Commit 243fd59a authored by bow's avatar bow
Browse files

Set default validation stringency to lenient in WipeReads

parent 634364dd
...@@ -165,6 +165,7 @@ object WipeReads extends MainCommand { ...@@ -165,6 +165,7 @@ object WipeReads extends MainCommand {
new SAMFileReader(inBAM, inBAMIndex) new SAMFileReader(inBAM, inBAMIndex)
else { else {
val sfr = new SAMFileReader(inBAM) val sfr = new SAMFileReader(inBAM)
sfr.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT)
if (!sfr.hasIndex) if (!sfr.hasIndex)
throw new IllegalStateException("Input BAM file must be indexed") throw new IllegalStateException("Input BAM file must be indexed")
else else
...@@ -312,6 +313,7 @@ object WipeReads extends MainCommand { ...@@ -312,6 +313,7 @@ object WipeReads extends MainCommand {
.setCreateIndex(writeIndex) .setCreateIndex(writeIndex)
.setUseAsyncIo(async) .setUseAsyncIo(async)
val templateBAM = new SAMFileReader(inBAM) val templateBAM = new SAMFileReader(inBAM)
templateBAM.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT)
val targetBAM = factory.makeBAMWriter(templateBAM.getFileHeader, true, outBAM) val targetBAM = factory.makeBAMWriter(templateBAM.getFileHeader, true, outBAM)
val filteredBAM = val filteredBAM =
if (filteredOutBAM != null) if (filteredOutBAM != null)
......
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