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data/bowtie-1.3.0+dfsg1/.travis.yml:                                              ASCII text, with very long lines
data/bowtie-1.3.0+dfsg1/AUTHORS:                                                  ASCII text
data/bowtie-1.3.0+dfsg1/LICENSE:                                                  ASCII text, with very long lines
data/bowtie-1.3.0+dfsg1/MANUAL:                                                   ASCII text
data/bowtie-1.3.0+dfsg1/MANUAL.markdown:                                          exported SGML document, ASCII text
data/bowtie-1.3.0+dfsg1/NEWS:                                                     ASCII text
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data/bowtie-1.3.0+dfsg1/aligner.h:                                                C++ source, ASCII text
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data/bowtie-1.3.0+dfsg1/aligner_seed_mm.h:                                        C++ source, ASCII text
data/bowtie-1.3.0+dfsg1/alphabet.cpp:                                             C source, ASCII text
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data/bowtie-1.3.0+dfsg1/assert_helpers.h:                                         C++ source, ASCII text
data/bowtie-1.3.0+dfsg1/binary_sa_search.h:                                       C source, ASCII text
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data/bowtie-1.3.0+dfsg1/blockwise_sa.h:                                           C++ source, ASCII text
data/bowtie-1.3.0+dfsg1/bowtie:                                                   Python script, ASCII text executable
data/bowtie-1.3.0+dfsg1/bowtie-build:                                             Python script, ASCII text executable
data/bowtie-1.3.0+dfsg1/bowtie-inspect:                                           Python script, ASCII text executable
data/bowtie-1.3.0+dfsg1/bowtie_build_main.cpp:                                    C++ source, ASCII text
data/bowtie-1.3.0+dfsg1/bowtie_inspect.cpp:                                       C++ source, ASCII text
data/bowtie-1.3.0+dfsg1/bowtie_main.cpp:                                          C++ source, ASCII text
data/bowtie-1.3.0+dfsg1/bt2_locks.cpp:                                            C source, ASCII text
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data/bowtie-1.3.0+dfsg1/btypes.h:                                                 C source, ASCII text
data/bowtie-1.3.0+dfsg1/ccnt_lut.cpp:                                             C source, ASCII text
data/bowtie-1.3.0+dfsg1/chaincat.cpp:                                             C++ source, ASCII text
data/bowtie-1.3.0+dfsg1/cpu_numa_info.cpp:                                        C source, ASCII text
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data/bowtie-1.3.0+dfsg1/diff_sample.h:                                            C++ source, ASCII text
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data/bowtie-1.3.0+dfsg1/doc/release.txt:                                          ASCII text
data/bowtie-1.3.0+dfsg1/doc/strip_markdown.pl:                                    Perl script text executable
data/bowtie-1.3.0+dfsg1/doc/style.css:                                            ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/css/style.css:                                ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/foot.ssi:                                     HTML document, ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/images/bowtie_logo.png:                       PNG image data, 356 x 155, 8-bit/color RGBA, non-interlaced
data/bowtie-1.3.0+dfsg1/doc/website/images/osi-certified.gif:                     GIF image data, version 89a, 90 x 75
data/bowtie-1.3.0+dfsg1/doc/website/images/sflogo.png:                            PNG image data, 210 x 62, 8-bit colormap, non-interlaced
data/bowtie-1.3.0+dfsg1/doc/website/images/university.small.horizontal.white.png: PNG image data, 1159 x 231, 8-bit/color RGBA, non-interlaced
data/bowtie-1.3.0+dfsg1/doc/website/index.html:                                   HTML document, ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/index.shtml:                                  HTML document, ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/latest-version.txt:                           ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/manual.html:                                  HTML document, ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/manual.shtml:                                 HTML document, ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/md5s.shtml:                                   HTML document, ASCII text
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data/bowtie-1.3.0+dfsg1/doc/website/old_news.ssi:                                 HTML document, ASCII text, with very long lines
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data/bowtie-1.3.0+dfsg1/doc/website/recent_news.ssi:                              HTML document, ASCII text, with very long lines
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data/bowtie-1.3.0+dfsg1/doc/website/tutorial.html:                                HTML document, ASCII text
data/bowtie-1.3.0+dfsg1/doc/website/tutorial.shtml:                               HTML document, ASCII text
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data/bowtie-1.3.0+dfsg1/ebwt.cpp:                                                 C++ source, ASCII text
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data/bowtie-1.3.0+dfsg1/genomes/NC_008253.fna:                                    ASCII text
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data/bowtie-1.3.0+dfsg1/indexes/e_coli.1.ebwt:                                    data
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data/bowtie-1.3.0+dfsg1/indexes/e_coli.3.ebwt:                                    data
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data/bowtie-1.3.0+dfsg1/indexes/e_coli.rev.1.ebwt:                                data
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data/bowtie-1.3.0+dfsg1/scripts/best_verify.pl:                                   Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/bowtie-hbb.sh:                                    Bourne-Again shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/bs_mapability.pl:                                 Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/build_test.sh:                                    POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/colorize_fasta.pl:                                Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/colorize_fastq.pl:                                Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/convert_quals.pl:                                 Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/fastq_to_tabbed.pl:                               Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/gen_2b_occ_lookup.pl:                             Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/gen_dnamasks2colormask.pl:                        Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/gen_occ_lookup.pl:                                Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/gen_solqual_lookup.pl:                            Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/infer_fraglen.pl:                                 Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/make_a_thaliana_tair.sh:                          POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_b_taurus_UMD3.sh:                            POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_c_elegans.sh:                                POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_canFam2.sh:                                  POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_d_melanogaster.sh:                           POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_e_coli.sh:                                   POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_galGal3.sh:                                  POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi36.sh:                         POSIX shell script, ASCII text executable, with very long lines
data/bowtie-1.3.0+dfsg1/scripts/make_h_sapiens_ncbi37.sh:                         POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_hg18.sh:                                     POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_hg19.sh:                                     POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_m_musculus_ncbi37.sh:                        POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_mm8.sh:                                      POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_mm9.sh:                                      POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_rn4.sh:                                      POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/make_s_cerevisiae.sh:                             POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/mapability.pl:                                    Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/pe_verify.pl:                                     Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/reconcile_alignments.pl:                          Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/reconcile_alignments_pe.pl:                       Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/run-hbb.sh:                                       POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/test/DNA.pm:                                      Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/test/all.sh:                                      POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/test/args.pl:                                     Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/test/big_data/reads/human_reads.fa:               ASCII text
data/bowtie-1.3.0+dfsg1/scripts/test/big_data/reads/mouse_reads.fa:               ASCII text
data/bowtie-1.3.0+dfsg1/scripts/test/btdata.py:                                   Python script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/test/btface.py:                                   Python script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/test/build_big.py:                                Python script, ASCII text executable
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data/bowtie-1.3.0+dfsg1/scripts/test/cs_trim.pl:                                  Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/test/dataface.py:                                 Python script, ASCII text executable
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data/bowtie-1.3.0+dfsg1/scripts/test/large_idx.py:                                Python script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/test/long_read.pl:                                Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests.pl:                      Perl script text executable
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data/bowtie-1.3.0+dfsg1/scripts/test/random_bowtie_tests_p.sh:                    POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/scripts/test/samtools.pl:                                 Perl script text executable
data/bowtie-1.3.0+dfsg1/scripts/test/simple_tests.pl:                             Perl script text executable
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data/bowtie-1.3.0+dfsg1/search_globals.h:                                         C source, ASCII text
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data/bowtie-1.3.0+dfsg1/sequence_io.h:                                            C++ source, ASCII text
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data/bowtie-1.3.0+dfsg1/timer.h:                                                  C++ source, UTF-8 Unicode text
data/bowtie-1.3.0+dfsg1/tinythread.cpp:                                           C++ source, ASCII text
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data/bowtie-1.3.0+dfsg1/debian/README.Debian:                                     ASCII text
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data/bowtie-1.3.0+dfsg1/debian/bowtie.dirs:                                       ASCII text
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data/bowtie-1.3.0+dfsg1/debian/changelog:                                         UTF-8 Unicode text
data/bowtie-1.3.0+dfsg1/debian/clean:                                             ASCII text
data/bowtie-1.3.0+dfsg1/debian/control:                                           ASCII text
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data/bowtie-1.3.0+dfsg1/debian/patches/2to3.patch:                                unified diff output, ASCII text
data/bowtie-1.3.0+dfsg1/debian/patches/build-as-Cpp03.patch:                      unified diff output, UTF-8 Unicode text
data/bowtie-1.3.0+dfsg1/debian/patches/no_hash_style_both_for_mips.patch:         unified diff output, ASCII text
data/bowtie-1.3.0+dfsg1/debian/patches/popcnt_capability.patch:                   unified diff output, UTF-8 Unicode text
data/bowtie-1.3.0+dfsg1/debian/patches/reproducible.patch:                        unified diff output, ASCII text
data/bowtie-1.3.0+dfsg1/debian/patches/seqan-popcount.patch:                      unified diff output, ASCII text
data/bowtie-1.3.0+dfsg1/debian/patches/seqan-rename-ChunkPool.patch:              unified diff output, ASCII text
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data/bowtie-1.3.0+dfsg1/debian/patches/spelling.patch:                            unified diff output, ASCII text
data/bowtie-1.3.0+dfsg1/debian/patches/strip_html5shiv.patch:                     unified diff output, ASCII text
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data/bowtie-1.3.0+dfsg1/debian/rules:                                             a /usr/bin/make -f script, ASCII text executable
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data/bowtie-1.3.0+dfsg1/debian/tests/example2.out:                                ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/example3.out:                                ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/example4.out:                                ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/example5.out:                                ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/example5.out.diff:                           unified diff output, ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/example6.out:                                ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/example7.out:                                ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/example8.out:                                ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/example9.out:                                ASCII text
data/bowtie-1.3.0+dfsg1/debian/tests/run-unit-test:                               POSIX shell script, ASCII text executable
data/bowtie-1.3.0+dfsg1/debian/upstream/edam:                                     ASCII text
data/bowtie-1.3.0+dfsg1/debian/upstream/metadata:                                 ASCII text
data/bowtie-1.3.0+dfsg1/debian/watch:                                             ASCII text
data/bowtie-1.3.0+dfsg1/.pc/.version:                                             ASCII text
data/bowtie-1.3.0+dfsg1/.pc/.quilt_patches:                                       ASCII text
data/bowtie-1.3.0+dfsg1/.pc/.quilt_series:                                        ASCII text
data/bowtie-1.3.0+dfsg1/.pc/applied-patches:                                      ASCII text
data/bowtie-1.3.0+dfsg1/.pc/strip_html5shiv.patch/doc/manual.html:                HTML document, ASCII text, with very long lines
data/bowtie-1.3.0+dfsg1/.pc/spelling.patch/ref_read.cpp:                          C source, ASCII text
data/bowtie-1.3.0+dfsg1/.pc/spelling.patch/doc/website/manual.ssi:                HTML document, ASCII text, with very long lines
data/bowtie-1.3.0+dfsg1/.pc/no_hash_style_both_for_mips.patch/Makefile:           makefile script, ASCII text
data/bowtie-1.3.0+dfsg1/.pc/use-dpkg-buildflags.patch/Makefile:                   makefile script, ASCII text
data/bowtie-1.3.0+dfsg1/.pc/reproducible.patch/Makefile:                          makefile script, ASCII text
data/bowtie-1.3.0+dfsg1/.pc/build-as-Cpp03.patch/Makefile:                        makefile script, ASCII text
data/bowtie-1.3.0+dfsg1/.pc/simple-test/scripts/test/simple_tests.pl:             Perl script text executable
data/bowtie-1.3.0+dfsg1/.pc/simple-test/Makefile:                                 makefile script, ASCII text
data/bowtie-1.3.0+dfsg1/.pc/popcnt_capability.patch/Makefile:                     makefile script, ASCII text
data/bowtie-1.3.0+dfsg1/ref_read.cpp:                                             C source, ASCII text
data/bowtie-1.3.0+dfsg1/Makefile:                                                 makefile script, ASCII text