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Project: halvade
(GitHub Link)
halvade-master
halvade_upload_tool
src
org
apache
tools
bzip2
CRC.java
CBZip2InputStream.java
CBZip2OutputStream.java
CBZip2InputStream.java~
BZip2Constants.java
be
ugent
intec
halvade
uploader
BaseInterleaveFiles.java
AWSUploader.java
Timer.java
HDFSInterleaveFiles.java
Logger.java
HalvadeUploader.java
input
SingleFastQReader.java
ReadBlock.java
PairedFastQReader.java
FileReaderFactory.java
BaseFileReader.java
AWSInterleaveFiles.java
build.xml
gpl.txt
lib
nbproject
project.xml
private
private.properties
private.xml
config.properties
project.properties
genfiles.properties
build-impl.xml
LICENSE
halvade
src
be
ugent
intec
halvade
utils
CommandGenerator.java
StreamGobbler.java
HalvadeFileUtils.java
HalvadeFileLock.java
Timer.java
ChromosomeRange.java
HalvadeConf.java
SAMRecordIterator.java
ProcessBuilderWrapper.java
Logger.java
ChromosomeSplitter.java
SAMStreamHandler.java
hadoop
partitioners
SimpleChrRegionComparator.java
GenomeSJGroupingComparator.java
ChrRgGroupingComparator.java
ChrRgSortComparator.java
GenomeSJSortComparator.java
ChrRgPartitioner.java
datatypes
GenomeSJ.java
ChromosomeRegion.java
mapreduce
BWAMemMapper.java
StarAlignPassXMapper.java
Bowtie2Mapper.java
HalvadeMapper.java
BamMergeReducer.java
CountReadsReducer.java
BWAAlnMapper.java
HalvadeReducer.java
HalvadeTextInputFormat.java
VCFCombineMapper.java
RnaGATKReducer.java
HalvadeCounters.java
Cushaw2Mapper.java
HTSeqCombineReducer.java
GATKReducer.java
RebuildStarGenomeReducer.java
DnaGATKReducer.java
VCFCombineReducer.java
AlignedBamMapper.java
HTSeqCombineMapper.java
Halvade.java
MapReduceRunner.java
HalvadeOptions.java
tools
Cushaw2Instance.java
QualityEncoding.java
ProcessException.java
Bowtie2Instance.java
BWAMemInstance.java
BWAAlnInstance.java
QualityException.java
AlignerInstance.java
DummyAlignerInstance.java
STARInstance.java
PreprocessingTools.java
GATKTools.java
HalvadeResourceManager.java
build.xml
gpl.txt
lib
nbproject
project.xml
private
private.properties
private.xml
config.properties
project.properties
genfiles.properties
build-impl.xml
README.md
scripts
example.config
halvade_bootstrap.sh
runHalvade.py
docs
Makefile
source
contents
run.rst
introduction.rst
hadoop~
options.rst
references.rst
preprocessing.rst
hadoop.rst
upload.rst
samples.rst
installation.rst
index.rst
conf.py
Halvade
The source code has moved to
https://github.com/biointec/halvade