Account for difference between hg19 and GRCh37 MT contigs

Author: bbimber

SequenceAnalysis/pipeline_code/sequence_tools_install.sh

@@ -486,10 +486,10 @@ then
     rm -Rf bcftools*
     rm -Rf $LKTOOLS_DIR/bcftools
 
-    wget $WGET_OPTS https://github.com/samtools/bcftools/releases/download/1.18/bcftools-1.18.tar.bz2
-    tar xjvf bcftools-1.18.tar.bz2
-    chmod 755 bcftools-1.18
-    cd bcftools-1.18
+    wget $WGET_OPTS https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
+    tar xjvf bcftools-1.20.tar.bz2
+    chmod 755 bcftools-1.20
+    cd bcftools-1.20
     rm -f plugins/liftover.c
     wget $WGET_OPTS -P plugins https://raw.githubusercontent.com/freeseek/score/master/liftover.c
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java

@@ -215,7 +215,7 @@ else if (_vcfFileType.isType(f.getFile()))
                 }
 
                 File lifted = new File(outDir, baseName + ".lifted-" + targetGenomeId + ext);
-                File unmappedOutput = doNotRetainUnmapped ? new File(outDir, baseName + ".unmapped-" + targetGenomeId + ext) : null;
+                File unmappedOutput = doNotRetainUnmapped ? null : new File(outDir, baseName + ".unmapped-" + targetGenomeId + ext);
 
                 try
                 {

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java

@@ -420,7 +420,8 @@ else if (refName.endsWith("_alt"))
             refName = StringUtils.join(Arrays.copyOfRange(tokens, 1, tokens.length), "_");
         }
 
-        if (refName.equals("chrM"))
+        // NOTE: hg19 and GRCh37 have different MT contigs. chrM is the legacy version.
+        if (refName.equals("chrMT"))
         {
             return "MT";
         }