MANIFEST.in
README.md
setup.py
BSBolt/__init__.py
BSBolt/__main__.py
BSBolt.egg-info/PKG-INFO
BSBolt.egg-info/SOURCES.txt
BSBolt.egg-info/dependency_links.txt
BSBolt.egg-info/entry_points.txt
BSBolt.egg-info/not-zip-safe
BSBolt.egg-info/requires.txt
BSBolt.egg-info/top_level.txt
BSBolt/Align/AlignReads.py
BSBolt/Align/AlignmentHelpers.py
BSBolt/Align/LaunchBowtie2Alignment.py
BSBolt/Align/ProcessSamReads.py
BSBolt/Align/SortDiscordantReads.py
BSBolt/Align/SortReads.py
BSBolt/Align/StreamTabFormat.py
BSBolt/Align/__init__.py
BSBolt/CallMethylation/CallMethylationValues.py
BSBolt/CallMethylation/CallMethylationVector.py
BSBolt/CallMethylation/ProcessContigs.py
BSBolt/CallMethylation/__init__.py
BSBolt/External/__init__.py
BSBolt/External/ART/art_comp.sh
BSBolt/External/ART/map2bed.pl
BSBolt/External/ART/ART_profiler_illumina/README
BSBolt/External/ART/ART_profiler_illumina/art_profiler_illumina
BSBolt/External/ART/ART_profiler_illumina/combinedAvg.pl
BSBolt/External/ART/ART_profiler_illumina/empDist.pl
BSBolt/External/ART/ART_profiler_illumina/fastqReadAvg.pl
BSBolt/External/ART/ART_profiler_illumina/summation.pl
BSBolt/External/ART/Illumina_profiles/Emp100R1.txt
BSBolt/External/ART/Illumina_profiles/Emp100R2.txt
BSBolt/External/ART/Illumina_profiles/Emp36R1.txt
BSBolt/External/ART/Illumina_profiles/Emp36R2.txt
BSBolt/External/ART/Illumina_profiles/Emp44R1.txt
BSBolt/External/ART/Illumina_profiles/Emp44R2.txt
BSBolt/External/ART/Illumina_profiles/Emp50R1.txt
BSBolt/External/ART/Illumina_profiles/Emp50R2.txt
BSBolt/External/ART/Illumina_profiles/Emp75R1.txt
BSBolt/External/ART/Illumina_profiles/Emp75R2.txt
BSBolt/External/ART/Illumina_profiles/EmpMiSeq250R1.txt
BSBolt/External/ART/Illumina_profiles/EmpMiSeq250R2.txt
BSBolt/External/ART/Illumina_profiles/EmpR36R1.txt
BSBolt/External/ART/Illumina_profiles/EmpR36R2.txt
BSBolt/External/ART/Illumina_profiles/EmpR44R1.txt
BSBolt/External/ART/Illumina_profiles/EmpR44R2.txt
BSBolt/External/ART/Illumina_profiles/EmpR50R1.txt
BSBolt/External/ART/Illumina_profiles/EmpR50R2.txt
BSBolt/External/ART/Illumina_profiles/EmpR75R1.txt
BSBolt/External/ART/Illumina_profiles/EmpR75R2.txt
BSBolt/External/ART/Illumina_profiles/HiSeq2500L125R1.txt
BSBolt/External/ART/Illumina_profiles/HiSeq2500L125R2.txt
BSBolt/External/ART/Illumina_profiles/HiSeq2500L150R1.txt
BSBolt/External/ART/Illumina_profiles/HiSeq2500L150R1filter.txt
BSBolt/External/ART/Illumina_profiles/HiSeq2500L150R2.txt
BSBolt/External/ART/Illumina_profiles/HiSeq2500L150R2filter.txt
BSBolt/External/ART/Illumina_profiles/HiSeq2kL100R1.txt
BSBolt/External/ART/Illumina_profiles/HiSeq2kL100R2.txt
BSBolt/External/ART/Illumina_profiles/HiSeqXPCRfreeL150R1.txt
BSBolt/External/ART/Illumina_profiles/HiSeqXPCRfreeL150R2.txt
BSBolt/External/ART/Illumina_profiles/HiSeqXtruSeqL150R1.txt
BSBolt/External/ART/Illumina_profiles/HiSeqXtruSeqL150R2.txt
BSBolt/External/ART/Illumina_profiles/MiSeqv3L250R1.txt
BSBolt/External/ART/Illumina_profiles/MiSeqv3L250R2.txt
BSBolt/External/ART/Illumina_profiles/MiniSeqTruSeqL50.txt
BSBolt/External/ART/Illumina_profiles/NextSeq500v2L75R1.txt
BSBolt/External/ART/Illumina_profiles/NextSeq500v2L75R2.txt
BSBolt/External/ART/art_illumina_src/.dirstamp
BSBolt/External/ART/art_illumina_src/art.h
BSBolt/External/ART/art_illumina_src/art_illumina.cpp
BSBolt/External/ART/art_illumina_src/art_illumina.o
BSBolt/External/ART/art_illumina_src/art_illumina_m.cpp
BSBolt/External/ART/art_illumina_src/art_qual_scale.cpp
BSBolt/External/ART/art_illumina_src/art_qual_scale.o
BSBolt/External/ART/art_illumina_src/empdist.cpp
BSBolt/External/ART/art_illumina_src/empdist.h
BSBolt/External/ART/art_illumina_src/empdist.o
BSBolt/External/ART/art_illumina_src/readSeqFile.cpp
BSBolt/External/ART/art_illumina_src/readSeqFile.h
BSBolt/External/ART/art_illumina_src/readSeqFile.o
BSBolt/External/ART/art_illumina_src/samRead.cpp
BSBolt/External/ART/art_illumina_src/samRead.h
BSBolt/External/ART/art_illumina_src/samRead.o
BSBolt/External/ART/art_illumina_src/seqRead.cpp
BSBolt/External/ART/art_illumina_src/seqRead.h
BSBolt/External/ART/art_illumina_src/seqRead.o
BSBolt/External/ART/art_illumina_src/.deps/.dirstamp
BSBolt/External/ART/art_illumina_src/.deps/art_illumina.Po
BSBolt/External/ART/art_illumina_src/.deps/art_qual_scale.Po
BSBolt/External/ART/art_illumina_src/.deps/empdist.Po
BSBolt/External/ART/art_illumina_src/.deps/readSeqFile.Po
BSBolt/External/ART/art_illumina_src/.deps/samRead.Po
BSBolt/External/ART/art_illumina_src/.deps/seqRead.Po
BSBolt/External/BT2/.DS_Store
BSBolt/External/BT2/AUTHORS
BSBolt/External/BT2/CMakeLists.txt
BSBolt/External/BT2/Dockerfile-aarch64
BSBolt/External/BT2/Makefile
BSBolt/External/BT2/NEWS
BSBolt/External/BT2/VERSION
BSBolt/External/BT2/aligner_bt.cpp
BSBolt/External/BT2/aligner_bt.h
BSBolt/External/BT2/aligner_cache.cpp
BSBolt/External/BT2/aligner_cache.h
BSBolt/External/BT2/aligner_driver.cpp
BSBolt/External/BT2/aligner_driver.h
BSBolt/External/BT2/aligner_metrics.h
BSBolt/External/BT2/aligner_report.h
BSBolt/External/BT2/aligner_result.cpp
BSBolt/External/BT2/aligner_result.h
BSBolt/External/BT2/aligner_seed.cpp
BSBolt/External/BT2/aligner_seed.h
BSBolt/External/BT2/aligner_seed2.cpp
BSBolt/External/BT2/aligner_seed2.h
BSBolt/External/BT2/aligner_seed_policy.cpp
BSBolt/External/BT2/aligner_seed_policy.h
BSBolt/External/BT2/aligner_sw.cpp
BSBolt/External/BT2/aligner_sw.h
BSBolt/External/BT2/aligner_sw_common.h
BSBolt/External/BT2/aligner_sw_driver.cpp
BSBolt/External/BT2/aligner_sw_driver.h
BSBolt/External/BT2/aligner_sw_nuc.h
BSBolt/External/BT2/aligner_swsse.cpp
BSBolt/External/BT2/aligner_swsse.h
BSBolt/External/BT2/aligner_swsse_ee_i16.cpp
BSBolt/External/BT2/aligner_swsse_ee_u8.cpp
BSBolt/External/BT2/aligner_swsse_loc_i16.cpp
BSBolt/External/BT2/aligner_swsse_loc_u8.cpp
BSBolt/External/BT2/aln_sink.cpp
BSBolt/External/BT2/aln_sink.h
BSBolt/External/BT2/alphabet.cpp
BSBolt/External/BT2/alphabet.h
BSBolt/External/BT2/assert_helpers.h
BSBolt/External/BT2/banded.cpp
BSBolt/External/BT2/banded.h
BSBolt/External/BT2/binary_sa_search.h
BSBolt/External/BT2/bitpack.h
BSBolt/External/BT2/blockwise_sa.h
BSBolt/External/BT2/bowtie2
BSBolt/External/BT2/bowtie2-build
BSBolt/External/BT2/bowtie2-inspect
BSBolt/External/BT2/bowtie_build_main.cpp
BSBolt/External/BT2/bowtie_main.cpp
BSBolt/External/BT2/bt2_build.cpp
BSBolt/External/BT2/bt2_dp.cpp
BSBolt/External/BT2/bt2_idx.cpp
BSBolt/External/BT2/bt2_idx.h
BSBolt/External/BT2/bt2_inspect.cpp
BSBolt/External/BT2/bt2_io.cpp
BSBolt/External/BT2/bt2_search.cpp
BSBolt/External/BT2/bt2_search.h
BSBolt/External/BT2/bt2_util.cpp
BSBolt/External/BT2/btypes.h
BSBolt/External/BT2/ccnt_lut.cpp
BSBolt/External/BT2/cpu_numa_info.cpp
BSBolt/External/BT2/cpu_numa_info.h
BSBolt/External/BT2/diff_sample.cpp
BSBolt/External/BT2/diff_sample.h
BSBolt/External/BT2/dp_framer.cpp
BSBolt/External/BT2/dp_framer.h
BSBolt/External/BT2/ds.cpp
BSBolt/External/BT2/ds.h
BSBolt/External/BT2/edit.cpp
BSBolt/External/BT2/edit.h
BSBolt/External/BT2/endian_swap.h
BSBolt/External/BT2/fast_mutex.h
BSBolt/External/BT2/filebuf.h
BSBolt/External/BT2/formats.h
BSBolt/External/BT2/group_walk.cpp
BSBolt/External/BT2/group_walk.h
BSBolt/External/BT2/ival_list.cpp
BSBolt/External/BT2/ival_list.h
BSBolt/External/BT2/limit.cpp
BSBolt/External/BT2/limit.h
BSBolt/External/BT2/ls.cpp
BSBolt/External/BT2/ls.h
BSBolt/External/BT2/mask.cpp
BSBolt/External/BT2/mask.h
BSBolt/External/BT2/mem_ids.h
BSBolt/External/BT2/mm.h
BSBolt/External/BT2/multikey_qsort.cpp
BSBolt/External/BT2/multikey_qsort.h
BSBolt/External/BT2/opts.h
BSBolt/External/BT2/outq.cpp
BSBolt/External/BT2/outq.h
BSBolt/External/BT2/pat.cpp
BSBolt/External/BT2/pat.h
BSBolt/External/BT2/pe.cpp
BSBolt/External/BT2/pe.h
BSBolt/External/BT2/presets.cpp
BSBolt/External/BT2/presets.h
BSBolt/External/BT2/processor_support.h
BSBolt/External/BT2/qual.cpp
BSBolt/External/BT2/qual.h
BSBolt/External/BT2/random_source.cpp
BSBolt/External/BT2/random_source.h
BSBolt/External/BT2/random_util.cpp
BSBolt/External/BT2/random_util.h
BSBolt/External/BT2/read.h
BSBolt/External/BT2/read_qseq.cpp
BSBolt/External/BT2/ref_coord.cpp
BSBolt/External/BT2/ref_coord.h
BSBolt/External/BT2/ref_read.cpp
BSBolt/External/BT2/ref_read.h
BSBolt/External/BT2/reference.cpp
BSBolt/External/BT2/reference.h
BSBolt/External/BT2/sam.cpp
BSBolt/External/BT2/sam.h
BSBolt/External/BT2/scoring.cpp
BSBolt/External/BT2/scoring.h
BSBolt/External/BT2/search_globals.h
BSBolt/External/BT2/sequence_io.h
BSBolt/External/BT2/shmem.cpp
BSBolt/External/BT2/shmem.h
BSBolt/External/BT2/simple_func.cpp
BSBolt/External/BT2/simple_func.h
BSBolt/External/BT2/sse_util.cpp
BSBolt/External/BT2/sse_util.h
BSBolt/External/BT2/sse_wrap.h
BSBolt/External/BT2/sstring.cpp
BSBolt/External/BT2/sstring.h
BSBolt/External/BT2/str_util.h
BSBolt/External/BT2/threading.h
BSBolt/External/BT2/timer.h
BSBolt/External/BT2/tinythread.cpp
BSBolt/External/BT2/tinythread.h
BSBolt/External/BT2/tokenize.h
BSBolt/External/BT2/unique.cpp
BSBolt/External/BT2/unique.h
BSBolt/External/BT2/util.h
BSBolt/External/BT2/word_io.h
BSBolt/External/BT2/zbox.h
BSBolt/External/BT2/third_party/cpuid.h
BSBolt/Impute/__init__.py
BSBolt/Impute/kNN_Impute.py
BSBolt/Impute/Imputation/EuclideanDistance.py
BSBolt/Impute/Imputation/GenomeImputation.py
BSBolt/Impute/Imputation/GenomeImputationWindows.py
BSBolt/Impute/Imputation/__init__.py
BSBolt/Impute/Impute_Utils/ImputationFunctions.py
BSBolt/Impute/Impute_Utils/__init__.py
BSBolt/Impute/Validation/ImputationAssessment.py
BSBolt/Impute/Validation/MaskValues.py
BSBolt/Impute/Validation/__init__.py
BSBolt/Index/IndexOutput.py
BSBolt/Index/ProcessCutSites.py
BSBolt/Index/RRBSGenomeBuild.py
BSBolt/Index/WholeGenomeBuild.py
BSBolt/Index/__init__.py
BSBolt/Matrix/MatrixAggregator.py
BSBolt/Matrix/__init__.py
BSBolt/Simulate/SetCyotsineMethylation.py
BSBolt/Simulate/SimulateMethylatedReads.py
BSBolt/Simulate/SimulationOutput.py
BSBolt/Simulate/__init__.py
BSBolt/Utils/AlnIterator.py
BSBolt/Utils/CGmapIterator.py
BSBolt/Utils/FastaIterator.py
BSBolt/Utils/FastqIterator.py
BSBolt/Utils/Launcher.py
BSBolt/Utils/MatrixIterator.py
BSBolt/Utils/Parser.py
BSBolt/Utils/TabFormatConversion.py
BSBolt/Utils/UtilityFunctions.py
BSBolt/Utils/__init__.py
BSBolt/Variant/__init__.py