.gitignore

notebooks/Scratch.ipynb
notebooks/VCF.ipynb

settings.local.json

*.py[cod]
__pycache__
*~
*.swn
*.swo
*.swp
*.tiles

# setup and build artifacts
*.egg-info/
.eggs/
dist/
build/
MANIFEST
docs/_templates
docs/_static
docs/_build
clodius/*.c
*.so

# test and coverage artifacts
.cache
.pytest_cache
.coverage
coverage.xml
htmlcov/

# OS-generated files
.DS_Store
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db

.ipynb_checkpoints/
.idea/
old
tmp
checkpoint
data/*
!data/Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool
!data/hic-resolutions.cool
!data/sample_htime.json
!data/gene_annotations.short.db
!data/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig
!data/points_density.h5
!data/corrected.geneListwithStrand.bed.multires
!data/labels.h5
!data/SRR1770413.sorted.short.bam
!data/SRR1770413.sorted.short.bam.bai
!data/SRR1770413.different_index_filename.bai
!data/SRR1770413.mismatched_bai.bam
!data/geneAnnotationsExonUnions.1000.bed.v3.beddb
!data/masterlist_DHSs_733samples_WM20180608_all_mean_signal_colorsMax.bed.bb
!data/GCA_000350705.1_Esch_coli_KTE11_V1_genomic.short.fna.fai
!data/GCA_002918705.1_ASM291870v1_genomic.gff.gz
!data/genomic.10k.gff
!data/genomic.10k.gff.gz
!data/chm13v1.chrom.sizes
!data/hg38.chrom.sizes
!data/test.1.vcf.gz
!data/no_item_rgb.bed
!data/regions.valid.bed.1.gz
!data/regions.valid.bed
!data/regions.valid.bed.gz
!data/regions.valid.bed.gz.tbi
!data/regions.spaces.bed
!data/genomic.10k.gff.gz.tbi
!data/GCA_000350705.1_Esch_coli_KTE11_V1_genomic.short.fna
output/
COMMANDS
npm-debug.log
output.tar
profile.dat
profile.png
aws_keys.py
.envrc

#test related
a.out
test/sample_data/3_header_100_testfile.bed.multires.mv5
test/sample_data/states_format_input_testfile.bed.multires.mv5