Cleanup LIBBWA mess: binary blob on root level and several references to the binary loader through hmftools/common/bwa helper

Author: brainstorm

esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/AssemblyConfig.java

@@ -1,9 +1,6 @@
 package com.hartwig.hmftools.esvee.assembly;
 
 import static com.hartwig.hmftools.common.bamops.BamToolName.BAMTOOL_PATH;
-import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH;
-import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH_DESC;
-import static com.hartwig.hmftools.common.bwa.BwaUtils.loadAlignerLibrary;
 import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.REF_GENOME;
 import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.addRefGenomeConfig;
 import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.loadRefGenome;
@@ -225,8 +222,6 @@ public AssemblyConfig(final ConfigBuilder configBuilder)
         AlignmentFile = AlignmentCache.filename(configBuilder);
         RunAlignment = AlignmentFile != null || WriteType.requiresAlignment(WriteTypes);
 
-        loadAlignerLibrary(configBuilder.getValue(BWA_LIB_PATH));
-
         setSequencingType(configBuilder);
         setLowBaseQualThreshold(configBuilder);
 
@@ -338,8 +333,6 @@ public static void registerConfig(final ConfigBuilder configBuilder)
         configBuilder.addPath(REF_GENOME_IMAGE, false, REFERENCE_BAM_DESC);
         configBuilder.addPath(DECOY_GENOME, false, "Decoy genome image file");
 
-        configBuilder.addPath(BWA_LIB_PATH, false, BWA_LIB_PATH_DESC);
-
         if(!configBuilder.isRegistered(WRITE_TYPES))
             configBuilder.addConfigItem(WRITE_TYPES, false, enumValueSelectionAsStr(WriteType.values(), "Write types"));
 

gene-utils/src/main/java/com/hartwig/hmftools/geneutils/mapping/BwaSeqTester.java

@@ -1,8 +1,6 @@
 package com.hartwig.hmftools.geneutils.mapping;
 
 import static com.hartwig.hmftools.common.bam.CigarUtils.calcCigarAlignedLength;
-import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH;
-import static com.hartwig.hmftools.common.bwa.BwaUtils.loadAlignerLibrary;
 import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.REF_GENOME;
 import static com.hartwig.hmftools.common.utils.PerformanceCounter.runTimeMinsStr;
 import static com.hartwig.hmftools.common.utils.file.FileDelimiters.TSV_DELIM;
@@ -36,7 +34,6 @@ public BwaSeqTester(final SeqTestConfig config, final ConfigBuilder configBuilde
 
         String refGenomeImageFile = configBuilder.getValue(REF_GENOME) + ".img";
 
-        loadAlignerLibrary(configBuilder.getValue(BWA_LIB_PATH));
         mAligner = initialiseBwaAligner(refGenomeImageFile);
     }
 

gene-utils/src/main/java/com/hartwig/hmftools/geneutils/mapping/SeqTestConfig.java

@@ -1,8 +1,6 @@
 package com.hartwig.hmftools.geneutils.mapping;
 
 import static com.hartwig.hmftools.common.blastn.BlastnRunner.registerBlastn;
-import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH;
-import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH_DESC;
 import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.REF_GENOME;
 import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.addRefGenomeFile;
 import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.deriveRefGenomeVersion;
@@ -47,7 +45,6 @@ public static void registerConfig(final ConfigBuilder configBuilder)
     {
         configBuilder.addPath(INPUT_FILE, true, "Input regions and sequences");
 
-        configBuilder.addPath(BWA_LIB_PATH, false, BWA_LIB_PATH_DESC);
         registerBlastn(configBuilder, false);
 
         addOutputOptions(configBuilder, false);