.codecov.yml
.gitignore
.readthedocs.yaml
LICENSE
README.md
pyproject.toml
setup.py
.github/workflows/publish.yml
.github/workflows/python-package.yml
docs/Makefile
docs/make.bat
docs/source/api.rst
docs/source/conf.py
docs/source/index.rst
docs/source/installation.rst
docs/source/release_notes.rst
docs/source/usage.rst
docs/source/_static/custom.css
docs/source/_static/img/logo.svg
docs/source/_static/img/tidesurf.svg
docs/source/_templates/autosummary/class.rst
docs/source/_templates/autosummary/module.rst
docs/source/api/tidesurf.counter.UMICounter.MIN_INTRON_OVERLAP.rst
docs/source/api/tidesurf.counter.UMICounter.count.rst
docs/source/api/tidesurf.counter.UMICounter.multi_mapped_reads.rst
docs/source/api/tidesurf.counter.UMICounter.orientation.rst
docs/source/api/tidesurf.counter.UMICounter.rst
docs/source/api/tidesurf.counter.UMICounter.transcript_index.rst
docs/source/api/tidesurf.counter.rst
docs/source/api/tidesurf.enums.ReadType.AMBIGUOUS_READ.rst
docs/source/api/tidesurf.enums.ReadType.EXON.rst
docs/source/api/tidesurf.enums.ReadType.EXON_EXON.rst
docs/source/api/tidesurf.enums.ReadType.INTRON.rst
docs/source/api/tidesurf.enums.ReadType.rst
docs/source/api/tidesurf.enums.SpliceType.AMBIGUOUS.rst
docs/source/api/tidesurf.enums.SpliceType.SPLICED.rst
docs/source/api/tidesurf.enums.SpliceType.UNSPLICED.rst
docs/source/api/tidesurf.enums.SpliceType.rst
docs/source/api/tidesurf.enums.Strand.MINUS.rst
docs/source/api/tidesurf.enums.Strand.PLUS.rst
docs/source/api/tidesurf.enums.Strand.rst
docs/source/api/tidesurf.enums.antisense.rst
docs/source/api/tidesurf.enums.rst
docs/source/api/tidesurf.transcript.Exon.chromosome.rst
docs/source/api/tidesurf.transcript.Exon.end.rst
docs/source/api/tidesurf.transcript.Exon.exon_id.rst
docs/source/api/tidesurf.transcript.Exon.exon_number.rst
docs/source/api/tidesurf.transcript.Exon.gene_id.rst
docs/source/api/tidesurf.transcript.Exon.gene_name.rst
docs/source/api/tidesurf.transcript.Exon.overlaps.rst
docs/source/api/tidesurf.transcript.Exon.rst
docs/source/api/tidesurf.transcript.Exon.start.rst
docs/source/api/tidesurf.transcript.Exon.strand.rst
docs/source/api/tidesurf.transcript.Exon.transcript_id.rst
docs/source/api/tidesurf.transcript.Exon.transcript_name.rst
docs/source/api/tidesurf.transcript.GTFLine.attributes.rst
docs/source/api/tidesurf.transcript.GTFLine.chromosome.rst
docs/source/api/tidesurf.transcript.GTFLine.end.rst
docs/source/api/tidesurf.transcript.GTFLine.feature.rst
docs/source/api/tidesurf.transcript.GTFLine.frame.rst
docs/source/api/tidesurf.transcript.GTFLine.rst
docs/source/api/tidesurf.transcript.GTFLine.score.rst
docs/source/api/tidesurf.transcript.GTFLine.source.rst
docs/source/api/tidesurf.transcript.GTFLine.start.rst
docs/source/api/tidesurf.transcript.GTFLine.strand.rst
docs/source/api/tidesurf.transcript.GenomicFeature.chromosome.rst
docs/source/api/tidesurf.transcript.GenomicFeature.end.rst
docs/source/api/tidesurf.transcript.GenomicFeature.gene_id.rst
docs/source/api/tidesurf.transcript.GenomicFeature.gene_name.rst
docs/source/api/tidesurf.transcript.GenomicFeature.overlaps.rst
docs/source/api/tidesurf.transcript.GenomicFeature.rst
docs/source/api/tidesurf.transcript.GenomicFeature.start.rst
docs/source/api/tidesurf.transcript.GenomicFeature.strand.rst
docs/source/api/tidesurf.transcript.GenomicFeature.transcript_id.rst
docs/source/api/tidesurf.transcript.GenomicFeature.transcript_name.rst
docs/source/api/tidesurf.transcript.Intron.chromosome.rst
docs/source/api/tidesurf.transcript.Intron.end.rst
docs/source/api/tidesurf.transcript.Intron.gene_id.rst
docs/source/api/tidesurf.transcript.Intron.gene_name.rst
docs/source/api/tidesurf.transcript.Intron.overlaps.rst
docs/source/api/tidesurf.transcript.Intron.rst
docs/source/api/tidesurf.transcript.Intron.start.rst
docs/source/api/tidesurf.transcript.Intron.strand.rst
docs/source/api/tidesurf.transcript.Intron.transcript_id.rst
docs/source/api/tidesurf.transcript.Intron.transcript_name.rst
docs/source/api/tidesurf.transcript.Transcript.add_exon.rst
docs/source/api/tidesurf.transcript.Transcript.chromosome.rst
docs/source/api/tidesurf.transcript.Transcript.end.rst
docs/source/api/tidesurf.transcript.Transcript.gene_id.rst
docs/source/api/tidesurf.transcript.Transcript.gene_name.rst
docs/source/api/tidesurf.transcript.Transcript.overlaps.rst
docs/source/api/tidesurf.transcript.Transcript.regions.rst
docs/source/api/tidesurf.transcript.Transcript.rst
docs/source/api/tidesurf.transcript.Transcript.sort_regions.rst
docs/source/api/tidesurf.transcript.Transcript.start.rst
docs/source/api/tidesurf.transcript.Transcript.strand.rst
docs/source/api/tidesurf.transcript.Transcript.transcript_id.rst
docs/source/api/tidesurf.transcript.Transcript.transcript_name.rst
docs/source/api/tidesurf.transcript.TranscriptIndex.get_overlapping_transcripts.rst
docs/source/api/tidesurf.transcript.TranscriptIndex.get_transcript.rst
docs/source/api/tidesurf.transcript.TranscriptIndex.read_gtf.rst
docs/source/api/tidesurf.transcript.TranscriptIndex.rst
docs/source/api/tidesurf.transcript.TranscriptIndex.transcripts.rst
docs/source/api/tidesurf.transcript.TranscriptIndex.transcripts_by_region.rst
docs/source/api/tidesurf.transcript.rst
src/tidesurf/__init__.py
src/tidesurf/counter.c
src/tidesurf/counter.pxd
src/tidesurf/counter.py
src/tidesurf/enums.c
src/tidesurf/enums.pxd
src/tidesurf/enums.pyx
src/tidesurf/main.c
src/tidesurf/main.py
src/tidesurf/transcript.c
src/tidesurf/transcript.pxd
src/tidesurf/transcript.py
src/tidesurf.egg-info/PKG-INFO
src/tidesurf.egg-info/SOURCES.txt
src/tidesurf.egg-info/dependency_links.txt
src/tidesurf.egg-info/entry_points.txt
src/tidesurf.egg-info/requires.txt
src/tidesurf.egg-info/scm_file_list.json
src/tidesurf.egg-info/scm_version.json
src/tidesurf.egg-info/top_level.txt
tests/conftest.py
tests/test_counter.py
tests/test_main.py
tests/test_read.py
tests/test_transcript.py
tests/test_data/adata_cr_out.h5ad
tests/test_data/adata_cr_out_3p.h5ad
tests/test_data/genes.gtf
tests/test_data/genes.gtf.gz
tests/test_data/whitelist.tsv
tests/test_data/whitelist_3p.tsv
tests/test_data/test_dir_count/outs/possorted_genome_bam.bam
tests/test_data/test_dir_count/outs/possorted_genome_bam.bam.bai
tests/test_data/test_dir_count/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
tests/test_data/test_dir_count_3p/outs/possorted_genome_bam.bam
tests/test_data/test_dir_count_3p/outs/possorted_genome_bam.bam.bai
tests/test_data/test_dir_count_3p/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
tests/test_data/test_dir_multi/outs/per_sample_outs/sample_1/count/sample_alignments.bam
tests/test_data/test_dir_multi/outs/per_sample_outs/sample_1/count/sample_alignments.bam.bai
tests/test_data/test_dir_multi/outs/per_sample_outs/sample_1/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz
tests/test_data/tidesurf_out/tidesurf_filter_cr.h5ad
tests/test_data/tidesurf_out/tidesurf_filter_cr_3p.h5ad
tests/test_data/tidesurf_out/tidesurf_filter_cr_mm.h5ad
tests/test_data/tidesurf_out/tidesurf_filter_cr_mm_3p.h5ad
tests/test_data/tidesurf_out/tidesurf_filter_umi.h5ad
tests/test_data/tidesurf_out/tidesurf_filter_umi_3p.h5ad
tests/test_data/tidesurf_out/tidesurf_filter_umi_mm.h5ad
tests/test_data/tidesurf_out/tidesurf_filter_umi_mm_3p.h5ad
tests/test_data/tidesurf_out/tidesurf_no_filter.h5ad
tests/test_data/tidesurf_out/tidesurf_no_filter_3p.h5ad
tests/test_data/tidesurf_out/tidesurf_no_filter_mm.h5ad
tests/test_data/tidesurf_out/tidesurf_no_filter_mm_3p.h5ad