Package org.broadinstitute.hellbender.tools.reference

Class CompareReferences.CompareReferencesOutputTableWriter

java.lang.Object

org.broadinstitute.hellbender.utils.tsv.TableWriter<ReferenceSequenceTable.TableRow>

org.broadinstitute.hellbender.tools.reference.CompareReferences.CompareReferencesOutputTableWriter

All Implemented Interfaces:

Closeable, AutoCloseable

Enclosing class:

CompareReferences

public static class CompareReferences.CompareReferencesOutputTableWriter
extends TableWriter<ReferenceSequenceTable.TableRow>

TableWriter to format and write the table output.

Field Summary

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

METADATA_TAG

Constructor Summary

Constructors

Constructor	Description
CompareReferencesOutputTableWriter(Writer writer, TableColumnCollection columns)
CompareReferencesOutputTableWriter(Path table, TableColumnCollection columns)

Method Summary

Modifier and Type	Method	Description
protected void	composeLine(ReferenceSequenceTable.TableRow 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

CompareReferencesOutputTableWriter

public CompareReferencesOutputTableWriter(Path table,
 TableColumnCollection columns)
                                   throws IOException

Throws:

IOException

CompareReferencesOutputTableWriter

public CompareReferencesOutputTableWriter(Writer writer,
 TableColumnCollection columns)
                                   throws IOException

Throws:

IOException

Method Details

composeLine

protected void composeLine(ReferenceSequenceTable.TableRow 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<ReferenceSequenceTable.TableRow>

Parameters:

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

dataLine - the destination data-line object.