├── .dockerignore ├── .gitignore ├── .readthedocs.yaml ├── CHANGES.rst ├── Dockerfile ├── INSTALL.rst ├── LICENSE ├── Makefile ├── README.rst ├── docs ├── Makefile ├── bin │ └── get_class_substitutions ├── requirements.txt └── source │ ├── CHANGES.rst │ ├── FAQ.rst │ ├── _static │ ├── css │ │ └── custom.css │ └── images │ │ ├── SRR609197_riboprofile_p_offsets.png │ │ ├── count_vectors_transcript_plot.png │ │ ├── demo_gene_expr_teff_vs_tx.png │ │ ├── demo_gene_expr_tl_vs_tx.png │ │ ├── demo_metagene_cds_start.png │ │ ├── kdeplot.png │ │ ├── kdeplot_log.png │ │ ├── maplot.png │ │ ├── mapping_rule_demo.png │ │ ├── metagene_aligned_vectors.png │ │ ├── metagene_average_profile.png │ │ ├── metagene_big_spike_demo.png │ │ ├── metagene_maximal_spanning_window.png │ │ ├── metagene_normalized_vectors.png │ │ ├── metagene_unnormalized_vectors.png │ │ ├── p_site_applied.png │ │ ├── p_site_map_cartoon.png │ │ ├── p_site_offset_by_length.png │ │ ├── profile_heatmap.png │ │ ├── scatterhist.png │ │ ├── stackedbar.png │ │ └── triangleplot.png │ ├── _templates │ └── layout.html │ ├── citing.rst │ ├── class_substitutions.txt │ ├── concepts │ ├── coordinates.rst │ ├── data.rst │ ├── gff3.rst │ ├── mapping_rules.rst │ └── multimappers.rst │ ├── conf.py │ ├── contact.rst │ ├── devinfo │ ├── contributing.rst │ └── entrypoints.rst │ ├── examples.rst │ ├── examples │ ├── a1_genome_setup.rst │ ├── a2_sample_processing.rst │ ├── count_vector.rst │ ├── gene_expression.rst │ ├── make_annotation.rst │ ├── metagene.rst │ ├── p_site.rst │ ├── phasing.rst │ ├── sequence.rst │ ├── using_masks.rst │ └── z_plotting.rst │ ├── generated │ ├── modules.rst │ ├── plastid.bin.counts_in_region.rst │ ├── plastid.bin.crossmap.rst │ ├── plastid.bin.cs.rst │ ├── plastid.bin.findjuncs.rst │ ├── plastid.bin.get_count_vectors.rst │ ├── plastid.bin.gff_parent_types.rst │ ├── plastid.bin.make_wiggle.rst │ ├── plastid.bin.metagene.rst │ ├── plastid.bin.phase_by_size.rst │ ├── plastid.bin.psite.rst │ ├── plastid.bin.reformat_transcripts.rst │ ├── plastid.bin.rst │ ├── plastid.bin.slidejuncs.rst │ ├── plastid.bin.test_table_equality.rst │ ├── plastid.genomics.c_common.rst │ ├── plastid.genomics.genome_array.rst │ ├── plastid.genomics.genome_hash.rst │ ├── plastid.genomics.map_factories.rst │ ├── plastid.genomics.roitools.rst │ ├── plastid.genomics.rst │ ├── plastid.genomics.seqtools.rst │ ├── plastid.genomics.splicing.rst │ ├── plastid.plotting.colors.rst │ ├── plastid.plotting.plots.rst │ ├── plastid.plotting.plotutils.rst │ ├── plastid.plotting.rst │ ├── plastid.readers.autosql.rst │ ├── plastid.readers.bbifile.rst │ ├── plastid.readers.bed.rst │ ├── plastid.readers.bigbed.rst │ ├── plastid.readers.bigwig.rst │ ├── plastid.readers.bowtie.rst │ ├── plastid.readers.common.rst │ ├── plastid.readers.gff.rst │ ├── plastid.readers.gff_tokens.rst │ ├── plastid.readers.psl.rst │ ├── plastid.readers.rst │ ├── plastid.readers.wiggle.rst │ ├── plastid.rst │ ├── plastid.util.io.binary.rst │ ├── plastid.util.io.filters.rst │ ├── plastid.util.io.openers.rst │ ├── plastid.util.io.rst │ ├── plastid.util.rst │ ├── plastid.util.scriptlib.argparsers.rst │ ├── plastid.util.scriptlib.help_formatters.rst │ ├── plastid.util.scriptlib.rst │ ├── plastid.util.scriptlib.template.rst │ ├── plastid.util.services.decorators.rst │ ├── plastid.util.services.exceptions.rst │ ├── plastid.util.services.lists.rst │ ├── plastid.util.services.mini2to3.rst │ ├── plastid.util.services.misc.rst │ ├── plastid.util.services.rst │ ├── plastid.util.services.sets.rst │ └── plastid.util.unique_fifo.rst │ ├── genometools_classnames.txt │ ├── glossary.rst │ ├── index.rst │ ├── installation.rst │ ├── license.rst │ ├── links.txt │ ├── quickstart.rst │ ├── related.rst │ ├── script_substitutions.txt │ ├── scriptlist.rst │ ├── test_dataset.rst │ ├── tour.rst │ ├── zreferences.bib │ └── zreferences.rst ├── kent ├── LICENSE └── src │ ├── README │ ├── htslib │ ├── INSTALL │ ├── LICENSE │ ├── Makefile │ ├── NEWS │ ├── README │ ├── bgzf.c │ ├── bgzip.c │ ├── config.h │ ├── config.h.in │ ├── config.log │ ├── config.mk │ ├── config.mk.in │ ├── config.status │ ├── configure │ ├── configure.ac │ ├── cram │ │ ├── cram.h │ │ ├── cram_codecs.c │ │ ├── cram_codecs.h │ │ ├── cram_decode.c │ │ ├── cram_decode.h │ │ ├── cram_encode.c │ │ ├── cram_encode.h │ │ ├── cram_external.c │ │ ├── cram_index.c │ │ ├── cram_index.h │ │ ├── cram_io.c │ │ ├── cram_io.c.00 │ │ ├── cram_io.h │ │ ├── cram_samtools.c │ │ ├── cram_samtools.h │ │ ├── cram_stats.c │ │ ├── cram_stats.h │ │ ├── cram_structs.h │ │ ├── files.c │ │ ├── mFILE.c │ │ ├── mFILE.h │ │ ├── misc.h │ │ ├── open_trace_file.c │ │ ├── open_trace_file.h │ │ ├── os.h │ │ ├── pooled_alloc.c │ │ ├── pooled_alloc.h │ │ ├── rANS_byte.h │ │ ├── rANS_static.c │ │ ├── rANS_static.h │ │ ├── sam_header.c │ │ ├── sam_header.h │ │ ├── string_alloc.c │ │ ├── string_alloc.h │ │ ├── thread_pool.c │ │ ├── thread_pool.h │ │ ├── vlen.c │ │ ├── vlen.h │ │ ├── zfio.c │ │ └── zfio.h │ ├── faidx.5 │ ├── faidx.c │ ├── hfile.c │ ├── hfile_internal.h │ ├── hfile_irods.c │ ├── hfile_libcurl.c │ ├── hfile_net.c │ ├── hts.c │ ├── hts_internal.h │ ├── htsfile.1 │ ├── htsfile.c │ ├── htslib.mk │ ├── htslib.pc.in │ ├── htslib │ │ ├── bgzf.h │ │ ├── cram.h │ │ ├── faidx.h │ │ ├── hfile.h │ │ ├── hts.h │ │ ├── hts_defs.h │ │ ├── kbitset.h │ │ ├── kfunc.h │ │ ├── khash.h │ │ ├── khash_str2int.h │ │ ├── klist.h │ │ ├── knetfile.h │ │ ├── kseq.h │ │ ├── ksort.h │ │ ├── kstring.h │ │ ├── regidx.h │ │ ├── sam.h │ │ ├── synced_bcf_reader.h │ │ ├── tbx.h │ │ ├── vcf.h │ │ ├── vcf_sweep.h │ │ └── vcfutils.h │ ├── htslib_vars.mk │ ├── kfunc.c │ ├── knetfile.c │ ├── kstring.c │ ├── md5.c │ ├── plugin.c │ ├── regidx.c │ ├── sam.5 │ ├── sam.c │ ├── synced_bcf_reader.c │ ├── tabix.1 │ ├── tabix.c │ ├── tbx.c │ ├── vcf.5 │ ├── vcf.c │ ├── vcf_sweep.c │ ├── vcfutils.c │ └── version.h │ ├── inc │ ├── LICENSE │ ├── ace.h │ ├── aliType.h │ ├── annoAssembly.h │ ├── annoFilter.h │ ├── annoFormatTab.h │ ├── annoFormatter.h │ ├── annoGrateWig.h │ ├── annoGrator.h │ ├── annoGratorQuery.h │ ├── annoOption.h │ ├── annoRow.h │ ├── annoStreamBigBed.h │ ├── annoStreamBigWig.h │ ├── annoStreamLongTabix.h │ ├── annoStreamTab.h │ ├── annoStreamVcf.h │ ├── annoStreamer.h │ ├── apacheLog.h │ ├── asParse.h │ ├── aveStats.h │ ├── axt.h │ ├── bPlusTree.h │ ├── bamFile.h │ ├── bandExt.h │ ├── base64.h │ ├── basicBed.h │ ├── bbiAlias.h │ ├── bbiFile.h │ ├── bedTabix.h │ ├── bigBed.h │ ├── bigWig.h │ ├── binRange.h │ ├── bits.h │ ├── blastParse.h │ ├── boxClump.h │ ├── boxLump.h │ ├── bwgInternal.h │ ├── cda.h │ ├── chain.h │ ├── chainBlock.h │ ├── chainConnect.h │ ├── chainToAxt.h │ ├── chainToPsl.h │ ├── cheapcgi.h │ ├── cirTree.h │ ├── codebias.h │ ├── common.h │ ├── correlate.h │ ├── crTree.h │ ├── crudeali.h │ ├── csv.h │ ├── diGraph.h │ ├── dlist.h │ ├── dnaLoad.h │ ├── dnaMarkov.h │ ├── dnaMotif.h │ ├── dnaseq.h │ ├── dnautil.h │ ├── dtdParse.h │ ├── dyOut.h │ ├── dystring.h │ ├── elmTree.h │ ├── emblParse.h │ ├── ens.h │ ├── errAbort.h │ ├── errCatch.h │ ├── fa.h │ ├── fieldedTable.h │ ├── filePath.h │ ├── flydna.h │ ├── fof.h │ ├── fq.h │ ├── fuzzyFind.h │ ├── gapCalc.h │ ├── gdf.h │ ├── genoFind.h │ ├── genomeRangeTree.h │ ├── gfClientLib.h │ ├── gfPcrLib.h │ ├── gfWebLib.h │ ├── gff.h │ ├── gff3.h │ ├── gfxPoly.h │ ├── gifLabel.h │ ├── hacTree.h │ ├── hash.h │ ├── hex.h │ ├── hgGene.h │ ├── hgap.h │ ├── hgdb.h │ ├── histogram.h │ ├── hmac.h │ ├── hmmPfamParse.h │ ├── hmmstats.h │ ├── htmlColor.h │ ├── htmlPage.h │ ├── htmshell.h │ ├── https.h │ ├── intValTree.h │ ├── internet.h │ ├── itsa.h │ ├── iupac.h │ ├── jointalign.h │ ├── jpegSize.h │ ├── jsonParse.h │ ├── jsonQuery.h │ ├── jsonWrite.h │ ├── keys.h │ ├── knetUdc.h │ ├── kxTok.h │ ├── linefile.h │ ├── localmem.h │ ├── log.h │ ├── longTabix.h │ ├── longToList.h │ ├── maDbRep.h │ ├── maToFf.h │ ├── maf.h │ ├── mailViaPipe.h │ ├── matrixMarket.h │ ├── md5.h │ ├── memalloc.h │ ├── memgfx.h │ ├── meta.h │ ├── metaWig.h │ ├── mime.h │ ├── net.h │ ├── nib.h │ ├── nibTwo.h │ ├── nt4.h │ ├── obscure.h │ ├── oldGff.h │ ├── oligoTm.h │ ├── ooc.h │ ├── options.h │ ├── pairDistance.h │ ├── pairHmm.h │ ├── paraFetch.h │ ├── patSpace.h │ ├── peakCluster.h │ ├── phyloTree.h │ ├── pipeline.h │ ├── portable.h │ ├── psGfx.h │ ├── psPoly.h │ ├── pscmGfx.h │ ├── psl.h │ ├── pslTbl.h │ ├── pslTransMap.h │ ├── pthreadDoList.h │ ├── pthreadWrap.h │ ├── qa.h │ ├── quickHeap.h │ ├── quotedP.h │ ├── ra.h │ ├── raToStruct.h │ ├── rainbow.h │ ├── rangeTree.h │ ├── rbTree.h │ ├── regexHelper.h │ ├── repMask.h │ ├── rle.h │ ├── rnautil.h │ ├── rql.h │ ├── rqlToSql.h │ ├── rudp.h │ ├── scoreWindow.h │ ├── seg.h │ ├── seqOut.h │ ├── seqStats.h │ ├── shaRes.h │ ├── sig.h │ ├── slog.h │ ├── snof.h │ ├── snofmake.h │ ├── spaceSaver.h │ ├── spacedColumn.h │ ├── spacedSeed.h │ ├── sparseMatrix.h │ ├── splatAli.h │ ├── splix.h │ ├── sqlList.h │ ├── sqlNum.h │ ├── sqlReserved.h │ ├── srcVersion.h │ ├── strex.h │ ├── subText.h │ ├── sufa.h │ ├── sufx.h │ ├── supStitch.h │ ├── synQueue.h │ ├── tabRow.h │ ├── tagSchema.h │ ├── tagStorm.h │ ├── tagToJson.h │ ├── tagToSql.h │ ├── textOut.h │ ├── tokenizer.h │ ├── trans3.h │ ├── trix.h │ ├── twoBit.h │ ├── udc.h │ ├── unfin.h │ ├── uuid.h │ ├── vGfx.h │ ├── vMatrix.h │ ├── vcf.h │ ├── vcfBits.h │ ├── verbose.h │ ├── windowsToAscii.h │ ├── wormdna.h │ ├── xAli.h │ ├── xa.h │ ├── xap.h │ ├── xenalign.h │ ├── xmlEscape.h │ ├── xp.h │ └── zlibFace.h │ └── lib │ ├── LICENSE │ ├── README │ ├── README-CSP3.txt │ ├── aliType.c │ ├── annoAssembly.c │ ├── annoFilter.c │ ├── annoFormatTab.c │ ├── annoFormatter.c │ ├── annoGrateWig.c │ ├── annoGrator.c │ ├── annoGratorQuery.c │ ├── annoOption.c │ ├── annoRow.c │ ├── annoStreamBigBed.c │ ├── annoStreamBigWig.c │ ├── annoStreamLongTabix.c │ ├── annoStreamTab.c │ ├── annoStreamVcf.c │ ├── annoStreamer.c │ ├── apacheLog.c │ ├── asParse.c │ ├── aveStats.c │ ├── axt.c │ ├── axtAffine.c │ ├── bPlusTree.c │ ├── bamFile.c │ ├── base64.c │ ├── basicBed.c │ ├── bbiAlias.c │ ├── bbiRead.c │ ├── bbiWrite.c │ ├── bedTabix.c │ ├── bigBed.c │ ├── binRange.c │ ├── bits.c │ ├── blastOut.c │ ├── blastParse.c │ ├── boxClump.c │ ├── boxLump.c │ ├── bwgCreate.c │ ├── bwgQuery.c │ ├── bwgValsOnChrom.c │ ├── cda.c │ ├── chain.c │ ├── chainBlock.c │ ├── chainConnect.c │ ├── chainToAxt.c │ ├── chainToPsl.c │ ├── cheapcgi.c │ ├── cirTree.c │ ├── codebias.c │ ├── colHash.c │ ├── colHash.h │ ├── common.c │ ├── common.ps │ ├── common.pss │ ├── correlate.c │ ├── crTree.c │ ├── csv.c │ ├── dgRange.c │ ├── diGraph.c │ ├── dlist.c │ ├── dnaLoad.c │ ├── dnaMarkov.c │ ├── dnaMotif.c │ ├── dnaseq.c │ ├── dnautil.c │ ├── dtdParse.c │ ├── dyOut.c │ ├── dystring.c │ ├── elmTree.c │ ├── emblParse.c │ ├── errAbort.c │ ├── errCatch.c │ ├── fa.c │ ├── ffAli.c │ ├── ffScore.c │ ├── fieldedTable.c │ ├── filePath.c │ ├── fixColor.c │ ├── flydna.c │ ├── fof.c │ ├── fq.c │ ├── freeType.c │ ├── freeType.h │ ├── fuzzyShow.c │ ├── gapCalc.c │ ├── gdf.c │ ├── gemfont.c │ ├── gemfont.h │ ├── genomeRangeTree.c │ ├── gfNet.c │ ├── gff.c │ ├── gff3.c │ ├── gfxPoly.c │ ├── gifLabel.c │ ├── gifcodes.h │ ├── gifcomp.c │ ├── gifdecomp.c │ ├── gifread.c │ ├── gifwrite.c │ ├── hacTree.c │ ├── hash.c │ ├── hex.c │ ├── histogram.c │ ├── hmac.c │ ├── hmmPfamParse.c │ ├── hmmstats.c │ ├── htmlColor.c │ ├── htmlPage.c │ ├── htmshell.c │ ├── https.c │ ├── intExp.c │ ├── intValTree.c │ ├── internet.c │ ├── itsa.c │ ├── iupac.c │ ├── jointalign.c │ ├── jpegSize.c │ ├── jsonParse.c │ ├── jsonQuery.c │ ├── jsonWrite.c │ ├── keys.c │ ├── knetUdc.c │ ├── kxTok.c │ ├── lineFileOnBigBed.c │ ├── linefile.c │ ├── localmem.c │ ├── log.c │ ├── longTabix.c │ ├── longToList.c │ ├── maf.c │ ├── maf.doc │ ├── mafFromAxt.c │ ├── mafScore.c │ ├── mailViaPipe.c │ ├── matrixMarket.c │ ├── md5.c │ ├── memalloc.c │ ├── memgfx.c │ ├── meta.c │ ├── metaWig.c │ ├── mgCircle.c │ ├── mgPolygon.c │ ├── mime.c │ ├── net.c │ ├── nib.c │ ├── nibTwo.c │ ├── nt4.c │ ├── numObscure.c │ ├── obscure.c │ ├── oldGff.c │ ├── oligoTm.c │ ├── options.c │ ├── osunix.c │ ├── oswin9x.c │ ├── pairDistance.c │ ├── pairHmm.c │ ├── paraFetch.c │ ├── peakCluster.c │ ├── phyloTree.c │ ├── pipeline.c │ ├── pngwrite.c │ ├── portimpl.c │ ├── portimpl.h │ ├── ppc │ └── placeHolder.c │ ├── psGfx.c │ ├── psPoly.c │ ├── pscmGfx.c │ ├── psl.c │ ├── pslGenoShow.c │ ├── pslShow.c │ ├── pslTbl.c │ ├── pslTransMap.c │ ├── pthreadDoList.c │ ├── pthreadWrap.c │ ├── qa.c │ ├── quickHeap.c │ ├── quotedP.c │ ├── ra.c │ ├── raToStruct.c │ ├── rainbow.c │ ├── rangeTree.c │ ├── rbTree.c │ ├── regexHelper.c │ ├── repMask.c │ ├── rle.c │ ├── rnautil.c │ ├── rqlEval.c │ ├── rqlParse.c │ ├── rqlToSql.c │ ├── rudp.c │ ├── scoreWindow.c │ ├── seg.c │ ├── seqOut.c │ ├── seqStats.c │ ├── servBrcMcw.c │ ├── servCrunx.c │ ├── servcis.c │ ├── servcl.c │ ├── servmsII.c │ ├── servpws.c │ ├── shaRes.c │ ├── slog.c │ ├── snof.c │ ├── snofmake.c │ ├── snofsig.c │ ├── spaceSaver.c │ ├── spacedColumn.c │ ├── spacedSeed.c │ ├── sparc │ └── placeHolder.c │ ├── sparseMatrix.c │ ├── splatAli.c │ ├── sqlList.c │ ├── sqlNum.c │ ├── sqlReserved.c │ ├── strex.c │ ├── strex.doc │ ├── subText.c │ ├── sufa.c │ ├── sufx.c │ ├── synQueue.c │ ├── tabRow.c │ ├── tagSchema.c │ ├── tagStorm.c │ ├── tagToJson.c │ ├── tagToSql.c │ ├── textOut.c │ ├── tokenizer.c │ ├── trix.c │ ├── twoBit.c │ ├── udc.c │ ├── uuid.c │ ├── vGfx.c │ ├── vGfxPrivate.h │ ├── vMatrix.c │ ├── vPng.c │ ├── vcf.c │ ├── vcfBits.c │ ├── verbose.c │ ├── wildcmp.c │ ├── windowsToAscii.c │ ├── wormdna.c │ ├── xAli.c │ ├── xa.c │ ├── xap.c │ ├── xenshow.c │ ├── xmlEscape.c │ ├── xp.c │ └── zlibFace.c ├── plastid ├── __init__.py ├── bin │ ├── __init__.py │ ├── counts_in_region.py │ ├── crossmap.py │ ├── cs.py │ ├── findjuncs.py │ ├── get_count_vectors.py │ ├── gff_parent_types.py │ ├── make_wiggle.py │ ├── metagene.py │ ├── phase_by_size.py │ ├── psite.py │ ├── reformat_transcripts.py │ ├── slidejuncs.py │ └── test_table_equality.py ├── genomics │ ├── __init__.py │ ├── c_common.pxd │ ├── c_common.pyx │ ├── genome_array.py │ ├── genome_hash.py │ ├── map_factories.pxd │ ├── map_factories.pyx │ ├── roitools.pxd │ ├── roitools.pyx │ ├── seqtools.py │ └── splicing.py ├── plotting │ ├── __init__.py │ ├── colors.py │ ├── plots.py │ └── plotutils.py ├── readers │ ├── __init__.py │ ├── autosql.py │ ├── bbifile.pxd │ ├── bbifile.pyx │ ├── bed.py │ ├── bigbed.pxd │ ├── bigbed.pyx │ ├── bigwig.pxd │ ├── bigwig.pyx │ ├── bowtie.py │ ├── common.py │ ├── gff.py │ ├── gff_tokens.py │ ├── psl.py │ └── wiggle.py ├── test │ ├── __init__.py │ ├── common.py │ ├── functional │ │ ├── __init__.py │ │ ├── base.py │ │ ├── test_counts_in_region.py │ │ ├── test_crossmap.py │ │ ├── test_cs.py │ │ ├── test_findjuncs.py │ │ ├── test_get_count_vectors.py │ │ ├── test_gff_parent_types.py │ │ ├── test_make_wiggle.py │ │ ├── test_metagene.py │ │ ├── test_phase_by_size.py │ │ ├── test_psite.py │ │ ├── test_reformat_transcripts.py │ │ ├── test_slidejuncs.py │ │ └── test_test_table_equality.py │ ├── ref_files.py │ └── unit │ │ ├── __init__.py │ │ ├── bin │ │ ├── __init__.py │ │ ├── test_crossmap.py │ │ ├── test_metagene.py │ │ ├── test_slidejuncs.py │ │ └── test_test_table_equality.py │ │ ├── genomics │ │ ├── __init__.py │ │ ├── test_genome_array.py │ │ ├── test_genome_hash.py │ │ ├── test_map_factories.py │ │ ├── test_roitools.py │ │ ├── test_seqtools.py │ │ └── test_splicing.py │ │ ├── plotting │ │ ├── __init__.py │ │ └── test_colors.py │ │ ├── readers │ │ ├── __init__.py │ │ ├── test_autosql.py │ │ ├── test_bed.py │ │ ├── test_bigbed.py │ │ ├── test_bigwig.py │ │ ├── test_common.py │ │ ├── test_gff.py │ │ ├── test_gff_tokens.py │ │ ├── test_psl.py │ │ └── test_wiggle.py │ │ └── util │ │ ├── __init__.py │ │ ├── io │ │ ├── __init__.py │ │ ├── test_binary.py │ │ ├── test_filters.py │ │ └── test_openers.py │ │ ├── scriptlib │ │ ├── __init__.py │ │ ├── test_argparsers.py │ │ └── test_help_formatters.py │ │ ├── services │ │ ├── __init__.py │ │ ├── test_decorators.py │ │ ├── test_lists.py │ │ ├── test_misc.py │ │ └── test_sets.py │ │ └── test_uniquefifo.py └── util │ ├── __init__.py │ ├── io │ ├── __init__.py │ ├── binary.py │ ├── filters.py │ └── openers.py │ ├── scriptlib │ ├── __init__.py │ ├── argparsers.py │ ├── help_formatters.py │ └── template.py │ ├── services │ ├── __init__.py │ ├── decorators.py │ ├── exceptions.py │ ├── lists.py │ ├── mini2to3.py │ ├── misc.py │ └── sets.py │ └── unique_fifo.py ├── pyproject.toml ├── requirements-test.txt ├── requirements.txt ├── setup.cfg ├── setup.py └── tox.ini /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/joshuagryphon/plastid/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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