python3-bcbio (1.2.9-4)

Details

Core information at a glance

Distribution
ubuntu
Origin
ubuntu-stonking
Repository
https://nl.archive.ubuntu.com/ubuntu
Codename
stonking
Component
multiverse
Source
bcbio
Architecture
i386
Section
multiverse/python
Priority
optional
Maintainer
Ubuntu Developers <[email protected]>

Size & integrity

Byte sizes and integrity verification

Installed size
4.8 kB
Size expected
1.3 MB
Size actual
1.3 MB
Size match

Dependencies

Required package dependencies

  • python3:any
  • python3-biopython
  • python3-cyvcf2
  • python3-joblib
  • python3-logbook
  • python3-matplotlib
  • python3-psutil
  • python3-pysam
  • python3-requests
  • python3-scipy
  • python3-six
  • python3-tornado

Suggested packages

Recommended additional packages

  • python3-bioblend
  • python3-dnapilib
  • python3-msgpack
  • python3-seqcluster

Description

library for analysing high-throughput sequencing data

Tags

Package classification tags

None

Checksums

Hash values and integrity verification status

TypeActualMatch
MD5b75e5468…b26dcd8d
SHA-147efaf57…3d4066aa
SHA-256d0cdcdae…5553ca85
SHA-5123b1598a8…9873f9e1

Contents

Files and directories included

.
usr
usr/lib
usr/lib/python3
usr/lib/python3/dist-packages
usr/lib/python3/dist-packages/bcbio
usr/lib/python3/dist-packages/bcbio/__init__.py
usr/lib/python3/dist-packages/bcbio/bam
usr/lib/python3/dist-packages/bcbio/bam/__init__.py
usr/lib/python3/dist-packages/bcbio/bam/callable.py
usr/lib/python3/dist-packages/bcbio/bam/counts.py
usr/lib/python3/dist-packages/bcbio/bam/coverage.py
usr/lib/python3/dist-packages/bcbio/bam/cram.py
usr/lib/python3/dist-packages/bcbio/bam/fasta.py
usr/lib/python3/dist-packages/bcbio/bam/fastq.py
usr/lib/python3/dist-packages/bcbio/bam/readstats.py
usr/lib/python3/dist-packages/bcbio/bam/ref.py
usr/lib/python3/dist-packages/bcbio/bam/skewer.py
usr/lib/python3/dist-packages/bcbio/bam/trim.py
usr/lib/python3/dist-packages/bcbio/bed
usr/lib/python3/dist-packages/bcbio/bed/__init__.py
usr/lib/python3/dist-packages/bcbio/broad
usr/lib/python3/dist-packages/bcbio/broad/__init__.py
usr/lib/python3/dist-packages/bcbio/broad/metrics.py
usr/lib/python3/dist-packages/bcbio/broad/picardrun.py
usr/lib/python3/dist-packages/bcbio/chipseq
usr/lib/python3/dist-packages/bcbio/chipseq/__init__.py
usr/lib/python3/dist-packages/bcbio/chipseq/antibodies.py
usr/lib/python3/dist-packages/bcbio/chipseq/atac.py
usr/lib/python3/dist-packages/bcbio/chipseq/macs2.py
usr/lib/python3/dist-packages/bcbio/chipseq/peaks.py
usr/lib/python3/dist-packages/bcbio/cwl
usr/lib/python3/dist-packages/bcbio/cwl/__init__.py
usr/lib/python3/dist-packages/bcbio/cwl/create.py
usr/lib/python3/dist-packages/bcbio/cwl/cwlutils.py
usr/lib/python3/dist-packages/bcbio/cwl/defs.py
usr/lib/python3/dist-packages/bcbio/cwl/hpc.py
usr/lib/python3/dist-packages/bcbio/cwl/inspect.py
usr/lib/python3/dist-packages/bcbio/cwl/main.py
usr/lib/python3/dist-packages/bcbio/cwl/tool.py
usr/lib/python3/dist-packages/bcbio/cwl/workflow.py
usr/lib/python3/dist-packages/bcbio/data
usr/lib/python3/dist-packages/bcbio/data/umis
usr/lib/python3/dist-packages/bcbio/data/umis/10x_v2-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/10x_v2-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/dropseq-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v2-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v2-cb2.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v2-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v3-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v3-cb2.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v3-sample_barcodes.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v3-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v31-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v31-cb2.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-indrop-v31-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-scrb-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/harvard-scrb-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/icell8-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/icell8-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/qiagen_smallRNA_umi-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/qiaseq-upx-384-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/qiaseq-upx-384-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/qiaseq-upx-96-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/qiaseq-upx-96-transform.json
usr/lib/python3/dist-packages/bcbio/data/umis/surecell-cb1.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/surecell-cb2.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/surecell-cb3.txt.gz
usr/lib/python3/dist-packages/bcbio/data/umis/surecell-transform.json
usr/lib/python3/dist-packages/bcbio/distributed
usr/lib/python3/dist-packages/bcbio/distributed/__init__.py
usr/lib/python3/dist-packages/bcbio/distributed/clargs.py
usr/lib/python3/dist-packages/bcbio/distributed/clusterk.py
usr/lib/python3/dist-packages/bcbio/distributed/ipython.py
usr/lib/python3/dist-packages/bcbio/distributed/ipythontasks.py
usr/lib/python3/dist-packages/bcbio/distributed/multi.py
usr/lib/python3/dist-packages/bcbio/distributed/multitasks.py
usr/lib/python3/dist-packages/bcbio/distributed/objectstore.py
usr/lib/python3/dist-packages/bcbio/distributed/prun.py
usr/lib/python3/dist-packages/bcbio/distributed/resources.py
usr/lib/python3/dist-packages/bcbio/distributed/runfn.py
usr/lib/python3/dist-packages/bcbio/distributed/split.py
usr/lib/python3/dist-packages/bcbio/distributed/transaction.py
usr/lib/python3/dist-packages/bcbio/dragen
usr/lib/python3/dist-packages/bcbio/dragen/__init__.py
usr/lib/python3/dist-packages/bcbio/dragen/dragen.py
usr/lib/python3/dist-packages/bcbio/galaxy
usr/lib/python3/dist-packages/bcbio/galaxy/__init__.py
usr/lib/python3/dist-packages/bcbio/galaxy/api.py
usr/lib/python3/dist-packages/bcbio/galaxy/loc.py
usr/lib/python3/dist-packages/bcbio/galaxy/nglims.py
usr/lib/python3/dist-packages/bcbio/graph
usr/lib/python3/dist-packages/bcbio/graph/__init__.py
usr/lib/python3/dist-packages/bcbio/graph/collectl.py
usr/lib/python3/dist-packages/bcbio/graph/graph.py
usr/lib/python3/dist-packages/bcbio/heterogeneity
usr/lib/python3/dist-packages/bcbio/heterogeneity/__init__.py
usr/lib/python3/dist-packages/bcbio/heterogeneity/bubbletree.py
usr/lib/python3/dist-packages/bcbio/heterogeneity/chromhacks.py
usr/lib/python3/dist-packages/bcbio/heterogeneity/loh.py
usr/lib/python3/dist-packages/bcbio/heterogeneity/phylowgs.py
usr/lib/python3/dist-packages/bcbio/heterogeneity/theta.py
usr/lib/python3/dist-packages/bcbio/hla
usr/lib/python3/dist-packages/bcbio/hla/__init__.py
usr/lib/python3/dist-packages/bcbio/hla/bwakit.py
usr/lib/python3/dist-packages/bcbio/hla/groups.py
usr/lib/python3/dist-packages/bcbio/hla/optitype.py
usr/lib/python3/dist-packages/bcbio/hmmer
usr/lib/python3/dist-packages/bcbio/hmmer/__init__.py
usr/lib/python3/dist-packages/bcbio/hmmer/search.py
usr/lib/python3/dist-packages/bcbio/illumina
usr/lib/python3/dist-packages/bcbio/illumina/__init__.py
usr/lib/python3/dist-packages/bcbio/illumina/demultiplex.py
usr/lib/python3/dist-packages/bcbio/illumina/flowcell.py
usr/lib/python3/dist-packages/bcbio/illumina/machine.py
usr/lib/python3/dist-packages/bcbio/illumina/samplesheet.py
usr/lib/python3/dist-packages/bcbio/illumina/transfer.py
usr/lib/python3/dist-packages/bcbio/install.py
usr/lib/python3/dist-packages/bcbio/log
usr/lib/python3/dist-packages/bcbio/log/__init__.py
usr/lib/python3/dist-packages/bcbio/log/logbook_zmqpush.py
usr/lib/python3/dist-packages/bcbio/ngsalign
usr/lib/python3/dist-packages/bcbio/ngsalign/__init__.py
usr/lib/python3/dist-packages/bcbio/ngsalign/alignprep.py
usr/lib/python3/dist-packages/bcbio/ngsalign/bbmap.py
usr/lib/python3/dist-packages/bcbio/ngsalign/bismark.py
usr/lib/python3/dist-packages/bcbio/ngsalign/bowtie.py
usr/lib/python3/dist-packages/bcbio/ngsalign/bowtie2.py
usr/lib/python3/dist-packages/bcbio/ngsalign/bsmap.py
usr/lib/python3/dist-packages/bcbio/ngsalign/bwa.py
usr/lib/python3/dist-packages/bcbio/ngsalign/hisat2.py
usr/lib/python3/dist-packages/bcbio/ngsalign/minimap2.py
usr/lib/python3/dist-packages/bcbio/ngsalign/mosaik.py
usr/lib/python3/dist-packages/bcbio/ngsalign/novoalign.py
usr/lib/python3/dist-packages/bcbio/ngsalign/postalign.py
usr/lib/python3/dist-packages/bcbio/ngsalign/rtg.py
usr/lib/python3/dist-packages/bcbio/ngsalign/snap.py
usr/lib/python3/dist-packages/bcbio/ngsalign/star.py
usr/lib/python3/dist-packages/bcbio/ngsalign/tophat.py
usr/lib/python3/dist-packages/bcbio/picard
usr/lib/python3/dist-packages/bcbio/picard/__init__.py
usr/lib/python3/dist-packages/bcbio/picard/metrics.py
usr/lib/python3/dist-packages/bcbio/picard/utils.py
usr/lib/python3/dist-packages/bcbio/pipeline
usr/lib/python3/dist-packages/bcbio/pipeline/__init__.py
usr/lib/python3/dist-packages/bcbio/pipeline/alignment.py
usr/lib/python3/dist-packages/bcbio/pipeline/archive.py
usr/lib/python3/dist-packages/bcbio/pipeline/cleanbam.py
usr/lib/python3/dist-packages/bcbio/pipeline/config_utils.py
usr/lib/python3/dist-packages/bcbio/pipeline/datadict.py
usr/lib/python3/dist-packages/bcbio/pipeline/disambiguate
usr/lib/python3/dist-packages/bcbio/pipeline/disambiguate/__init__.py
usr/lib/python3/dist-packages/bcbio/pipeline/disambiguate/run.py
usr/lib/python3/dist-packages/bcbio/pipeline/fastq.py
usr/lib/python3/dist-packages/bcbio/pipeline/genome.py
usr/lib/python3/dist-packages/bcbio/pipeline/main.py
usr/lib/python3/dist-packages/bcbio/pipeline/merge.py
usr/lib/python3/dist-packages/bcbio/pipeline/qcsummary.py
usr/lib/python3/dist-packages/bcbio/pipeline/region.py
usr/lib/python3/dist-packages/bcbio/pipeline/rnaseq.py
usr/lib/python3/dist-packages/bcbio/pipeline/run_info.py
usr/lib/python3/dist-packages/bcbio/pipeline/sample.py
usr/lib/python3/dist-packages/bcbio/pipeline/shared.py
usr/lib/python3/dist-packages/bcbio/pipeline/sra.py
usr/lib/python3/dist-packages/bcbio/pipeline/tools.py
usr/lib/python3/dist-packages/bcbio/pipeline/variation.py
usr/lib/python3/dist-packages/bcbio/pipeline/version.py
usr/lib/python3/dist-packages/bcbio/provenance
usr/lib/python3/dist-packages/bcbio/provenance/__init__.py
usr/lib/python3/dist-packages/bcbio/provenance/data.py
usr/lib/python3/dist-packages/bcbio/provenance/diagnostics.py
usr/lib/python3/dist-packages/bcbio/provenance/do.py
usr/lib/python3/dist-packages/bcbio/provenance/profile.py
usr/lib/python3/dist-packages/bcbio/provenance/programs.py
usr/lib/python3/dist-packages/bcbio/provenance/system.py
usr/lib/python3/dist-packages/bcbio/provenance/versioncheck.py
usr/lib/python3/dist-packages/bcbio/qc
usr/lib/python3/dist-packages/bcbio/qc/__init__.py
usr/lib/python3/dist-packages/bcbio/qc/atac.py
usr/lib/python3/dist-packages/bcbio/qc/atropos.py
usr/lib/python3/dist-packages/bcbio/qc/chipseq.py
usr/lib/python3/dist-packages/bcbio/qc/contamination.py
usr/lib/python3/dist-packages/bcbio/qc/coverage.py
usr/lib/python3/dist-packages/bcbio/qc/damage.py
usr/lib/python3/dist-packages/bcbio/qc/fastqc.py
usr/lib/python3/dist-packages/bcbio/qc/kraken.py
usr/lib/python3/dist-packages/bcbio/qc/multiqc.py
usr/lib/python3/dist-packages/bcbio/qc/picard.py
usr/lib/python3/dist-packages/bcbio/qc/preseq.py
usr/lib/python3/dist-packages/bcbio/qc/qsignature.py
usr/lib/python3/dist-packages/bcbio/qc/qualimap.py
usr/lib/python3/dist-packages/bcbio/qc/samtools.py
usr/lib/python3/dist-packages/bcbio/qc/srna.py
usr/lib/python3/dist-packages/bcbio/qc/umi.py
usr/lib/python3/dist-packages/bcbio/qc/variant.py
usr/lib/python3/dist-packages/bcbio/qc/viral.py
usr/lib/python3/dist-packages/bcbio/rnaseq
usr/lib/python3/dist-packages/bcbio/rnaseq/__init__.py
usr/lib/python3/dist-packages/bcbio/rnaseq/annotate_gtf.py
usr/lib/python3/dist-packages/bcbio/rnaseq/arriba.py
usr/lib/python3/dist-packages/bcbio/rnaseq/bcbiornaseq.py
usr/lib/python3/dist-packages/bcbio/rnaseq/count.py
usr/lib/python3/dist-packages/bcbio/rnaseq/cpat.py
usr/lib/python3/dist-packages/bcbio/rnaseq/cufflinks.py
usr/lib/python3/dist-packages/bcbio/rnaseq/dexseq.py
usr/lib/python3/dist-packages/bcbio/rnaseq/ericscript.py
usr/lib/python3/dist-packages/bcbio/rnaseq/express.py
usr/lib/python3/dist-packages/bcbio/rnaseq/featureCounts.py
usr/lib/python3/dist-packages/bcbio/rnaseq/gtf.py
usr/lib/python3/dist-packages/bcbio/rnaseq/kallisto.py
usr/lib/python3/dist-packages/bcbio/rnaseq/oncofuse.py
usr/lib/python3/dist-packages/bcbio/rnaseq/pizzly.py
usr/lib/python3/dist-packages/bcbio/rnaseq/qc.py
usr/lib/python3/dist-packages/bcbio/rnaseq/rapmap.py
usr/lib/python3/dist-packages/bcbio/rnaseq/rsem.py
usr/lib/python3/dist-packages/bcbio/rnaseq/sailfish.py
usr/lib/python3/dist-packages/bcbio/rnaseq/salmon.py
usr/lib/python3/dist-packages/bcbio/rnaseq/singlecellexperiment.py
usr/lib/python3/dist-packages/bcbio/rnaseq/spikein.py
usr/lib/python3/dist-packages/bcbio/rnaseq/stringtie.py
usr/lib/python3/dist-packages/bcbio/rnaseq/umi.py
usr/lib/python3/dist-packages/bcbio/rnaseq/variation.py
usr/lib/python3/dist-packages/bcbio/scripts
usr/lib/python3/dist-packages/bcbio/scripts/R
usr/lib/python3/dist-packages/bcbio/scripts/R/bcbio2se.R
usr/lib/python3/dist-packages/bcbio/scripts/R/se2qc.Rmd
usr/lib/python3/dist-packages/bcbio/server
usr/lib/python3/dist-packages/bcbio/server/__init__.py
usr/lib/python3/dist-packages/bcbio/server/background.py
usr/lib/python3/dist-packages/bcbio/server/main.py
usr/lib/python3/dist-packages/bcbio/server/run.py
usr/lib/python3/dist-packages/bcbio/setpath.py
usr/lib/python3/dist-packages/bcbio/srna
usr/lib/python3/dist-packages/bcbio/srna/__init__.py
usr/lib/python3/dist-packages/bcbio/srna/group.py
usr/lib/python3/dist-packages/bcbio/srna/mirdeep.py
usr/lib/python3/dist-packages/bcbio/srna/mirge.py
usr/lib/python3/dist-packages/bcbio/srna/qc.py
usr/lib/python3/dist-packages/bcbio/srna/sample.py
usr/lib/python3/dist-packages/bcbio/srna/umis.py
usr/lib/python3/dist-packages/bcbio/structural
usr/lib/python3/dist-packages/bcbio/structural/__init__.py
usr/lib/python3/dist-packages/bcbio/structural/annotate.py
usr/lib/python3/dist-packages/bcbio/structural/battenberg.py
usr/lib/python3/dist-packages/bcbio/structural/cn_mops.py
usr/lib/python3/dist-packages/bcbio/structural/cnvkit.py
usr/lib/python3/dist-packages/bcbio/structural/convert.py
usr/lib/python3/dist-packages/bcbio/structural/delly.py
usr/lib/python3/dist-packages/bcbio/structural/gatkcnv.py
usr/lib/python3/dist-packages/bcbio/structural/gridss.py
usr/lib/python3/dist-packages/bcbio/structural/hydra.py
usr/lib/python3/dist-packages/bcbio/structural/lumpy.py
usr/lib/python3/dist-packages/bcbio/structural/manta.py
usr/lib/python3/dist-packages/bcbio/structural/metasv.py
usr/lib/python3/dist-packages/bcbio/structural/pindel.py
usr/lib/python3/dist-packages/bcbio/structural/plot.py
usr/lib/python3/dist-packages/bcbio/structural/prioritize.py
usr/lib/python3/dist-packages/bcbio/structural/purecn.py
usr/lib/python3/dist-packages/bcbio/structural/purple.py
usr/lib/python3/dist-packages/bcbio/structural/regions.py
usr/lib/python3/dist-packages/bcbio/structural/scramble.py
usr/lib/python3/dist-packages/bcbio/structural/seq2c.py
usr/lib/python3/dist-packages/bcbio/structural/shared.py
usr/lib/python3/dist-packages/bcbio/structural/titancna.py
usr/lib/python3/dist-packages/bcbio/structural/validate.py
usr/lib/python3/dist-packages/bcbio/structural/wham.py
usr/lib/python3/dist-packages/bcbio/upload
usr/lib/python3/dist-packages/bcbio/upload/__init__.py
usr/lib/python3/dist-packages/bcbio/upload/filesystem.py
usr/lib/python3/dist-packages/bcbio/upload/galaxy.py
usr/lib/python3/dist-packages/bcbio/upload/irods.py
usr/lib/python3/dist-packages/bcbio/upload/s3.py
usr/lib/python3/dist-packages/bcbio/upload/shared.py
usr/lib/python3/dist-packages/bcbio/utils.py
usr/lib/python3/dist-packages/bcbio/variation
usr/lib/python3/dist-packages/bcbio/variation/__init__.py
usr/lib/python3/dist-packages/bcbio/variation/annotation.py
usr/lib/python3/dist-packages/bcbio/variation/bamprep.py
usr/lib/python3/dist-packages/bcbio/variation/bedutils.py
usr/lib/python3/dist-packages/bcbio/variation/cortex.py
usr/lib/python3/dist-packages/bcbio/variation/coverage.py
usr/lib/python3/dist-packages/bcbio/variation/damage.py
usr/lib/python3/dist-packages/bcbio/variation/deepvariant.py
usr/lib/python3/dist-packages/bcbio/variation/effects.py
usr/lib/python3/dist-packages/bcbio/variation/ensemble.py
usr/lib/python3/dist-packages/bcbio/variation/freebayes.py
usr/lib/python3/dist-packages/bcbio/variation/gatk.py
usr/lib/python3/dist-packages/bcbio/variation/gatkfilter.py
usr/lib/python3/dist-packages/bcbio/variation/gatkjoint.py
usr/lib/python3/dist-packages/bcbio/variation/genotype.py
usr/lib/python3/dist-packages/bcbio/variation/germline.py
usr/lib/python3/dist-packages/bcbio/variation/joint.py
usr/lib/python3/dist-packages/bcbio/variation/multi.py
usr/lib/python3/dist-packages/bcbio/variation/mutect.py
usr/lib/python3/dist-packages/bcbio/variation/mutect2.py
usr/lib/python3/dist-packages/bcbio/variation/naming.py
usr/lib/python3/dist-packages/bcbio/variation/normalize.py
usr/lib/python3/dist-packages/bcbio/variation/octopus.py
usr/lib/python3/dist-packages/bcbio/variation/peddy.py
usr/lib/python3/dist-packages/bcbio/variation/pisces.py
usr/lib/python3/dist-packages/bcbio/variation/platypus.py
usr/lib/python3/dist-packages/bcbio/variation/ploidy.py
usr/lib/python3/dist-packages/bcbio/variation/population.py
usr/lib/python3/dist-packages/bcbio/variation/prioritize.py
usr/lib/python3/dist-packages/bcbio/variation/qsnp.py
usr/lib/python3/dist-packages/bcbio/variation/realign.py
usr/lib/python3/dist-packages/bcbio/variation/recalibrate.py
usr/lib/python3/dist-packages/bcbio/variation/samtools.py
usr/lib/python3/dist-packages/bcbio/variation/scalpel.py
usr/lib/python3/dist-packages/bcbio/variation/sentieon.py
usr/lib/python3/dist-packages/bcbio/variation/smcounter2.py
usr/lib/python3/dist-packages/bcbio/variation/split.py
usr/lib/python3/dist-packages/bcbio/variation/strelka2.py
usr/lib/python3/dist-packages/bcbio/variation/validate.py
usr/lib/python3/dist-packages/bcbio/variation/validateplot.py
usr/lib/python3/dist-packages/bcbio/variation/vardict.py
usr/lib/python3/dist-packages/bcbio/variation/varscan.py
usr/lib/python3/dist-packages/bcbio/variation/vcfanno.py
usr/lib/python3/dist-packages/bcbio/variation/vcfutils.py
usr/lib/python3/dist-packages/bcbio/variation/vfilter.py
usr/lib/python3/dist-packages/bcbio/wgbsseq
usr/lib/python3/dist-packages/bcbio/wgbsseq/__init__.py
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