bowtie-0.11.3
.............\aligner_0mm.h
.............\aligner_1mm.h
.............\aligner_23mm.h
.............\aligner.h
.............\aligner_metrics.h
.............\aligner_seed_mm.h
.............\alphabet.h
.............\annot.h
.............\assert_helpers.h
.............\auto_array.h
.............\binary_sa_search.h
.............\bitpack.h
.............\bitset.h
.............\blockwise_sa.h
.............\diff_sample.h
.............\ebwt.h
.............\ebwt_search_backtrack.h
.............\ebwt_search_util.h
.............\edit.h
.............\endian_swap.h
.............\filebuf.h
.............\formats.h
.............\hit.h
.............\hit_set.h
.............\log.h
.............\mm.h
.............\multikey_qsort.h
.............\pat.h
.............\pool.h
.............\qual.h
.............\random_source.h
.............\range_cache.h
.............\range_chaser.h
.............\range.h
.............\range_source.h
.............\ref_aligner.h
.............\reference.h
.............\refmap.h
.............\ref_read.h
.............\row_chaser.h
.............\sam.h
.............\sequence_io.h
.............\shmem.h
.............\spinlock.h
.............\str_util.h
.............\threading.h
.............\timer.h
.............\tokenize.h
.............\word_io.h
.............\zbox.h
.............\alphabet.c
.............\search_1mm_phase1.c
.............\search_1mm_phase2.c
.............\search_23mm_phase1.c
.............\search_23mm_phase2.c
.............\search_23mm_phase3.c
.............\search_exact.c
.............\search_seeded_phase1.c
.............\search_seeded_phase2.c
.............\search_seeded_phase3.c
.............\search_seeded_phase4.c
.............\annot.cpp
.............\bowtie_build_main.cpp
.............\bowtie_inspect.cpp
.............\bowtie_main.cpp
.............\ccnt_lut.cpp
.............\chaincat.cpp
.............\ebwt_build.cpp
.............\ebwt.cpp
.............\ebwt_search.cpp
.............\ebwt_search_util.cpp
.............\edit.cpp
.............\hit.cpp
.............\hit_set.cpp
.............\log.cpp
.............\map_tool.cpp
.............\pat.cpp
.............\qual.cpp
.............\ref_aligner.cpp
.............\refmap.cpp
.............\ref_read.cpp
.............\sam.cpp
.............\shmem.cpp
.............\maq_convert
.............\...........\bfa.h
.............\...........\const.h
.............\...........\maqmap.h
.............\...........\read_bfq.h
.............\...........\algo.hh
.............\...........\const.c
.............\...........\bfa.cpp
.............\...........\bowtie_convert.cpp
.............\SeqAn-1.1
.............\.........\platform_linux_gcc.h
.............\.........\platform_windows_mingw.h
.............\.........\platform_windows_vs.h
.............\.........\seqan
.............\.........\.....\basic.h
.............\.........\.....\file.h