Package org.broadinstitute.hellbender.tools.walkers.contamination

Class PileupSummary.PileupSummaryTableWriter

java.lang.Object

org.broadinstitute.hellbender.utils.tsv.TableWriter<PileupSummary>

org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary.PileupSummaryTableWriter

All Implemented Interfaces:

Closeable, AutoCloseable

Enclosing class:

PileupSummary

public static class PileupSummary.PileupSummaryTableWriter
extends TableWriter<PileupSummary>

Field Summary

Fields inherited from class org.broadinstitute.hellbender.utils.tsv.TableWriter

METADATA_TAG

Constructor Summary

Constructors

Constructor	Description
PileupSummaryTableWriter(Path output)

Method Summary

Modifier and Type	Method	Description
protected void	composeLine(PileupSummary record, DataLine dataLine)	Composes the data-line to write into the output to represent a given record

Methods inherited from class org.broadinstitute.hellbender.utils.tsv.TableWriter

close, flush, writeAllRecords, writeComment, writeHeaderIfApplies, writeMetadata, writeRecord

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

PileupSummaryTableWriter

public PileupSummaryTableWriter(Path output)
                         throws IOException

Throws:

IOException

Method Details

composeLine

protected void composeLine(PileupSummary record,
 DataLine dataLine)

Description copied from class: TableWriter

Composes the data-line to write into the output to represent a given record

Also the first element cannot contain the comment prefix. If that is a genuine valid value for the first column you shall consider to re-order the columns or change the encoding of the first column to avoid this issue.

Both inputs, record and dataLine are guaranteed not to be nulls.

Specified by:

composeLine in class TableWriter<PileupSummary>

Parameters:

record - the record to write into the data-line.

dataLine - the destination data-line object.