add an alignment record to be emitted by the writer . concode_field_sep int DEAFULT_MAX_RECORDS_IN_RAM concode_elem_sep int maxRecordsInRam concode_elem_sep SortingCollection<SAMRecord> alignmentSorter concode_elem_sep ProgressLoggerInterface progressLogger concode_elem_sep SAMSortOrderChecker sortOrderChecker concode_elem_sep SAMFileHeader.SortOrder sortOrder concode_elem_sep boolean isClosed concode_elem_sep SAMFileHeader header concode_elem_sep boolean presorted concode_elem_sep File tmpDir concode_field_sep void writeHeader concode_elem_sep void setProgressLogger concode_elem_sep void setSortOrder concode_elem_sep void setTempDirectory concode_elem_sep SAMRecordComparator makeComparator concode_elem_sep void setDefaultMaxRecordsInRam concode_elem_sep SAMFileHeader.SortOrder getSortOrder concode_elem_sep void setMaxRecordsInRam concode_elem_sep void setHeader concode_elem_sep String getFilename concode_elem_sep void assertPresorted concode_elem_sep void finish concode_elem_sep SAMFileHeader getFileHeader concode_elem_sep void close concode_elem_sep void writeAlignment concode_elem_sep int getDefaultMaxRecordsInRam
void function ( final SAMRecord arg0 ) { arg0 . setHeaderStrict ( header ) ; if ( sortOrder . equals ( SAMFileHeader . SortOrder . unsorted ) ) { writeAlignment ( arg0 ) ; } else if ( presorted ) { assertPresorted ( arg0 ) ; writeAlignment ( arg0 ) ; } else { alignmentSorter . add ( arg0 ) ; } }