MANIFEST.in
Readme.md
distribute_setup.py
setup.cfg
setup.py
GEMTools/.cproject
GEMTools/.project
GEMTools/Makefile
GEMTools/Makefile.mk
GEMTools/Makefile.mk.in
GEMTools/Tasks.todo
GEMTools/config.log
GEMTools/config.status
GEMTools/configure
GEMTools/configure.ac
GEMTools/.settings/language.settings.xml
GEMTools/datasets/Bowtie.Illumina.sam
GEMTools/datasets/Bowtie.PE.sam
GEMTools/datasets/Bowtie.SE.sam
GEMTools/datasets/Bowtie2.454.sam
GEMTools/datasets/MrsFast.PE.sam
GEMTools/datasets/MrsFast.SE.sam
GEMTools/datasets/SMALT.454.sam
GEMTools/datasets/SMALT.Illumina.sam
GEMTools/datasets/TMAP.454.sam
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/datasets/small_fastq.fastq
GEMTools/datasets/stampy.454.sam
GEMTools/datasets/strampy.Illuimina.sam
GEMTools/include/gem_tools.h
GEMTools/include/gt_alignment.h
GEMTools/include/gt_alignment_utils.h
GEMTools/include/gt_attributes.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_counters_utils.h
GEMTools/include/gt_dna_read.h
GEMTools/include/gt_dna_string.h
GEMTools/include/gt_error.h
GEMTools/include/gt_essentials.h
GEMTools/include/gt_fm.h
GEMTools/include/gt_gemIdx_loader.h
GEMTools/include/gt_generic_printer.h
GEMTools/include/gt_gtf.h
GEMTools/include/gt_hash.h
GEMTools/include/gt_ihash.h
GEMTools/include/gt_input_fasta_parser.h
GEMTools/include/gt_input_file.h
GEMTools/include/gt_input_generic_parser.h
GEMTools/include/gt_input_map_parser.h
GEMTools/include/gt_input_map_utils.h
GEMTools/include/gt_input_parser.h
GEMTools/include/gt_input_sam_parser.h
GEMTools/include/gt_json.h
GEMTools/include/gt_map.h
GEMTools/include/gt_map_align.h
GEMTools/include/gt_map_metrics.h
GEMTools/include/gt_map_score.h
GEMTools/include/gt_map_utils.h
GEMTools/include/gt_misms.h
GEMTools/include/gt_mm.h
GEMTools/include/gt_output_buffer.h
GEMTools/include/gt_output_fasta.h
GEMTools/include/gt_output_file.h
GEMTools/include/gt_output_generic_printer.h
GEMTools/include/gt_output_map.h
GEMTools/include/gt_output_printer.h
GEMTools/include/gt_output_sam.h
GEMTools/include/gt_profiler.h
GEMTools/include/gt_sam_attributes.h
GEMTools/include/gt_segmented_sequence.h
GEMTools/include/gt_sequence_archive.h
GEMTools/include/gt_shash.h
GEMTools/include/gt_stats.h
GEMTools/include/gt_stats_vector.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/resources/include/bgzf.h
GEMTools/resources/include/check.h
GEMTools/resources/include/gt_uthash.h
GEMTools/resources/include/json.h
GEMTools/resources/include/uthash.h
GEMTools/resources/lib/libcheck.a
GEMTools/resources/lib/mac/libcheck.a
GEMTools/resources/src/Makefile
GEMTools/resources/src/bgzf.c
GEMTools/resources/src/json.c
GEMTools/src/Makefile
GEMTools/src/gem_tools.c
GEMTools/src/gt_alignment.c
GEMTools/src/gt_alignment_utils.c
GEMTools/src/gt_attributes.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_counters_utils.c
GEMTools/src/gt_data_attributes.c
GEMTools/src/gt_dna_read.c
GEMTools/src/gt_dna_string.c
GEMTools/src/gt_error.c
GEMTools/src/gt_fm.c
GEMTools/src/gt_gemIdx_loader.c
GEMTools/src/gt_generic_printer.c
GEMTools/src/gt_gtf.c
GEMTools/src/gt_hash.c
GEMTools/src/gt_ihash.c
GEMTools/src/gt_input_fasta_parser.c
GEMTools/src/gt_input_file.c
GEMTools/src/gt_input_generic_parser.c
GEMTools/src/gt_input_map_parser.c
GEMTools/src/gt_input_map_utils.c
GEMTools/src/gt_input_parser.c
GEMTools/src/gt_input_sam_parser.c
GEMTools/src/gt_json.c
GEMTools/src/gt_map.c
GEMTools/src/gt_map_align.c
GEMTools/src/gt_map_metrics.c
GEMTools/src/gt_map_score.c
GEMTools/src/gt_map_utils.c
GEMTools/src/gt_misms.c
GEMTools/src/gt_mm.c
GEMTools/src/gt_output_buffer.c
GEMTools/src/gt_output_fasta.c
GEMTools/src/gt_output_file.c
GEMTools/src/gt_output_generic_printer.c
GEMTools/src/gt_output_map.c
GEMTools/src/gt_output_printer.c
GEMTools/src/gt_output_sam.c
GEMTools/src/gt_profiler.c
GEMTools/src/gt_sam_attributes.c
GEMTools/src/gt_sam_data_attributes.c
GEMTools/src/gt_segmented_sequence.c
GEMTools/src/gt_sequence_archive.c
GEMTools/src/gt_shash.c
GEMTools/src/gt_stats.c
GEMTools/src/gt_stats_vector.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_gtf.c
GEMTools/test/gt_suite_ihash.c
GEMTools/test/gt_suite_input_map_parser.c
GEMTools/test/gt_suite_input_tag_parser.c
GEMTools/test/gt_suite_template_utils.c
GEMTools/test/gt_utest_commons.c
GEMTools/test/gt_utest_core_structures.c
GEMTools/test/gt_utest_gtf.c
GEMTools/test/gt_utest_parsers.c
GEMTools/test/script/gt_itest_map_parser.sh
GEMTools/test/script/test_gtfcounts.sh
GEMTools/test/testdata/chr1.gtf
GEMTools/test/testdata/counts.gtf
GEMTools/test/testdata/counts.map
GEMTools/test/testdata/result_counts_p.txt
GEMTools/test/testdata/result_counts_p_e_0.5.txt
GEMTools/test/testdata/result_counts_p_e_0.5_s.txt
GEMTools/test/testdata/result_counts_p_e_1.0.txt
GEMTools/test/testdata/result_counts_p_e_1.0_m.txt
GEMTools/test/testdata/result_counts_p_m.txt
GEMTools/test/testdata/result_counts_p_m_s.txt
GEMTools/test/testdata/result_counts_p_m_w.txt
GEMTools/test/testdata/result_counts_p_m_w_s.txt
GEMTools/test/testdata/result_counts_p_s.txt
GEMTools/test/testdata/single_paired.map
GEMTools/test/testdata/single_paired_casava_additional.fastq
GEMTools/test/testdata/single_paired_casava_additional.map
GEMTools/tools/Makefile
GEMTools/tools/align_stats.c
GEMTools/tools/align_stats.h
GEMTools/tools/get_coverage.c
GEMTools/tools/get_coverage.h
GEMTools/tools/gt.construct.c
GEMTools/tools/gt.filter.c
GEMTools/tools/gt.gtfcount.c
GEMTools/tools/gt.map2sam.c
GEMTools/tools/gt.mapset.c
GEMTools/tools/gt.region.c
GEMTools/tools/gt.scorereads.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/entry_points.txt
python/Gemtools.egg-info/not-zip-safe
python/Gemtools.egg-info/requires.txt
python/Gemtools.egg-info/top_level.txt
python/gem/__init__.py
python/gem/__main__.py
python/gem/commands.py
python/gem/files.py
python/gem/filter.py
python/gem/junctions.py
python/gem/pipeline.py
python/gem/production.py
python/gem/reports.py
python/gem/splits.py
python/gem/utils.py
python/src/gemapi.pxd
python/src/gemtools.pyx
python/src/gemtools_binding.c
python/src/gemtools_binding.h
python/test/__init__.py
python/test/__init__.pyc
python/test/conversion_tests.py
python/test/conversion_tests.pyc
python/test/cpu_info_tests.py
python/test/cpu_info_tests.pyc
python/test/files_tests.py
python/test/files_tests.pyc
python/test/filters_tests.py
python/test/filters_tests.pyc
python/test/gem_utils_tests.py
python/test/gem_utils_tests.pyc
python/test/gemtools_filehandles_tests.py
python/test/gemtools_filehandles_tests.pyc
python/test/gemtools_template_tests.py
python/test/gemtools_template_tests.pyc
python/test/hash_and_junctions_tests.py
python/test/hash_and_junctions_tests.pyc
python/test/indexer_tests.py
python/test/indexer_tests.pyc
python/test/mapper_tests.py
python/test/mapper_tests.pyc
python/test/merger_tests.py
python/test/merger_tests.pyc
python/test/parameter_converter_tests.py
python/test/parameter_converter_tests.pyc
python/test/testfiles.py
python/test/testfiles.pyc
python/testdata/20t.map.gz
python/testdata/20t_sub.map.gz
python/testdata/bedconvert.map
python/testdata/chr21_mapping_denovo.map
python/testdata/chr21_mapping_initial.map
python/testdata/chr21_mapping_initial_split.map
python/testdata/chr21_mapping_trim_20.map
python/testdata/chr21_mapping_trim_20_split.map
python/testdata/cpuinfo_core2.txt
python/testdata/cpuinfo_i3.txt
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/split_filter_test_paired.map
python/testdata/splitmap_old_format.map
python/testdata/stats.txt
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
python/testdata/test_unmapped.map
python/testdata/test_xs.fa
python/testdata/test_xs.sam
python/testdata/teststats.stats.json