MANIFEST.in
setup.cfg
setup.py
GEMTools/.cproject
GEMTools/.project
GEMTools/Makefile
GEMTools/Makefile.mk
GEMTools/Tasks.todo
GEMTools/bin/gem-tools-examples
GEMTools/bin/gt.filter
GEMTools/bin/gt.stats
GEMTools/build/gem_tools.o
GEMTools/build/gt_alignment.o
GEMTools/build/gt_alignment_utils.o
GEMTools/build/gt_buffered_input_file.o
GEMTools/build/gt_commons.o
GEMTools/build/gt_dna_string.o
GEMTools/build/gt_error.o
GEMTools/build/gt_ihash.o
GEMTools/build/gt_input_file.o
GEMTools/build/gt_input_map_parser.o
GEMTools/build/gt_map.o
GEMTools/build/gt_misms.o
GEMTools/build/gt_shash.o
GEMTools/build/gt_string.o
GEMTools/build/gt_template.o
GEMTools/build/gt_template_utils.o
GEMTools/build/gt_vector.o
GEMTools/datasets/gem.new.PE.Illumina.Dall.map
GEMTools/datasets/gem.new.PE.map
GEMTools/datasets/gem.new.PE.scored.map
GEMTools/datasets/gem.new.SE.454.map
GEMTools/datasets/gem.new.SE.map
GEMTools/datasets/gem.new.SE.splits.map
GEMTools/datasets/gem.old.SE.map
GEMTools/datasets/gem.old.splitmaps.map
GEMTools/include/gem_tools.h
GEMTools/include/gt_alignment.h
GEMTools/include/gt_alignment_utils.h
GEMTools/include/gt_buffered_input_file.h
GEMTools/include/gt_buffered_output_file.h
GEMTools/include/gt_commons.h
GEMTools/include/gt_compact_dna_string.h
GEMTools/include/gt_dna_read.h
GEMTools/include/gt_dna_string.h
GEMTools/include/gt_error.h
GEMTools/include/gt_generic_printer.h
GEMTools/include/gt_hash.h
GEMTools/include/gt_ihash.h
GEMTools/include/gt_input_fastq_parser.h
GEMTools/include/gt_input_file.h
GEMTools/include/gt_input_map_parser.h
GEMTools/include/gt_input_parser.h
GEMTools/include/gt_input_sam_parser.h
GEMTools/include/gt_map.h
GEMTools/include/gt_map_align.h
GEMTools/include/gt_map_score.h
GEMTools/include/gt_misms.h
GEMTools/include/gt_output_buffer.h
GEMTools/include/gt_output_file.h
GEMTools/include/gt_output_map.h
GEMTools/include/gt_output_sam.h
GEMTools/include/gt_sequence_archive.h
GEMTools/include/gt_shash.h
GEMTools/include/gt_string.h
GEMTools/include/gt_template.h
GEMTools/include/gt_template_utils.h
GEMTools/include/gt_test.h
GEMTools/include/gt_vector.h
GEMTools/lib/libgemtools.a
GEMTools/resources/include/check.h
GEMTools/resources/include/uthash.h
GEMTools/resources/lib/libcheck.a
GEMTools/src/Makefile
GEMTools/src/gem_tools.c
GEMTools/src/gt_alignment.c
GEMTools/src/gt_alignment_utils.c
GEMTools/src/gt_buffered_input_file.c
GEMTools/src/gt_buffered_output_file.c
GEMTools/src/gt_commons.c
GEMTools/src/gt_compact_dna_string.c
GEMTools/src/gt_dna_read.c
GEMTools/src/gt_dna_string.c
GEMTools/src/gt_error.c
GEMTools/src/gt_generic_printer.c
GEMTools/src/gt_ihash.c
GEMTools/src/gt_input_fastq_parser.c
GEMTools/src/gt_input_file.c
GEMTools/src/gt_input_map_parser.c
GEMTools/src/gt_input_sam_parser.c
GEMTools/src/gt_map.c
GEMTools/src/gt_map_align.c
GEMTools/src/gt_map_score.c
GEMTools/src/gt_misms.c
GEMTools/src/gt_output_buffer.c
GEMTools/src/gt_output_file.c
GEMTools/src/gt_output_map.c
GEMTools/src/gt_output_sam.c
GEMTools/src/gt_sequence_archive.c
GEMTools/src/gt_shash.c
GEMTools/src/gt_string.c
GEMTools/src/gt_template.c
GEMTools/src/gt_template_utils.c
GEMTools/src/gt_vector.c
GEMTools/test/Makefile
GEMTools/test/gt_suite_alignment.c
GEMTools/test/gt_suite_ihash.c
GEMTools/test/gt_suite_input_map_parser.c
GEMTools/test/gt_utest_commons.c
GEMTools/test/gt_utest_core_structures.c
GEMTools/test/gt_utest_parsers.c
GEMTools/test/script/gt_itest_map_parser.sh
GEMTools/tools/Makefile
GEMTools/tools/gem-source.c
GEMTools/tools/gem-tools-examples.c
GEMTools/tools/gt.filter.c
GEMTools/tools/gt.stats.c
python/Gemtools.egg-info/PKG-INFO
python/Gemtools.egg-info/SOURCES.txt
python/Gemtools.egg-info/dependency_links.txt
python/Gemtools.egg-info/not-zip-safe
python/Gemtools.egg-info/top_level.txt
python/gem/__init__.py
python/gem/__main__.py
python/gem/files.py
python/gem/filter.py
python/gem/junctions.py
python/gem/splits.py
python/gem/utils.py
python/gem/gembinaries/gem-2-sam
python/gem/gembinaries/gem-indexer
python/gem/gembinaries/gem-indexer_bwt-dna
python/gem/gembinaries/gem-indexer_fasta2meta+cont
python/gem/gembinaries/gem-indexer_generate
python/gem/gembinaries/gem-info
python/gem/gembinaries/gem-map-2-map
python/gem/gembinaries/gem-mapper
python/gem/gembinaries/gem-retriever
python/gem/gembinaries/gem-rna-mapper
python/gem/gembinaries/gtf-2-junctions
python/gem/gembinaries/splits-2-junctions
python/src/gemtoolsmodule.c
python/src/py_alignment.c
python/src/py_alignment.h
python/src/py_iterator.c
python/src/py_iterator.h
python/src/py_map.c
python/src/py_map.h
python/src/py_mappings_iterator.c
python/src/py_mappings_iterator.h
python/src/py_mismatch.c
python/src/py_mismatch.h
python/src/py_template.c
python/src/py_template.h
python/src/py_template_iterator.c
python/src/py_template_iterator.h
python/test/__init__.py
python/test/conversion_tests.py
python/test/files_tests.py
python/test/filters_tests.py
python/test/gemtools_alignment_tests.py
python/test/gemtools_filehandles_tests.py
python/test/gemtools_map_tests.py
python/test/gemtools_template_tests.py
python/test/gemtools_test.py
python/test/mapper_tests.py
python/test/parameter_converter_tests.py
python/test/testfiles.py
python/testdata/bedconvert.map
python/testdata/genome.fa
python/testdata/genome.gem
python/testdata/genome.hash
python/testdata/paired_sm_mm.map
python/testdata/paired_w_splitmap.map
python/testdata/reads_1.bam
python/testdata/reads_1.fastq
python/testdata/reads_1.fastq.gz
python/testdata/reads_1.sam
python/testdata/reads_2.fastq
python/testdata/reads_2.fastq.gz
python/testdata/refseq.gtf
python/testdata/splitmap_old_format.map
python/testdata/subsetBWA.sam
python/testdata/test.fastq
python/testdata/test.map
python/testdata/test.map.gz
python/testdata/test_merge_source_1.map
python/testdata/test_merge_source_2.map
python/testdata/test_merge_target.map