Support lossy_names for SamtoolsCramConverter

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsCramConverter.java

@@ -31,7 +31,7 @@ public File convert(File inputBam, File outputCram, File gzippedFasta, boolean d
         params.add("view");
 
         params.add("--output-fmt");
-        params.add("cram,version=3.0");
+        params.add("cram,version=3.0" + (archivalMode ? ",lossy_names=1" : ""));
 
         params.add("-o");
         params.add(outputCram.getPath());