protected UnmappedReads < Read > getUnmappedMatesOfMappedReads ( String readsetId ) throws GeneralSecurityException , IOException { LOG . info ( "Collecting unmapped mates of mapped reads for injection" ) ; final Iterable < Read > unmappedReadsIterable = getUnmappedReadsIterator ( readsetId ) ; final UnmappedReads < Read > unmappedReads = createUnmappedReads ( ) ; for ( Read read : unmappedReadsIterable ) { unmappedReads . maybeAddRead ( read ) ; } LOG . info ( "Finished collecting unmapped mates of mapped reads: " + unmappedReads . getReadCount ( ) + " found." ) ; return unmappedReads ; }
Gets unmapped mates so we can inject them besides their mapped pairs .