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cramtools-master
src
main
java
htsjdk
samtools
API.java
BAMIndexFactory.java
CRAMContainerAsynchWriter.java
CRAMContainerStreamWriter.java
CRAMFileWriter.java
FileFormat.java
IndexAggregate.java
IndexFormat.java
cram
CramContext.java
CramLossyOptions.java
CramSerilization.java
build
CramNormalizer.java
encoding
reader
AbstractFastqReader.java
BAMNameCollate.java
BAMRead.java
BAMRecordView.java
BamFlags.java
CramFlags.java
FastqNameCollate.java
FastqRead.java
FastqReader.java
FastqView.java
MultiFastqOutputter.java
NameCollate.java
ReadFeatureBuffer.java
ReaderToBAM.java
ReaderToFasta.java
ReaderToFastq.java
lossy
Binning.java
QualityScorePreservation.java
paralell
BamToCram.java
BamToCram_OBA_Function.java
Bam_OBA_Supplier.java
ConsumerJob.java
Conveyer.java
CramContainer_OBA_Supplier.java
CramToBam.java
CramToBam_OBA_Function.java
IOrder.java
Job.java
OBAWriteConsumer.java
OrderedByteArray.java
OrderingConveyer.java
SAMFileHeader_Utils.java
StreamPump.java
SupplierJob.java
TransformerJob.java
ref
ReferenceTracks.java
structure
SliceIO_Accessor.java
net
sf
cram
AlignmentSliceQuery.java
AlignmentsTags.java
Bam2Cram.java
Cram2Bam.java
Cram2Fastq.java
CramFixHeader.java
CramTools.java
Crambone.java
DecomposeBAM.java
DetectFeatureB.java
DetectMultiref.java
DownloadReferences.java
FastqSAMFileWriter.java
FixBAMFileHeader.java
Merge.java
QualityScoreStats.java
ReadNotFoundException.java
RefRepo.java
Refless.java
Transcode.java
ValidateCramFile.java
cg
CigEl.java
DedupIterator.java
Evidence2SAM.java
EvidenceRecord.java
EvidenceRecordFileIterator.java
Read.java
Splitter.java
Utils.java
common
Utils.java
fasta
BGZF_FastaIndexer.java
BGZF_ReferenceSequenceFile.java
FAIDX_FastaIndexEntry.java
index
BAMQueryFilteringIterator.java
BaiIndexer.java
CraiIndexer.java
CramIndex.java
CramIndexer.java
mask
ArrayPositionMask.java
DefaultReadMaskFactory.java
FastaByteArrayMaskFactory.java
IntegerListMaskFactory.java
PositionMask.java
ReadMaskException.java
ReadMaskFactory.java
ReadMaskFormatException.java
ReadMaskReader.java
RefMaskUtils.java
SingleLineMaskReader.java
ref
InMemoryReferenceSequenceFile.java
PathPattern.java
ReferenceRegion.java
ReferenceSequenceFromSeekable.java
ReferenceSource.java
select
BoundSAMRecordIterator.java
Dibify.java
FIELD_TYPE.java
SAMFieldSelector.java
SAMRecordField.java
SamRecordComparision.java
test
java
htsjdk
samtools
cram
encoding
reader
BAMRecordViewTest.java
lossy
TestQualityScorePreservation.java
net
sf
cram
AlignmentsTagsTest.java
DataToDB.java
TestBAMRecordView.java
fasta
TestRandomAccess.java
index
TestIndex.java
ref
ReferenceRegionTest.java
package htsjdk.samtools.cram.paralell; interface IOrder { public long order(); }