public final class FastqToBam extends WithReadGroup
| Constructor and Description |
|---|
FastqToBam(File fastqFile,
File bamFile,
String readGroupId,
String readGroupSample,
String readGroupLibrary,
String readGroupPlatformUnit,
Integer readGroupInsertSize,
List<String> readGroupBarcodes)
Convert DNA sequences in FASTQ format to unaligned BAM format.
|
FastqToBam(Path fastqPath,
File bamFile,
String readGroupId,
String readGroupSample,
String readGroupLibrary,
String readGroupPlatformUnit,
Integer readGroupInsertSize,
List<String> readGroupBarcodes)
Convert DNA sequences in FASTQ format to unaligned BAM format.
|
| Modifier and Type | Method and Description |
|---|---|
Integer |
call() |
(package private) htsjdk.samtools.SAMRecord |
convert(org.biojava.bio.program.fastq.Fastq fastq) |
static void |
main(String[] args)
Main.
|
createReadGroupBarcodesArgument, createReadGroupIdArgument, createReadGroupInsertSizeArgument, createReadGroupLibraryArgument, createReadGroupPlatformUnitArgument, createReadGroupSampleArgument, getReadGroupBarcodes, getReadGroupId, getReadGroupInsertSize, getReadGroupLibrary, getReadGroupPlatformUnit, getReadGroupSample, toReadGroup, toReadGroupOptpublic FastqToBam(@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 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 FastqToBam(@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 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 anyCopyright (c) 2013-2023 held jointly by the individual authors. Licensed under the GNU Lesser General Public License (LGPL).