README.rst
setup.cfg
setup.py
/homeroot/joshua/projects/plastid/plastid/genomics/c_common.c
/homeroot/joshua/projects/plastid/plastid/genomics/map_factories.c
/homeroot/joshua/projects/plastid/plastid/genomics/roitools.c
plastid/__init__.py
plastid.egg-info/PKG-INFO
plastid.egg-info/SOURCES.txt
plastid.egg-info/dependency_links.txt
plastid.egg-info/entry_points.txt
plastid.egg-info/requires.txt
plastid.egg-info/top_level.txt
plastid/bin/__init__.py
plastid/bin/counts_in_region.py
plastid/bin/crossmap.py
plastid/bin/cs.py
plastid/bin/findjuncs.py
plastid/bin/get_count_vectors.py
plastid/bin/gff_parent_types.py
plastid/bin/make_wiggle.py
plastid/bin/metagene.py
plastid/bin/phase_by_size.py
plastid/bin/psite.py
plastid/bin/reformat_transcripts.py
plastid/bin/slidejuncs.py
plastid/bin/test_table_equality.py
plastid/genomics/__init__.py
plastid/genomics/c_common.c
plastid/genomics/c_common.pxd
plastid/genomics/c_common.pyx
plastid/genomics/genome_array.py
plastid/genomics/genome_hash.py
plastid/genomics/map_factories.c
plastid/genomics/map_factories.pxd
plastid/genomics/map_factories.pyx
plastid/genomics/roitools.c
plastid/genomics/roitools.pxd
plastid/genomics/roitools.pyx
plastid/genomics/seqtools.py
plastid/genomics/splicing.py
plastid/plotting/__init__.py
plastid/plotting/colors.py
plastid/plotting/plots.py
plastid/plotting/plotutils.py
plastid/readers/__init__.py
plastid/readers/autosql.py
plastid/readers/bed.py
plastid/readers/bigbed.py
plastid/readers/bowtie.py
plastid/readers/common.py
plastid/readers/gff.py
plastid/readers/gff_tokens.py
plastid/readers/psl.py
plastid/readers/wiggle.py
plastid/test/__init__.py
plastid/test/ref_files.py
plastid/test/data/__init__.py
plastid/test/data/annotations/__init__.py
plastid/test/data/annotations/juncs/__init__.py
plastid/test/data/command_line/__init__.py
plastid/test/data/command_line/gen_count_vectors/__init__.py
plastid/test/data/ebwt/__init__.py
plastid/test/data/mini/__init__.py
plastid/test/data/mini/align/__init__.py
plastid/test/data/mini/bed/__init__.py
plastid/test/data/mini/count_vectors/__init__.py
plastid/test/data/mini/fasta/__init__.py
plastid/test/data/mini/juncs/__init__.py
plastid/test/data/mini/wig/__init__.py
plastid/test/functional/__init__.py
plastid/test/functional/base.py
plastid/test/functional/test_counts_in_region.py
plastid/test/functional/test_crossmap.py
plastid/test/functional/test_cs.py
plastid/test/functional/test_findjuncs.py
plastid/test/functional/test_get_count_vectors.py
plastid/test/functional/test_gff_parent_types.py
plastid/test/functional/test_make_wiggle.py
plastid/test/functional/test_metagene.py
plastid/test/functional/test_phase_by_size.py
plastid/test/functional/test_psite.py
plastid/test/functional/test_reformat_transcripts.py
plastid/test/functional/test_slidejuncs.py
plastid/test/functional/test_test_table_equality.py
plastid/test/unit/__init__.py
plastid/test/unit/bin/__init__.py
plastid/test/unit/bin/test_crossmap.py
plastid/test/unit/bin/test_metagene.py
plastid/test/unit/bin/test_slidejuncs.py
plastid/test/unit/bin/test_test_table_equality.py
plastid/test/unit/genomics/__init__.py
plastid/test/unit/genomics/test_genome_array.py
plastid/test/unit/genomics/test_genome_hash.py
plastid/test/unit/genomics/test_mapping_rules.py
plastid/test/unit/genomics/test_roitools.py
plastid/test/unit/genomics/test_seqtools.py
plastid/test/unit/genomics/test_splicing.py
plastid/test/unit/readers/__init__.py
plastid/test/unit/readers/test_autosql.py
plastid/test/unit/readers/test_bed.py
plastid/test/unit/readers/test_bigbed.py
plastid/test/unit/readers/test_common.py
plastid/test/unit/readers/test_gff.py
plastid/test/unit/readers/test_gff_tokens.py
plastid/test/unit/readers/test_psl.py
plastid/test/unit/readers/test_wiggle.py
plastid/test/unit/util/__init__.py
plastid/test/unit/util/test_uniquefifo.py
plastid/test/unit/util/io/__init__.py
plastid/test/unit/util/io/test_binary.py
plastid/test/unit/util/io/test_filters.py
plastid/test/unit/util/scriptlib/__init__.py
plastid/test/unit/util/scriptlib/test_argparsers.py
plastid/test/unit/util/scriptlib/test_help_formatters.py
plastid/test/unit/util/services/__init__.py
plastid/test/unit/util/services/test_colors.py
plastid/test/unit/util/services/test_decorators.py
plastid/test/unit/util/services/test_lists.py
plastid/test/unit/util/services/test_misc.py
plastid/test/unit/util/services/test_sets.py
plastid/util/__init__.py
plastid/util/unique_fifo.py
plastid/util/io/__init__.py
plastid/util/io/binary.py
plastid/util/io/filters.py
plastid/util/io/openers.py
plastid/util/scriptlib/__init__.py
plastid/util/scriptlib/argparsers.py
plastid/util/scriptlib/help_formatters.py
plastid/util/scriptlib/template.py
plastid/util/services/__init__.py
plastid/util/services/decorators.py
plastid/util/services/exceptions.py
plastid/util/services/lists.py
plastid/util/services/mini2to3.py
plastid/util/services/misc.py
plastid/util/services/sets.py