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MANIFEST
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.dockerignore
.travis.yml
bin/addVagrentContext.pl
bin/Admin_CacheFileBuilder.pl
bin/Admin_EnsemblReferenceFileGenerator.pl
bin/Admin_EnsemblTranscriptFilter.pl
bin/Admin_GeneRegionBedDumper.pl
bin/AnnotateVcf.pl
bin/cpanm
build/opt-build-local.sh
build/opt-build.sh
CHANGES.md
Dockerfile
docs.tar.gz
lib/Sanger/CGP/Vagrent.pm
lib/Sanger/CGP/Vagrent/Annotators/AbstractAnnotator.pm
lib/Sanger/CGP/Vagrent/Annotators/AnnotatorCollection.pm
lib/Sanger/CGP/Vagrent/Annotators/ComplexIndelAnnotator.pm
lib/Sanger/CGP/Vagrent/Annotators/DeletionAnnotator.pm
lib/Sanger/CGP/Vagrent/Annotators/InsertionAnnotator.pm
lib/Sanger/CGP/Vagrent/Annotators/SimpleSubstitutionAnnotator.pm
lib/Sanger/CGP/Vagrent/Bookmarkers/AbstractBookmarker.pm
lib/Sanger/CGP/Vagrent/Bookmarkers/MostDeleteriousBookmarker.pm
lib/Sanger/CGP/Vagrent/Bookmarkers/RepresentativeTranscriptBookmarker.pm
lib/Sanger/CGP/Vagrent/Data/AbstractGenomicPosition.pm
lib/Sanger/CGP/Vagrent/Data/AbstractVariation.pm
lib/Sanger/CGP/Vagrent/Data/Annotation.pm
lib/Sanger/CGP/Vagrent/Data/AnnotationGroup.pm
lib/Sanger/CGP/Vagrent/Data/ComplexIndel.pm
lib/Sanger/CGP/Vagrent/Data/Deletion.pm
lib/Sanger/CGP/Vagrent/Data/Exon.pm
lib/Sanger/CGP/Vagrent/Data/GenomicRegion.pm
lib/Sanger/CGP/Vagrent/Data/Insertion.pm
lib/Sanger/CGP/Vagrent/Data/Substitution.pm
lib/Sanger/CGP/Vagrent/Data/Transcript.pm
lib/Sanger/CGP/Vagrent/GenomicRegionDumper/AbstractGenomicRegionDumper.pm
lib/Sanger/CGP/Vagrent/GenomicRegionDumper/IndelGenomicRegionDumper.pm
lib/Sanger/CGP/Vagrent/GenomicRegionDumper/SubstitutionGenomicRegionDumper.pm
lib/Sanger/CGP/Vagrent/IO/AnnotationWriter.pm
lib/Sanger/CGP/Vagrent/IO/GenomicRegionWriter.pm
lib/Sanger/CGP/Vagrent/IO/GenomicRegionWriter/BedWriter.pm
lib/Sanger/CGP/Vagrent/IO/Writer/CsvFileWriter.pm
lib/Sanger/CGP/Vagrent/IO/Writer/SingleLineCsvFileWriter.pm
lib/Sanger/CGP/Vagrent/Ontology/SequenceOntologyClassifier.pm
lib/Sanger/CGP/Vagrent/TranscriptSource/AbstractTranscriptSource.pm
lib/Sanger/CGP/Vagrent/TranscriptSource/FileBasedTranscriptSource.pm
LICENSE.TXT
Makefile.PL
MANIFEST This list of files
MANIFEST.SKIP
patches/vcfToolsProcessLog.diff
prerelease.sh
README.md
setup.sh
share/SequenceOntologySummary.ini
t/1_pm_compile.t
t/2_pl_compile.t
t/3_stable_sort.t
t/AnnotationTestUtils.pm
t/complex.t
t/deletion.t
t/insertion.t
t/substitution.t
t/testAll.pl
testData/stable.cache.gz
testData/stable.cache.gz.tbi
testData/stable.fa
testData/stable.fa.fai
testData/stable.vcf.gz
testData/stable.vcf.gz.tbi
testData/test_transcript.cache.gz
testData/test_transcript.cache.gz.tbi
testData/test_transcript.fa
testData/test_transcript.fa.fai