.gitignore

#Randome files
.DS_Store


# Editor files
*.swp
.mypy_cache/
mypy.ini
.idea

# Docs
*/_build/*

# Python files
*~
*.pyc
.pytest_cache/

# Extras
nohup.out
*\#*
twistd.pid

# Testing
test/common/*.vcf~
test/common/dump/
.coverage
coverage.xml
*test_run.vcf*
xx-*
test-*
c57*
.nox/

# Build files
*egg-info*
build/
dist/
env.yaml
trtools/version.py

# Files generated by examples
NA12878_eh_reader.vcf.gz
NA12878_eh_reader.vcf.gz.tbi
NA12891_eh_reader.vcf.gz
NA12891_eh_reader.vcf.gz.tbi
NA12892_eh_reader.vcf.gz
NA12892_eh_reader.vcf.gz.tbi
advntr_vs_advntr-bubble-periodALL.pdf
advntr_vs_advntr-callcompare.tab
advntr_vs_advntr-locuscompare.pdf
advntr_vs_advntr-locuscompare.tab
advntr_vs_advntr-overall.tab
advntr_vs_advntr-samplecompare.pdf
advntr_vs_advntr-samplecompare.tab
hipstr_vs_eh-bubble-periodALL.pdf
hipstr_vs_eh-callcompare.tab
hipstr_vs_eh-locuscompare.pdf
hipstr_vs_eh-locuscompare.tab
hipstr_vs_eh-overall.tab
hipstr_vs_eh-samplecompare.pdf
hipstr_vs_eh-samplecompare.tab
hipstr_vs_gangstr-bubble-periodALL.pdf
hipstr_vs_gangstr-callcompare.tab
hipstr_vs_gangstr-locuscompare.pdf
hipstr_vs_gangstr-locuscompare.tab
hipstr_vs_gangstr-overall.tab
hipstr_vs_gangstr-samplecompare.pdf
hipstr_vs_gangstr-samplecompare.tab
popstr_vs_popstr-bubble-periodALL.pdf
popstr_vs_popstr-callcompare.tab
popstr_vs_popstr-locuscompare.pdf
popstr_vs_popstr-locuscompare.tab
popstr_vs_popstr-overall.tab
popstr_vs_popstr-samplecompare.pdf
popstr_vs_popstr-samplecompare.tab
sample1_advntr_reheader.vcf.gz
sample1_advntr_reheader.vcf.gz.tbi
sample2_advntr_reheader.vcf.gz
sample2_advntr_reheader.vcf.gz.tbi
test_dumpstr_advntr.loclog.tab
test_dumpstr_advntr.samplog.tab
test_dumpstr_advntr.vcf
test_dumpstr_eh.loclog.tab
test_dumpstr_eh.samplog.tab
test_dumpstr_eh.vcf
test_dumpstr_gangstr.loclog.tab
test_dumpstr_gangstr.samplog.tab
test_dumpstr_gangstr.vcf
test_dumpstr_hipstr.loclog.tab
test_dumpstr_hipstr.samplog.tab
test_dumpstr_hipstr.vcf
test_dumpstr_popstr.loclog.tab
test_dumpstr_popstr.samplog.tab
test_dumpstr_popstr.vcf
test_merge_advntr.vcf
test_merge_eh.vcf
test_merge_gangstr.vcf
test_merge_hipstr.vcf
test_merge_popstr.vcf
test_qc_advntr-chrom-callnum.pdf
test_qc_advntr-diffref-bias.pdf
test_qc_advntr-diffref-histogram.pdf
test_qc_advntr-quality.pdf
test_qc_advntr-sample-callnum.pdf
test_qc_eh-chrom-callnum.pdf
test_qc_eh-diffref-bias.pdf
test_qc_eh-diffref-histogram.pdf
test_qc_eh-sample-callnum.pdf
test_qc_gangstr-chrom-callnum.pdf
test_qc_gangstr-diffref-bias.pdf
test_qc_gangstr-diffref-histogram.pdf
test_qc_gangstr-quality-per-locus.pdf
test_qc_gangstr-sample-callnum.pdf
test_qc_hipstr-chrom-callnum.pdf
test_qc_hipstr-diffref-bias.pdf
test_qc_hipstr-diffref-histogram.pdf
test_qc_hipstr-quality.pdf
test_qc_hipstr-sample-callnum.pdf
test_qc_popstr-chrom-callnum.pdf
test_qc_popstr-diffref-bias.pdf
test_qc_popstr-diffref-histogram.pdf
test_qc_popstr-quality.pdf
test_qc_popstr-sample-callnum.pdf
NA12878_advntr_reheader.vcf.gz
NA12878_advntr_reheader.vcf.gz.tbi
NA12878_eh_reheader.vcf.gz
NA12878_eh_reheader.vcf.gz.tbi
NA12891_advntr_reheader.vcf.gz
NA12891_advntr_reheader.vcf.gz.tbi
NA12891_eh_reheader.vcf.gz
NA12891_eh_reheader.vcf.gz.tbi
NA12892_advntr_reheader.vcf.gz
NA12892_advntr_reheader.vcf.gz.tbi
NA12892_eh_reheader.vcf.gz
NA12892_eh_reheader.vcf.gz.tbi
stats_eh.tab
stats_gangstr.tab
stats_popstr.tab
test.tab
test_association_results.tsv
test_association_results.tsv.temp
association_results.tsv
association_results.tsv.temp