├── .gitignore ├── .travis.yml ├── .travis_before_install.sh ├── .travis_deploy.sh ├── .travis_install.sh ├── .travis_pypirc ├── .travis_test.sh ├── LICENSE ├── MANIFEST.in ├── README.rst ├── RELEASE_CHECKOUT ├── VERSION ├── deploywheels.sh ├── example_data ├── Homo_sapiens.GRCh37.56_chrom1.gtf ├── SRR001432_head.bam ├── SRR001432_head_sorted.bam ├── SRR001432_head_sorted.bam.bai ├── Saccharomyces_cerevisiae.SGD1.01.56.gtf.gz ├── bamfile_no_qualities.bam ├── bamfile_no_qualities.gtf ├── bamfile_no_qualities.sam ├── bamfile_no_qualities.tsv ├── fastaEx.fa ├── fastaExLong.fa ├── fastqEx.fastq ├── fastqExgzip.fastq.gz ├── feature_list.txt ├── htseq-count-multimap-test_byName.bam ├── htseq-count-multimap-test_byPos.bam ├── inconsistent_mate.bam ├── short_test_ccs.bam ├── yeast_RNASeq_excerpt.sam ├── yeast_RNASeq_excerpt_sequence.txt ├── yeast_RNASeq_excerpt_withNH.sam ├── yeast_RNASeq_excerpt_withNH_counts.tsv ├── yeast_RNASeq_excerpt_withNH_counts_YPR036W-A.tsv ├── yeast_RNASeq_excerpt_withNH_counts_additional_attributes.tsv ├── yeast_RNASeq_excerpt_withNH_counts_ignore_secondary.tsv ├── yeast_RNASeq_excerpt_withNH_counts_nonunique.tsv ├── yeast_RNASeq_excerpt_withNH_counts_nonunique_fraction.tsv ├── yeast_RNASeq_excerpt_withNH_counts_twocolumns.tsv ├── yeast_RNASeq_excerpt_withbarcodes.sam └── yeast_RNASeq_excerpt_withbarcodes.tsv ├── python2 ├── HTSeq │ ├── _HTSeq_internal.py │ ├── __init__.py │ ├── _version.py │ └── scripts │ │ ├── __init__.py │ │ ├── count.py │ │ ├── count_with_barcodes.py │ │ └── qa.py ├── doc │ ├── GenomicArrayOfSets.svg │ ├── Makefile │ ├── add_counter.py │ ├── alignments.rst │ ├── cigar.png │ ├── conf.py.bak │ ├── contrib.rst │ ├── count.rst │ ├── count_modes.odg │ ├── count_modes.png │ ├── counting.rst │ ├── features.rst │ ├── genomic.rst │ ├── history.rst │ ├── index.rst │ ├── install.rst │ ├── misc.rst │ ├── otherparsers.rst │ ├── overview.rst │ ├── qa.rst │ ├── qa_example.png │ ├── qualplot.png │ ├── refoverview.rst │ ├── sequences.rst │ ├── tour.rst │ ├── tss.rst │ ├── tss1.py │ ├── tss2.py │ ├── tss3.py │ ├── tss_fig1.png │ ├── tss_fig2.png │ ├── tss_fig3.png │ └── tss_fig4.png ├── scripts │ ├── flake8.sh │ ├── htseq-count │ ├── htseq-count-barcodes │ └── htseq-qa ├── src │ ├── AutoPyObjPtr.i │ ├── HTSeq │ │ ├── _HTSeq.pxd │ │ ├── _HTSeq.pyx │ │ └── __init__.py │ ├── StepVector.i │ ├── StepVector.py │ ├── StepVector_wrap.cxx │ ├── _HTSeq.c │ └── step_vector.h ├── test │ ├── test.py │ ├── test_general.py │ ├── test_htseq-count.py │ └── tss_test.py └── tests │ ├── __init__.py │ ├── __init__.pyc │ └── test_loading.py ├── python3 ├── HTSeq │ ├── StepVector.py │ ├── _HTSeq_internal.py │ ├── __init__.py │ ├── _version.py │ └── scripts │ │ ├── __init__.py │ │ ├── count.py │ │ ├── count_with_barcodes.py │ │ └── qa.py ├── doc │ ├── GenomicArrayOfSets.svg │ ├── Makefile │ ├── add_counter.py │ ├── alignments.rst │ ├── cigar.png │ ├── conf.py │ ├── contrib.rst │ ├── count.rst │ ├── count_modes.odg │ ├── count_modes.png │ ├── counting.rst │ ├── features.rst │ ├── genomic.rst │ ├── history.rst │ ├── index.rst │ ├── install.rst │ ├── misc.rst │ ├── otherparsers.rst │ ├── overview.rst │ ├── qa.rst │ ├── qa_example.png │ ├── qualplot.png │ ├── refoverview.rst │ ├── sequences.rst │ ├── tour.rst │ ├── tss.rst │ ├── tss1.py │ ├── tss2.py │ ├── tss3.py │ ├── tss_fig1.png │ ├── tss_fig2.png │ ├── tss_fig3.png │ └── tss_fig4.png ├── scripts │ ├── htseq-count │ ├── htseq-count-barcodes │ └── htseq-qa ├── src │ ├── AutoPyObjPtr.i │ ├── HTSeq │ │ ├── _HTSeq.pxd │ │ ├── _HTSeq.pyx │ │ └── __init__.py │ ├── StepVector.i │ ├── StepVector.py │ ├── StepVector_wrap.cxx │ ├── _HTSeq.c │ └── step_vector.h └── test │ ├── test.py │ ├── test_general.py │ ├── test_htseq-count.py │ └── tss_test.py ├── requirements.txt ├── setup.py ├── testwheels.sh └── todo.txt /.gitignore: -------------------------------------------------------------------------------- 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