomeAnalysisTK.jar  -T HaplotypeCaller \
+-R /data/broad/samples/joint_variant_calling/broad_reference/Homo_sapiens_assembly19.fasta \
+-I /data/simulated/sim1M_pairs_final.bam \
+--dbsnp /data/broad/samples/joint_variant_calling/dbSNP/00-All.vcf \
+-stand_call_conf 50.0 \
+-stand_emit_conf 10.0 \
+--pair_hmm_implementation JNI_LOGLESS_CACHING \
+-o output.raw.snps.indels.vcf
+
+#--pair_hmm_implementation JNI_LOGLESS_CACHING \
+#-I /data/simulated/sim1M_pairs_final.bam \
+#-I /data/broad/samples/joint_variant_calling/NA12878_low_coverage_alignment/NA12878.chrom11.ILLUMINA.bwa.CEU.low_coverage.20121211.bam \