software.zip
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__MACOSX
software
._.DS_Store
120 Bytes
._bwa-0.7.15
212 Bytes
ATAC_BAM_shifter_gappedAlign
._.DS_Store
120 Bytes
bwa-0.7.15
._.gitignore
212 Bytes
._.travis.yml
212 Bytes
._COPYING
212 Bytes
._ChangeLog
212 Bytes
._Makefile
212 Bytes
._NEWS.md
212 Bytes
._QSufSort.c
212 Bytes
._QSufSort.h
212 Bytes
._README-alt.md
212 Bytes
._README.md
212 Bytes
._bamlite.c
212 Bytes
._bamlite.h
212 Bytes
._bntseq.c
212 Bytes
._bntseq.h
212 Bytes
._bwa.1
212 Bytes
._bwa.c
212 Bytes
._bwa.h
212 Bytes
._bwakit
212 Bytes
._bwamem.c
212 Bytes
._bwamem.h
212 Bytes
._bwamem_extra.c
212 Bytes
._bwamem_pair.c
212 Bytes
._bwape.c
212 Bytes
._bwase.c
212 Bytes
._bwase.h
212 Bytes
._bwaseqio.c
212 Bytes
._bwashm.c
212 Bytes
._bwt.c
212 Bytes
._bwt.h
212 Bytes
._bwt_gen.c
212 Bytes
._bwt_lite.c
212 Bytes
._bwt_lite.h
212 Bytes
._bwtaln.c
212 Bytes
._bwtaln.h
212 Bytes
._bwtgap.c
212 Bytes
._bwtgap.h
212 Bytes
._bwtindex.c
212 Bytes
._bwtsw2.h
212 Bytes
._bwtsw2_aux.c
212 Bytes
._bwtsw2_chain.c
212 Bytes
._bwtsw2_core.c
212 Bytes
._bwtsw2_main.c
212 Bytes
._bwtsw2_pair.c
212 Bytes
._example.c
212 Bytes
._fastmap.c
212 Bytes
._is.c
212 Bytes
._kbtree.h
212 Bytes
._khash.h
212 Bytes
._kopen.c
212 Bytes
._kseq.h
212 Bytes
._ksort.h
212 Bytes
._kstring.c
212 Bytes
._kstring.h
212 Bytes
._ksw.c
212 Bytes
._ksw.h
212 Bytes
._kthread.c
212 Bytes
._kvec.h
212 Bytes
._main.c
212 Bytes
._malloc_wrap.c
212 Bytes
._malloc_wrap.h
212 Bytes
._maxk.c
212 Bytes
._pemerge.c
212 Bytes
._qualfa2fq.pl
212 Bytes
._rle.c
212 Bytes
._rle.h
212 Bytes
._rope.c
212 Bytes
._rope.h
212 Bytes
._utils.c
212 Bytes
._utils.h
212 Bytes
._xa2multi.pl
212 Bytes
bwakit
._README.md
212 Bytes
._bwa-postalt.js
212 Bytes
._run-HLA
212 Bytes
._run-bwamem
212 Bytes
._run-gen-ref
212 Bytes
._typeHLA-selctg.js
212 Bytes
._typeHLA.js
212 Bytes
._typeHLA.sh
212 Bytes
picard
._.DS_Store
120 Bytes
samtools-1.3.1
._AUTHORS
212 Bytes
._ChangeLog.old
212 Bytes
._HowToInstallBedTools.rtf
120 Bytes
._aclocal.m4
212 Bytes
._bam.c
212 Bytes
._bam.h
212 Bytes
._bam2bcf.c
212 Bytes
._bam2bcf.h
212 Bytes
._bam2bcf_indel.c
212 Bytes
._bam2depth.c
212 Bytes
._bam_addrprg.c
212 Bytes
._bam_aux.c
212 Bytes
._bam_cat.c
212 Bytes
._bam_color.c
212 Bytes
._bam_endian.h
212 Bytes
._bam_flags.c
212 Bytes
._bam_import.c
212 Bytes
._bam_index.c
212 Bytes
._bam_lpileup.c
212 Bytes
._bam_lpileup.h
212 Bytes
._bam_mate.c
212 Bytes
._bam_md.c
212 Bytes
._bam_plbuf.c
212 Bytes
._bam_plbuf.h
212 Bytes
._bam_plcmd.c
212 Bytes
._bam_quickcheck.c
212 Bytes
._bam_reheader.c
212 Bytes
._bam_rmdup.c
212 Bytes
._bam_rmdupse.c
212 Bytes
._bam_sort.c
212 Bytes
._bam_split.c
212 Bytes
._bam_stat.c
212 Bytes
._bam_tview.c
212 Bytes
._bam_tview.h
212 Bytes
._bam_tview_curses.c
212 Bytes
._bam_tview_html.c
212 Bytes
._bamshuf.c
212 Bytes
._bamtk.c
212 Bytes
._bedcov.c
212 Bytes
._bedidx.c
212 Bytes
._config.h.in
212 Bytes
._config.mk.in
212 Bytes
._configure
212 Bytes
._configure.ac
212 Bytes
._cut_target.c
212 Bytes
._dict.c
212 Bytes
._errmod.c
212 Bytes
._errmod.h
212 Bytes
._examples
212 Bytes
._faidx.c
212 Bytes
examples
._00README.txt
212 Bytes
._ex1.fa
212 Bytes
._ex1.sam.gz
212 Bytes
._toy.fa
212 Bytes
._toy.sam
212 Bytes
htslib-1.3.1
._INSTALL
212 Bytes
._LICENSE
212 Bytes
._Makefile
212 Bytes
._NEWS
212 Bytes
._README
212 Bytes
._bgzf.c
212 Bytes
._bgzip.c
212 Bytes
._config.h.in
212 Bytes
._config.mk.in
212 Bytes
._configure
212 Bytes
._configure.ac
212 Bytes
._cram
212 Bytes
._faidx.5
212 Bytes
._faidx.c
212 Bytes
._hfile.c
212 Bytes
._hfile_internal.h
212 Bytes
._hfile_irods.c
212 Bytes
._hfile_libcurl.c
212 Bytes
._hfile_net.c
212 Bytes
._hts.c
212 Bytes
._hts_internal.h
212 Bytes
._htsfile.1
212 Bytes
._htsfile.c
212 Bytes
._htslib
212 Bytes
._htslib.mk
212 Bytes
._htslib.pc.in
212 Bytes
._htslib_vars.mk
212 Bytes
._kfunc.c
212 Bytes
._knetfile.c
212 Bytes
._kstring.c
212 Bytes
._md5.c
212 Bytes
._plugin.c
212 Bytes
._regidx.c
212 Bytes
._sam.5
212 Bytes
._sam.c
212 Bytes
._synced_bcf_reader.c
212 Bytes
._tabix.1
212 Bytes
._tabix.c
212 Bytes
._tbx.c
212 Bytes
cram
._cram.h
212 Bytes
._cram_codecs.c
212 Bytes
._cram_codecs.h
212 Bytes
._cram_decode.c
212 Bytes
._cram_decode.h
212 Bytes
._cram_encode.c
212 Bytes
._cram_encode.h
212 Bytes
._cram_external.c
212 Bytes
._cram_index.c
212 Bytes
._cram_index.h
212 Bytes
._cram_io.c
212 Bytes
._cram_io.h
212 Bytes
._cram_samtools.c
212 Bytes
._cram_samtools.h
212 Bytes
._cram_stats.c
212 Bytes
._cram_stats.h
212 Bytes
._cram_structs.h
212 Bytes
._files.c
212 Bytes
._mFILE.c
212 Bytes
._mFILE.h
212 Bytes
._misc.h
212 Bytes
._open_trace_file.c
212 Bytes
._open_trace_file.h
212 Bytes
._os.h
212 Bytes
._pooled_alloc.c
212 Bytes
._pooled_alloc.h
212 Bytes
._rANS_byte.h
212 Bytes
._rANS_static.c
212 Bytes
._rANS_static.h
212 Bytes
._sam_header.c
212 Bytes
._sam_header.h
212 Bytes
._string_alloc.c
212 Bytes
._string_alloc.h
212 Bytes
._thread_pool.c
212 Bytes
._thread_pool.h
212 Bytes
._vlen.c
212 Bytes
._vlen.h
212 Bytes
._zfio.c
212 Bytes
._zfio.h
212 Bytes
htslib
._bgzf.h
212 Bytes
._cram.h
212 Bytes
._faidx.h
212 Bytes
._hfile.h
212 Bytes
._hts.h
212 Bytes
._hts_defs.h
212 Bytes
._kbitset.h
212 Bytes
._kfunc.h
212 Bytes
._khash.h
212 Bytes
._khash_str2int.h
212 Bytes
._klist.h
212 Bytes
._knetfile.h
212 Bytes
._kseq.h
212 Bytes
._ksort.h
212 Bytes
._kstring.h
212 Bytes
._regidx.h
212 Bytes
._sam.h
212 Bytes
._synced_bcf_reader.h
212 Bytes
._tbx.h
212 Bytes
._vcf.h
212 Bytes
._vcf_sweep.h
212 Bytes
._vcfutils.h
212 Bytes
test
._aux#aux_java.cram
212 Bytes
._auxf#values.sam
212 Bytes
._auxf.fa
212 Bytes
._auxf.fa.fai
212 Bytes
._c1#bounds.sam
212 Bytes
._c1#clip.sam
212 Bytes
._c1#noseq.sam
212 Bytes
._c1#pad1.sam
212 Bytes
._c1#pad2.sam
212 Bytes
._c1#pad3.sam
212 Bytes
._c1#unknown.sam
212 Bytes
._c1.fa
212 Bytes
software
.DS_Store
18.4 kB
ATAC_BAM_shifter_gappedAlign
.DS_Store
6.1 kB
ATAC_BAM_shifter_gappedAlign.pl
9.1 kB
FastQC
Configuration
adapter_list.txt
1.3 kB
contaminant_list.txt
13.3 kB
limits.txt
2.6 kB
Help
1 Introduction
1.1 What is FastQC.html
1.2 kB
2 Basic Operations
2.1 Opening a sequence file.html
2.0 kB
2.2 Evaluating Results.html
1.2 kB
2.3 Saving a Report.html
1.2 kB
3 Analysis Modules
1 Basic Statistics.html
1.8 kB
10 Adapter Content.html
2.4 kB
11 Kmer Content.html
2.5 kB
12 Per Tile Sequence Quality.html
2.3 kB
2 Per Base Sequence Quality.html
3.7 kB
3 Per Sequence Quality Scores.html
1.7 kB
4 Per Base Sequence Content.html
2.9 kB
5 Per Sequence GC Content.html
1.9 kB
6 Per Base N Content.html
1.9 kB
7 Sequence Length Distribution.html
1.2 kB
8 Duplicate Sequences.html
6.1 kB
9 Overrepresented Sequences.html
2.4 kB
duplication_levels.png
20.5 kB
kmer_profiles.png
76.4 kB
per_base_gc_content.png
14.7 kB
per_base_n_content.png
13.7 kB
per_base_quality.png
10.1 kB
per_base_sequence_content.png
18.4 kB
per_sequence_gc_content.png
20.8 kB
per_sequence_quality.png
21.4 kB
per_tile_quality.png
11.8 kB
sequence_length_distribution.png
19.6 kB
INSTALL.txt
5.6 kB
LICENSE.txt
35.8 kB
README.txt
2.1 kB
RELEASE_NOTES.txt
31.8 kB
Templates
Icons
error.png
1.6 kB
fastqc_icon.png
1.2 kB
tick.png
1.7 kB
warning.png
1.4 kB
fastqc2fo.xsl
2.4 kB
header_template.html
2.8 kB
fastqc
12.8 kB
fastqc_icon.ico
2.2 kB
jbzip2-0.9.jar
50.1 kB
net
sourceforge
iharder
base64
Base64$1.class
1.3 kB
Base64$InputStream.class
2.2 kB
Base64$OutputStream.class
2.5 kB
Base64.class
21.7 kB
org
apache
commons
math3
analysis
UnivariateFunction.class
174 Bytes
solvers
AbstractUnivariateSolver.class
1.0 kB
AllowedSolution.class
1.4 kB
BaseAbstractUnivariateSolver.class
5.5 kB
BaseUnivariateSolver.class
716 Bytes
BracketedUnivariateSolver.class
852 Bytes
BrentSolver.class
2.8 kB
UnivariateSolver.class
386 Bytes
UnivariateSolverUtils.class
6.2 kB
distribution
AbstractIntegerDistribution.class
3.8 kB
AbstractRealDistribution$1.class
942 Bytes
AbstractRealDistribution.class
4.0 kB
BetaDistribution.class
3.3 kB
BinomialDistribution.class
2.5 kB
CauchyDistribution.class
3.1 kB
ChiSquaredDistribution.class
2.1 kB
FDistribution.class
3.6 kB
GammaDistribution.class
2.8 kB
HypergeometricDistribution.class
4.7 kB
IntegerDistribution.class
678 Bytes
NormalDistribution.class
3.7 kB
PascalDistribution.class
2.6 kB
PoissonDistribution.class
3.2 kB
RealDistribution.class
755 Bytes
SaddlePointExpansion.class
2.6 kB
TDistribution.class
2.9 kB
WeibullDistribution.class
3.9 kB
ZipfDistribution.class
3.0 kB
exception
ConvergenceException.class
1.1 kB
DimensionMismatchException.class
1.3 kB
MathArithmeticException.class
1.6 kB
MathIllegalArgumentException.class
1.3 kB
MathIllegalNumberException.class
986 Bytes
MathIllegalStateException.class
1.8 kB
MathInternalError.class
1.4 kB
MaxCountExceededException.class
1.4 kB
NoBracketingException.class
1.6 kB
NotFiniteNumberException.class
1.0 kB
NotPositiveException.class
983 Bytes
NotStrictlyPositiveException.class
1.0 kB
NullArgumentException.class
924 Bytes
NumberIsTooLargeException.class
1.5 kB
NumberIsTooSmallException.class
1.5 kB
OutOfRangeException.class
1.4 kB
TooManyEvaluationsException.class
980 Bytes
util
ArgUtils.class
927 Bytes
ExceptionContext.class
6.0 kB
ExceptionContextProvider.class
253 Bytes
Localizable.class
290 Bytes
LocalizedFormats.class
42.5 kB
random
AbstractWell.class
2.2 kB
BitsStreamGenerator.class
2.4 kB
RandomData.class
618 Bytes
RandomDataImpl.class
14.0 kB
RandomGenerator.class
395 Bytes
Well19937c.class
1.6 kB
special
Beta$1.class
956 Bytes
Beta.class
1.9 kB
Erf.class
1.1 kB
Gamma$1.class
747 Bytes
Gamma.class
3.4 kB
util
ArithmeticUtils.class
8.6 kB
ContinuedFraction.class
2.7 kB
DoubleArray.class
365 Bytes
FastMath$ExpFracTable.class
818 Bytes
FastMath$ExpIntTable.class
811 Bytes
FastMath$lnMant.class
658 Bytes
FastMath.class
36.0 kB
FastMathCalc.class
8.4 kB
FastMathLiteralArrays.class
149.4 kB
Incrementor$1.class
819 Bytes
Incrementor$MaxCountExceededCallback.class
288 Bytes
Incrementor.class
1.7 kB
MathUtils.class
3.2 kB
Precision.class
5.1 kB
ResizableDoubleArray.class
9.1 kB
run_fastqc.bat
101 Bytes
sam-1.103.jar
644.8 kB
uk
ac
babraham
FastQC
Analysis
AnalysisListener.class
527 Bytes
AnalysisQueue.class
2.9 kB
AnalysisRunner.class
3.6 kB
OfflineRunner.class
6.7 kB
Dialogs
AboutDialog$1.class
878 Bytes
AboutDialog.class
1.8 kB
FastQCTitlePanel$SmoothJLabel.class
1.2 kB
FastQCTitlePanel.class
3.4 kB
WelcomePanel.class
1.3 kB
FastQCApplication$1.class
1.0 kB
FastQCApplication.class
10.0 kB
FastQCConfig.class
3.1 kB
FastQCMenuBar.class
3.7 kB
FileFilters
BAMFileFilter.class
600 Bytes
CasavaFastQFileFilter.class
794 Bytes
FastQFileFilter.class
590 Bytes
GobyFileFilter.class
600 Bytes
MappedBAMFileFilter.class
626 Bytes
SequenceFileFilter.class
1.2 kB
Graphs
BaseGroup.class
3.2 kB
LineGraph.class
5.6 kB
QualityBoxPlot.class
4.5 kB
TileGraph.class
3.9 kB
Help
HelpDialog.class
3.3 kB
HelpIndexRoot$FileSorter.class
2.0 kB
HelpIndexRoot.class
3.0 kB
HelpPage.class
2.9 kB
HelpPageDisplay$HelpEditor.class
1.2 kB
HelpPageDisplay.class
2.3 kB
HelpSearchPanel.class
3.9 kB
Modules
AbstractQCModule.class
3.3 kB
AdapterContent$Adapter.class
1.6 kB
AdapterContent$ResultsTable.class
1.8 kB
AdapterContent.class
9.9 kB
BasicStats$ResultsTable.class
3.0 kB
BasicStats.class
4.8 kB
DuplicationLevel.class
7.7 kB
GCModel
GCModel.class
1.5 kB
GCModelValue.class
590 Bytes
KmerContent$Kmer.class
3.1 kB
KmerContent$ResultsTable.class
2.2 kB
KmerContent.class
11.0 kB
ModuleConfig.class
5.2 kB
NContent.class
5.3 kB
OverRepresentedSeqs$OverrepresentedSeq.class
2.1 kB
OverRepresentedSeqs$ResultsTable.class
2.0 kB
OverRepresentedSeqs.class
6.8 kB
PerBaseQualityScores.class
7.6 kB
PerBaseSequenceContent.class
6.3 kB
PerSequenceGCContent.class
6.8 kB
PerSequenceQualityScores.class
6.2 kB
PerTileQualityScores.class
8.9 kB
QCModule.class
610 Bytes
SequenceLengthDistribution.class
6.0 kB
Report
HTMLReportArchive.class
11.9 kB
stylesheet.txt
943 Bytes
Resources
error.png
1.6 kB
fastqc_icon.png
1.2 kB
fastqc_icon.svg
6.6 kB
fastqc_icon_100.png
3.5 kB
tick.png
1.7 kB
warning.png
1.4 kB
Results
ResultsPanel$ModuleRenderer.class
1.9 kB
ResultsPanel.class
5.0 kB
Sequence
BAMFile.class
4.5 kB
Contaminant
Contaminant.class
2.9 kB
ContaminantHit.class
1.7 kB
ContaminentFinder.class
3.3 kB
FastQFile.class
6.5 kB
QualityEncoding
PhredEncoding.class
2.7 kB
Sequence.class
1.7 kB
SequenceFactory.class
2.3 kB
SequenceFile.class
437 Bytes
SequenceFileGroup.class
2.5 kB
SequenceFormatException.class
423 Bytes
Statistics
NormalDistribution.class
739 Bytes
PearsonCorrelation.class
1.5 kB
Utilities
CasavaBasename.class
2.7 kB
HotColdColourGradient.class
2.0 kB
ImageToBase64.class
1.4 kB
MultiMemberGZIPInputStream.class
2.0 kB
NameFormatException.class
349 Bytes
QualityCount.class
1.4 kB
RGB.class
438 Bytes
MACS2-2.1.0.20140616
COPYING
1.6 kB
ChangeLog
67.2 kB
INSTALL.rst
4.9 kB
MACS2
Constants.py
901 Bytes
IO
BinKeeper.py
11.1 kB
WiggleIO.py
7.7 kB
__init__.py
0 Bytes
cBedGraph.c
823.6 kB
cBedGraph.pyx
44.4 kB
cBedGraphIO.c
191.4 kB
cBedGraphIO.pyx
5.2 kB
cCallPeakUnit.c
1.2 MB
cCallPeakUnit.pyx
111.2 kB
cCompositeScoreTrack.pyx
50.1 kB
cDiffScore.pyx
74.6 kB
cFixWidthTrack.c
1.0 MB
cFixWidthTrack.pyx
40.0 kB
cPairedEndTrack.c
769.1 kB
cPairedEndTrack.pyx
22.0 kB
cParser.c
1.2 MB
cParser.h
512 Bytes
cParser.pyx
51.9 kB
cPeakIO.c
1.0 MB
cPeakIO.pyx
48.3 kB
cScoreTrack.c
1.7 MB
cScoreTrack.pyx
70.7 kB
OptValidator.py
23.6 kB
OutputWriter.py
11.0 kB
Poisson.c
349.5 kB
Poisson.pyx
7.8 kB
__init__.py
24 Bytes
bdgbroadcall.py
2.6 kB
bdgcmp.py
3.4 kB
bdgdiff.py
4.5 kB
bdgpeakcall.py
2.2 kB
cArray.c
176.4 kB
cArray.pyx
4.0 kB
cPeakDetect.c
358.9 kB
cPeakDetect.pyx
21.2 kB
cPeakModel.c
613.3 kB
cPeakModel.pyx
22.2 kB
cPileup.c
699.5 kB
cPileup.pyx
26.8 kB
cPoisson.c
3.4 kB
cPoisson.h
215 Bytes
cProb.c
474.4 kB
cProb.pxd
1.2 kB
cProb.pyx
19.7 kB
cSignal.c
507.3 kB
cSignal.pyx
13.3 kB
cStat.py
5.4 kB
cTimeSeries.pyx
4.9 kB
callpeak.py
19.3 kB
data
__init__.py
1.0 kB
diffpeak.py
10.0 kB
filterdup.py
3.7 kB
hashtable.c
408.7 kB
hashtable.pyx
7.8 kB
khash.h
21.0 kB
khash.pxd
3.3 kB
pileup.py
3.4 kB
predictd.py
3.3 kB
randsample.py
2.8 kB
refinepeak.py
6.9 kB
MANIFEST
1.3 kB
PKG-INFO
673 Bytes
README.rst
21.7 kB
bin
macs2
52.0 kB
setup.py
4.1 kB
bwa-0.7.15
.gitignore
55 Bytes
.travis.yml
53 Bytes
COPYING
35.1 kB
ChangeLog
125.7 kB
Makefile
3.2 kB
NEWS.md
39.5 kB
QSufSort.c
12.6 kB
QSufSort.h
1.6 kB
QSufSort.o
18.9 kB
README-alt.md
9.4 kB
README.md
8.5 kB
bamlite.c
6.1 kB
bamlite.h
3.1 kB
bamlite.o
14.5 kB
bntseq.c
13.8 kB
bntseq.h
2.8 kB
bntseq.o
37.0 kB
bwa
399.3 kB
bwa.1
26.2 kB
bwa.c
13.7 kB
bwa.h
2.0 kB
bwa.o
40.4 kB
bwakit
README.md
6.0 kB
bwa-postalt.js
18.0 kB
run-HLA
411 Bytes
run-bwamem
6.6 kB
run-gen-ref
1.7 kB
typeHLA-selctg.js
1.7 kB
typeHLA.js
16.9 kB
typeHLA.sh
1.5 kB
bwamem.c
46.5 kB
bwamem.h
7.9 kB
bwamem.o
204.3 kB
bwamem_extra.c
4.4 kB
bwamem_extra.o
21.4 kB
bwamem_pair.c
17.2 kB
bwamem_pair.o
41.5 kB
bwape.c
29.4 kB
bwape.o
57.4 kB
bwase.c
19.6 kB
bwase.h
1.0 kB
bwase.o
50.5 kB
bwaseqio.c
6.9 kB
bwaseqio.o
23.5 kB
bwashm.c
5.8 kB
bwashm.o
16.2 kB
bwt.c
15.3 kB
bwt.h
5.0 kB
bwt.o
34.7 kB
bwt_gen.c
53.9 kB
bwt_gen.o
60.7 kB
bwt_lite.c
2.7 kB
bwt_lite.h
653 Bytes
bwt_lite.o
8.7 kB
bwtaln.c
11.0 kB
bwtaln.h
3.8 kB
bwtaln.o
27.8 kB
bwtgap.c
9.2 kB
bwtgap.h
999 Bytes
bwtgap.o
25.9 kB
bwtindex.c
9.8 kB
bwtindex.o
22.6 kB
bwtsw2.h
1.5 kB
bwtsw2_aux.c
25.0 kB
bwtsw2_aux.o
66.5 kB
bwtsw2_chain.c
3.1 kB
bwtsw2_chain.o
21.3 kB
bwtsw2_core.c
19.0 kB
bwtsw2_core.o
80.7 kB
bwtsw2_main.c
3.8 kB
bwtsw2_main.o
11.1 kB
bwtsw2_pair.c
10.3 kB
bwtsw2_pair.o
20.3 kB
example.c
1.8 kB
fastmap.c
18.4 kB
fastmap.o
36.9 kB
is.c
6.7 kB
is.o
18.8 kB
kbtree.h
15.9 kB
khash.h
20.9 kB
kopen.c
9.7 kB
kopen.o
23.5 kB
kseq.h
8.9 kB
ksort.h
9.7 kB
kstring.c
703 Bytes
kstring.h
2.3 kB
kstring.o
4.1 kB
ksw.c
26.1 kB
ksw.h
5.1 kB
ksw.o
41.1 kB
kthread.c
3.7 kB
kthread.o
9.4 kB
kvec.h
2.9 kB
libbwa.a
673.3 kB
main.c
4.6 kB
main.o
8.9 kB
malloc_wrap.c
1.4 kB
malloc_wrap.h
1.2 kB
malloc_wrap.o
6.2 kB
maxk.c
1.6 kB
maxk.o
8.7 kB
pemerge.c
8.8 kB
pemerge.o
21.0 kB
qualfa2fq.pl
617 Bytes
rle.c
4.8 kB
rle.h
1.9 kB
rle.o
22.8 kB
rope.c
9.0 kB
rope.h
1.5 kB
rope.o
25.6 kB
utils.c
6.9 kB
utils.h
3.8 kB
utils.o
57.2 kB
xa2multi.pl
731 Bytes
picard
.DS_Store
6.1 kB
1.95
AddOrReplaceReadGroups.jar
909.6 kB
BamIndexStats.jar
908.6 kB
BamToBfq.jar
922.8 kB
BuildBamIndex.jar
907.4 kB
CalculateHsMetrics.jar
979.7 kB
CheckIlluminaDirectory.jar
1.1 MB
CleanSam.jar
913.7 kB
CollectAlignmentSummaryMetrics.jar
957.4 kB
CollectGcBiasMetrics.jar
941.1 kB
CollectInsertSizeMetrics.jar
958.9 kB
CollectMultipleMetrics.jar
994.1 kB
CollectRnaSeqMetrics.jar
1.0 MB
CollectTargetedPcrMetrics.jar
983.2 kB
CompareSAMs.jar
876.6 kB
CreateSequenceDictionary.jar
925.0 kB
DownsampleSam.jar
909.6 kB
EstimateLibraryComplexity.jar
926.3 kB
ExtractIlluminaBarcodes.jar
1.1 MB
ExtractSequences.jar
931.6 kB
FastqToSam.jar
929.8 kB
FilterSamReads.jar
921.7 kB
FixMateInformation.jar
936.8 kB
IlluminaBasecallsToFastq.jar
1.1 MB
IlluminaBasecallsToSam.jar
1.1 MB
IntervalListTools.jar
917.5 kB
MarkDuplicates.jar
972.2 kB
MeanQualityByCycle.jar
940.2 kB
MergeBamAlignment.jar
997.8 kB
MergeSamFiles.jar
930.6 kB
MergeVcfs.jar
1.6 MB
NormalizeFasta.jar
923.7 kB
QualityScoreDistribution.jar
938.4 kB
ReorderSam.jar
926.1 kB
ReplaceSamHeader.jar
909.1 kB
RevertSam.jar
911.4 kB
SamFormatConverter.jar
908.8 kB
SamToFastq.jar
917.4 kB
SortSam.jar
908.7 kB
SplitVcfs.jar
1.5 MB
ValidateSamFile.jar
976.9 kB
VcfFormatConverter.jar
1.5 MB
ViewSam.jar
908.3 kB
apache-ant-1.8.2-bzip2.jar
30.4 kB
cofoja-1.0-r139.jar
378.2 kB
commons-jexl-2.1.1.jar
267.6 kB
commons-logging-1.1.1.jar
60.7 kB
picard-1.95.jar
1.7 MB
sam-1.95.jar
620.3 kB
snappy-java-1.0.3-rc3.jar
990.3 kB
tribble-1.95.jar
265.5 kB
variant-1.95.jar
556.2 kB
samtools-1.3.1
AUTHORS
828 Bytes
ChangeLog.old
116.4 kB
HowToInstallBedTools.rtf
2.1 kB
aclocal.m4
30.1 kB
bam.c
8.8 kB
bam.h
21.0 kB
bam.o
17.4 kB
bam2bcf.c
31.5 kB
bam2bcf.h
5.1 kB
bam2bcf.o
49.7 kB
bam2bcf_indel.c
24.0 kB
bam2bcf_indel.o
59.4 kB
bam2depth.c
12.7 kB
bam2depth.o
21.3 kB
bam_addrprg.c
14.5 kB
bam_addrprg.o
26.4 kB
bam_aux.c
2.8 kB
bam_aux.o
6.6 kB
bam_cat.c
17.9 kB
bam_cat.o
32.6 kB
bam_color.c
5.0 kB
bam_color.o
8.8 kB
bam_endian.h
2.3 kB
bam_flags.c
3.1 kB
bam_flags.o
4.9 kB
bam_import.c
2.3 kB
bam_import.o
9.0 kB
bam_index.c
4.1 kB
bam_index.o
10.2 kB
bam_lpileup.c
7.0 kB
bam_lpileup.h
2.1 kB
bam_lpileup.o
25.2 kB
bam_mate.c
14.9 kB
bam_mate.o
26.6 kB
bam_md.c
18.4 kB
bam_md.o
40.7 kB
bam_plbuf.c
2.1 kB
bam_plbuf.h
1.8 kB
bam_plbuf.o
6.0 kB
bam_plcmd.c
44.5 kB
bam_plcmd.o
73.6 kB
bam_quickcheck.c
5.0 kB
bam_quickcheck.o
11.9 kB
bam_reheader.c
16.1 kB
bam_reheader.o
28.8 kB
bam_rmdup.c
10.5 kB
bam_rmdup.o
39.9 kB
bam_rmdupse.c
7.3 kB
bam_rmdupse.o
33.6 kB
bam_sort.c
69.2 kB
bam_sort.o
183.2 kB
bam_split.c
20.1 kB
bam_split.o
38.2 kB
bam_stat.c
7.4 kB
bam_stat.o
16.0 kB
bam_tview.c
16.5 kB
bam_tview.h
3.4 kB
bam_tview.o
39.3 kB
bam_tview_curses.c
11.5 kB
bam_tview_curses.o
23.1 kB
bam_tview_html.c
10.9 kB
bam_tview_html.o
22.3 kB
bamshuf.c
9.0 kB
bamshuf.o
41.2 kB
bamtk.c
9.4 kB
bamtk.o
13.4 kB
bedcov.c
5.9 kB
bedcov.o
18.2 kB
bedidx.c
8.7 kB
bedidx.o
37.6 kB
config.h
85 Bytes
config.h.in
1.5 kB
config.mk
1.7 kB
config.mk.in
2.0 kB
configure
154.7 kB
configure.ac
4.0 kB
cut_target.c
8.5 kB
cut_target.o
17.8 kB
dict.c
5.1 kB
dict.o
17.6 kB
errmod.c
6.5 kB
errmod.h
1.7 kB
errmod.o
25.0 kB
examples
00README.txt
1.3 kB
ex1.fa
3.2 kB
ex1.sam.gz
114.6 kB
toy.fa
98 Bytes
toy.sam
786 Bytes
faidx.c
2.8 kB
faidx.o
5.5 kB
htslib-1.3.1
INSTALL
4.5 kB
LICENSE
3.5 kB
Makefile
18.2 kB
NEWS
4.8 kB
README
273 Bytes
bgzf.c
41.9 kB
bgzf.o
74.0 kB
bgzip.c
11.5 kB
config.h
43 Bytes
config.h.in
1.2 kB
config.mk.in
3.4 kB
configure
158.2 kB
configure.ac
7.6 kB
cram
cram.h
2.4 kB
cram_codecs.c
48.4 kB
cram_codecs.h
6.1 kB
cram_codecs.o
109.4 kB
cram_decode.c
83.2 kB
cram_decode.h
3.5 kB
cram_decode.o
162.9 kB
cram_encode.c
87.4 kB
cram_encode.h
3.3 kB
cram_encode.o
144.0 kB
cram_external.c
12.5 kB
cram_external.o
42.6 kB
cram_index.c
14.8 kB
cram_index.h
3.3 kB
cram_index.o
39.9 kB
cram_io.c
112.9 kB
cram_io.h
19.1 kB
cram_io.o
195.1 kB
cram_samtools.c
4.9 kB
cram_samtools.h
3.6 kB
cram_samtools.o
12.0 kB
cram_stats.c
12.2 kB
cram_stats.h
2.3 kB
cram_stats.o
33.6 kB
cram_structs.h
22.8 kB
files.c
2.5 kB
files.o
5.6 kB
mFILE.c
16.8 kB
mFILE.h
3.0 kB
mFILE.o
25.8 kB
misc.h
4.3 kB
open_trace_file.c
11.7 kB
open_trace_file.h
5.0 kB
open_trace_file.o
15.2 kB
os.h
9.4 kB
pooled_alloc.c
4.6 kB
pooled_alloc.h
2.2 kB
pooled_alloc.o
5.7 kB
rANS_byte.h
11.8 kB
rANS_static.c
21.1 kB
rANS_static.h
2.0 kB
rANS_static.o
44.8 kB
sam_header.c
29.7 kB
sam_header.h
14.0 kB
sam_header.o
72.7 kB
string_alloc.c
4.2 kB
string_alloc.h
2.3 kB
string_alloc.o
6.3 kB
thread_pool.c
17.9 kB
thread_pool.h
6.7 kB
thread_pool.o
16.1 kB
vlen.c
12.2 kB
vlen.h
1.8 kB
vlen.o
7.0 kB
zfio.c
4.9 kB
zfio.h
2.1 kB
zfio.o
8.2 kB
faidx.5
4.8 kB
faidx.c
15.1 kB
faidx.o
44.7 kB
hfile.c
21.0 kB
hfile.o
42.4 kB
hfile_internal.h
5.6 kB
hfile_irods.c
7.4 kB
hfile_libcurl.c
25.8 kB
hfile_net.c
3.2 kB
hfile_net.o
7.3 kB
hts.c
63.0 kB
hts.o
164.9 kB
hts_internal.h
3.7 kB
htsfile.1
3.1 kB
htsfile.c
6.8 kB
htslib
bgzf.h
11.4 kB
cram.h
14.6 kB
faidx.h
4.6 kB
hfile.h
7.1 kB
hts.h
21.9 kB
hts_defs.h
2.5 kB
kbitset.h
4.2 kB
kfunc.h
2.7 kB
khash.h
21.5 kB
khash_str2int.h
4.0 kB
klist.h
5.1 kB
knetfile.h
2.8 kB
kseq.h
8.9 kB
ksort.h
10.1 kB
kstring.h
7.1 kB
regidx.h
5.8 kB
sam.h
17.1 kB
synced_bcf_reader.h
12.7 kB
tbx.h
2.9 kB
vcf.h
39.9 kB
vcf_sweep.h
1.6 kB
vcfutils.h
4.7 kB
htslib.mk
5.3 kB
htslib.pc.in
265 Bytes
htslib_vars.mk
2.7 kB
kfunc.c
9.2 kB
kfunc.o
23.8 kB
knetfile.c
18.8 kB
knetfile.o
26.5 kB
kstring.c
7.3 kB
kstring.o
17.6 kB
libhts.a
2.1 MB
md5.c
10.6 kB
md5.o
11.4 kB
plugin.c
5.0 kB
regidx.c
10.2 kB
regidx.o
31.8 kB
sam.5
2.8 kB
sam.c
69.5 kB
sam.o
183.9 kB
synced_bcf_reader.c
42.0 kB
synced_bcf_reader.o
73.1 kB
tabix.1
5.7 kB
tabix.c
19.9 kB
tbx.c
10.6 kB
tbx.o
22.9 kB
test
aux#aux_java.cram
3.8 kB
auxf#values.sam
727 Bytes
auxf.fa
29 Bytes
auxf.fa.fai
18 Bytes
c1#bounds.sam
148 Bytes
c1#clip.sam
337 Bytes
c1#noseq.sam
433 Bytes
c1#pad1.sam
388 Bytes
c1#pad2.sam
527 Bytes
c1#pad3.sam
665 Bytes
c1#unknown.sam
429 Bytes
c1.fa
15 Bytes
c1.fa.fai
14 Bytes