HISTORY.md
LICENSE.txt
MANIFEST.in
README.rst
TODO.md
requirements.txt
setup.py
bcbio/__init__.py
bcbio/convert.py
bcbio/install.py
bcbio/utils.py
bcbio/bam/__init__.py
bcbio/bam/callable.py
bcbio/bam/counts.py
bcbio/bam/cram.py
bcbio/bam/fastq.py
bcbio/bam/trim.py
bcbio/broad/__init__.py
bcbio/broad/metrics.py
bcbio/broad/picardrun.py
bcbio/chipseq/__init__.py
bcbio/distributed/__init__.py
bcbio/distributed/ipython.py
bcbio/distributed/ipythontasks.py
bcbio/distributed/lsf.py
bcbio/distributed/manage.py
bcbio/distributed/messaging.py
bcbio/distributed/multitasks.py
bcbio/distributed/sge.py
bcbio/distributed/split.py
bcbio/distributed/tasks.py
bcbio/distributed/transaction.py
bcbio/galaxy/__init__.py
bcbio/galaxy/api.py
bcbio/hmmer/__init__.py
bcbio/hmmer/search.py
bcbio/log/__init__.py
bcbio/log/logbook_zmqpush.py
bcbio/ngsalign/__init__.py
bcbio/ngsalign/alignprep.py
bcbio/ngsalign/bowtie.py
bcbio/ngsalign/bowtie2.py
bcbio/ngsalign/bwa.py
bcbio/ngsalign/mosaik.py
bcbio/ngsalign/novoalign.py
bcbio/ngsalign/star.py
bcbio/ngsalign/tophat.py
bcbio/picard/__init__.py
bcbio/picard/metrics.py
bcbio/picard/utils.py
bcbio/pipeline/__init__.py
bcbio/pipeline/alignment.py
bcbio/pipeline/cleanbam.py
bcbio/pipeline/config_utils.py
bcbio/pipeline/demultiplex.py
bcbio/pipeline/fastq.py
bcbio/pipeline/genome.py
bcbio/pipeline/lane.py
bcbio/pipeline/main.py
bcbio/pipeline/merge.py
bcbio/pipeline/qcsummary.py
bcbio/pipeline/region.py
bcbio/pipeline/run_info.py
bcbio/pipeline/sample.py
bcbio/pipeline/shared.py
bcbio/pipeline/storage.py
bcbio/pipeline/toplevel.py
bcbio/pipeline/variation.py
bcbio/pipeline/version.py
bcbio/pipeline/disambiguate/__init__.py
bcbio/pipeline/disambiguate/run.py
bcbio/provenance/__init__.py
bcbio/provenance/diagnostics.py
bcbio/provenance/do.py
bcbio/provenance/programs.py
bcbio/provenance/system.py
bcbio/provenance/versioncheck.py
bcbio/rnaseq/__init__.py
bcbio/rnaseq/count.py
bcbio/rnaseq/cufflinks.py
bcbio/rnaseq/qc.py
bcbio/server/__init__.py
bcbio/server/main.py
bcbio/server/run.py
bcbio/solexa/__init__.py
bcbio/solexa/flowcell.py
bcbio/solexa/samplesheet.py
bcbio/structural/__init__.py
bcbio/structural/cn_mops.py
bcbio/structural/hydra.py
bcbio/structural/lumpy.py
bcbio/upload/__init__.py
bcbio/upload/filesystem.py
bcbio/upload/galaxy.py
bcbio/upload/s3.py
bcbio/upload/shared.py
bcbio/variation/__init__.py
bcbio/variation/annotation.py
bcbio/variation/bamprep.py
bcbio/variation/cortex.py
bcbio/variation/coverage.py
bcbio/variation/effects.py
bcbio/variation/ensemble.py
bcbio/variation/freebayes.py
bcbio/variation/genotype.py
bcbio/variation/multi.py
bcbio/variation/mutect.py
bcbio/variation/phasing.py
bcbio/variation/ploidy.py
bcbio/variation/population.py
bcbio/variation/realign.py
bcbio/variation/recalibrate.py
bcbio/variation/samtools.py
bcbio/variation/split.py
bcbio/variation/validate.py
bcbio/variation/varscan.py
bcbio/variation/vcfutils.py
bcbio/variation/vfilter.py
bcbio/workflow/__init__.py
bcbio/workflow/stormseq.py
bcbio/workflow/template.py
bcbio/workflow/xprize.py
bcbio_nextgen.egg-info/PKG-INFO
bcbio_nextgen.egg-info/SOURCES.txt
bcbio_nextgen.egg-info/dependency_links.txt
bcbio_nextgen.egg-info/namespace_packages.txt
bcbio_nextgen.egg-info/not-zip-safe
bcbio_nextgen.egg-info/requires.txt
bcbio_nextgen.egg-info/top_level.txt
config/bcbio_sample.yaml
config/bcbio_system.yaml
config/transfer_info.yaml
config/universe_wsgi.ini
scripts/bam_to_wiggle.py
scripts/barcode_sort_trim.py
scripts/bcbio_nextgen.py
scripts/illumina_finished_msg.py
scripts/nextgen_analysis_server.py
scripts/solexa_qseq_to_fastq.py
tests/test_SequencingDump.py
tests/test_automated_analysis.py
tests/test_pipeline.py
tests/data/illumina_samplesheet.csv
tests/data/illumina_samplesheet_fcid_mixed.csv
tests/data/illumina_samplesheet_sampleref_mixed.csv
tests/data/automated/post_process-sample.yaml
tests/data/automated/run_info-bam.yaml
tests/data/automated/run_info-bamclean.yaml
tests/data/automated/run_info-cancer.yaml
tests/data/automated/run_info-chipseq.yaml
tests/data/automated/run_info-empty.yaml
tests/data/automated/run_info-explant.yaml
tests/data/automated/run_info-rnaseq.yaml
tests/data/automated/run_info-variantcall.yaml
tests/data/automated/run_info.yaml
tests/data/automated/universe_wsgi.ini
tests/data/automated/tool-data/bowtie2_indices.loc
tests/data/automated/tool-data/bowtie_indices.loc
tests/data/automated/tool-data/bwa_index.loc
tests/data/automated/tool-data/mosaik_index.loc
tests/data/automated/tool-data/sam_fa_indices.loc