public final class InterleavedFastqToBam extends WithReadGroup
| Constructor and Description |
|---|
InterleavedFastqToBam(File fastqFile,
File bamFile,
String readGroupId,
String readGroupSample,
String readGroupLibrary,
String readGroupPlatformUnit,
Integer readGroupInsertSize,
List<String> readGroupBarcodes)
Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
|
InterleavedFastqToBam(Path fastqPath,
File bamFile,
String readGroupId,
String readGroupSample,
String readGroupLibrary,
String readGroupPlatformUnit,
Integer readGroupInsertSize,
List<String> readGroupBarcodes)
Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
|
| Modifier and Type | Method and Description |
|---|---|
Integer |
call() |
(package private) htsjdk.samtools.SAMRecord |
convertLeft(org.biojava.bio.program.fastq.Fastq left) |
(package private) htsjdk.samtools.SAMRecord |
convertRight(org.biojava.bio.program.fastq.Fastq right) |
static void |
main(String[] args)
Main.
|
createReadGroupBarcodesArgument, createReadGroupIdArgument, createReadGroupInsertSizeArgument, createReadGroupLibraryArgument, createReadGroupPlatformUnitArgument, createReadGroupSampleArgument, getReadGroupBarcodes, getReadGroupId, getReadGroupInsertSize, getReadGroupLibrary, getReadGroupPlatformUnit, getReadGroupSample, toReadGroup, toReadGroupOptpublic InterleavedFastqToBam(@Nullable File fastqFile, @Nullable File bamFile, @Nullable String readGroupId, @Nullable String readGroupSample, @Nullable String readGroupLibrary, @Nullable String readGroupPlatformUnit, @Nullable Integer readGroupInsertSize, @Nullable List<String> readGroupBarcodes)
fastqFile - input interleaved FASTQ file, if anybamFile - output BAM file, if anyreadGroupId - read group id, if anyreadGroupSample - read group sample, if anyreadGroupLibrary - read group library, if anyreadGroupPlatformUnit - read group platform unit, if anyreadGroupInsertSize - read group insert size, if anyreadGroupBarcodes - read group barcodes, if anypublic InterleavedFastqToBam(@Nullable Path fastqPath, @Nullable File bamFile, @Nullable String readGroupId, @Nullable String readGroupSample, @Nullable String readGroupLibrary, @Nullable String readGroupPlatformUnit, @Nullable Integer readGroupInsertSize, @Nullable List<String> readGroupBarcodes)
fastqPath - input interleaved FASTQ path, if anybamFile - output BAM file, if anyreadGroupId - read group id, if anyreadGroupSample - read group sample, if anyreadGroupLibrary - read group library, if anyreadGroupPlatformUnit - read group platform unit, if anyreadGroupInsertSize - read group insert size, if anyreadGroupBarcodes - read group barcodes, if anyhtsjdk.samtools.SAMRecord convertLeft(org.biojava.bio.program.fastq.Fastq left)
htsjdk.samtools.SAMRecord convertRight(org.biojava.bio.program.fastq.Fastq right)
public static void main(String[] args)
args - command line argsCopyright (c) 2013-2023 held jointly by the individual authors. Licensed under the GNU Lesser General Public License (LGPL).