Support CRAM for DepthOfCoverageHandler

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/DepthOfCoverageHandler.java

@@ -59,7 +59,7 @@ public DepthOfCoverageHandler()
     @Override
     public boolean canProcess(SequenceOutputFile o)
     {
-        return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bam.getFileType().isType(o.getFile());
+        return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bamOrCram.getFileType().isType(o.getFile());
     }
 
     @Override

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

@@ -83,6 +83,7 @@ public static enum FILETYPE
         fasta(Arrays.asList(".fasta", ".fa", ".fna"), true),
         bam(".bam"),
         cram(".cram"),
+        bamOrCram(Arrays.asList(".bam", ".cram"), false),
         sff(".sff"),
         gtf(Collections.singletonList(".gtf"), true),
         gff(Arrays.asList(".gff", ".gff3"), true),