.ci_deploy.sh
.ci_deps.sh
.ci_install.sh
.ci_postdeploy_install.sh
.ci_test.sh
.gitignore
.readthedocs.yaml
.travis.yml
.travis_pypirc
LICENSE
MANIFEST.in
README.md
RELEASE_CHECKOUT
VERSION
buildwheels.sh
deploywheels.sh
installwheels.sh
prepare_docker.sh
requirements.txt
setup.py
test.sh
testwheels.sh
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/ci.yml
.github/workflows/deploy.yml
HTSeq/StepVector.py
HTSeq/StretchVector.py
HTSeq/_HTSeq_internal.py
HTSeq/__init__.py
HTSeq/_version.py
HTSeq/features.py
HTSeq/utils.py
HTSeq.egg-info/PKG-INFO
HTSeq.egg-info/SOURCES.txt
HTSeq.egg-info/dependency_links.txt
HTSeq.egg-info/requires.txt
HTSeq.egg-info/top_level.txt
HTSeq/scripts/__init__.py
HTSeq/scripts/count.py
HTSeq/scripts/count_with_barcodes.py
HTSeq/scripts/qa.py
HTSeq/scripts/utils.py
HTSeq/scripts/count_features/__init__.py
HTSeq/scripts/count_features/count_features_per_file.py
HTSeq/scripts/count_features/reads_io_processor.py
HTSeq/scripts/count_features/reads_stats.py
doc/GenomicArrayOfSets.svg
doc/Makefile
doc/add_counter.py
doc/alignments.rst
doc/conf.py
doc/contrib.rst
doc/count_modes.odg
doc/counting.rst
doc/features.rst
doc/genomic.rst
doc/history.rst
doc/htseqcount.rst
doc/htseqcount_with_barcodes.rst
doc/index.rst
doc/install.rst
doc/misc.rst
doc/otherparsers.rst
doc/overview.rst
doc/qa.rst
doc/refoverview.rst
doc/requirements.txt
doc/sequences.rst
doc/tour.rst
doc/tutorials.rst
doc/code_examples/tss1.py
doc/code_examples/tss2.py
doc/code_examples/tss3.py
doc/images/cigar.png
doc/images/count_modes.png
doc/images/highc_fig1.png
doc/images/highc_fig2.png
doc/images/highc_fig3.png
doc/images/highc_fig4.png
doc/images/qa_example.png
doc/images/qualplot.png
doc/images/tss_fig1.png
doc/images/tss_fig2.png
doc/images/tss_fig3.png
doc/images/tss_fig4.png
doc/tutorials/bam_reader.rst
doc/tutorials/exon_example.rst
doc/tutorials/fastx_reader.rst
doc/tutorials/highc.rst
doc/tutorials/step_vs_stretch_vector.rst
doc/tutorials/tss.rst
doc/tutorials/tutorial_exon_level.rst
example_data/Homo_sapiens.GRCh37.56_chrom1.gtf
example_data/SRR001432_head.bam
example_data/SRR001432_head_sorted.bam
example_data/SRR001432_head_sorted.bam.bai
example_data/Saccharomyces_cerevisiae.SGD1.01.56.gtf.gz
example_data/bamfile_no_qualities.bam
example_data/bamfile_no_qualities.gtf
example_data/bamfile_no_qualities.h5ad
example_data/bamfile_no_qualities.loom
example_data/bamfile_no_qualities.mtx
example_data/bamfile_no_qualities.sam
example_data/bamfile_no_qualities.tsv
example_data/example_bedgraph.bedgraph
example_data/example_bigwig.bw
example_data/fastaEx.fa
example_data/fastaExLong.fa
example_data/fastqEx.fastq
example_data/fastqExgzip.fastq.gz
example_data/feature_list.txt
example_data/htseq-count-multimap-test_byName.bam
example_data/htseq-count-multimap-test_byPos.bam
example_data/inconsistent_mate.bam
example_data/short_test_ccs.bam
example_data/yeast_RNASeq_excerpt.sam
example_data/yeast_RNASeq_excerpt_sequence.txt
example_data/yeast_RNASeq_excerpt_some_empty_seqs.sam
example_data/yeast_RNASeq_excerpt_some_empty_seqs.tsv
example_data/yeast_RNASeq_excerpt_withNH.sam
example_data/yeast_RNASeq_excerpt_withNH_counts.tsv
example_data/yeast_RNASeq_excerpt_withNH_counts_YPR036W-A.tsv
example_data/yeast_RNASeq_excerpt_withNH_counts_additional_attributes.tsv
example_data/yeast_RNASeq_excerpt_withNH_counts_additional_attributes_chromosome_info.tsv
example_data/yeast_RNASeq_excerpt_withNH_counts_exon_level_and_additional_attributes.tsv
example_data/yeast_RNASeq_excerpt_withNH_counts_ignore_secondary.tsv
example_data/yeast_RNASeq_excerpt_withNH_counts_nonunique.tsv
example_data/yeast_RNASeq_excerpt_withNH_counts_nonunique_fraction.tsv
example_data/yeast_RNASeq_excerpt_withNH_counts_twocolumns.tsv
example_data/yeast_RNASeq_excerpt_withbarcodes.h5ad
example_data/yeast_RNASeq_excerpt_withbarcodes.loom
example_data/yeast_RNASeq_excerpt_withbarcodes.sam
example_data/yeast_RNASeq_excerpt_withbarcodes.tsv
example_data/yeast_RNASeq_excerpt_withbarcodes_chromosome_info.tsv
example_data/yeast_RNASeq_excerpt_withbarcodes_correctUMI_1.tsv
scripts/htseq-count
scripts/htseq-count-barcodes
scripts/htseq-qa
src/AutoPyObjPtr.i
src/StepVector.i
src/StepVector.py
src/StepVector_wrap.cxx
src/_HTSeq.c
src/step_vector.h
src/HTSeq/_HTSeq.pxd
src/HTSeq/_HTSeq.pyx
src/HTSeq/__init__.py
test/conftest.py
test/test_general.py
test/test_genomic.py
test/test_htseq-count.py
test/test_parsers.py
test/test_stretch_vector.py
test/tss_test.py