diff --git a/Makefile b/Makefile index 965e0c3c..26e3858f 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/aligner_bt.cpp b/aligner_bt.cpp index 4ed12403..6247dd42 100644 --- a/aligner_bt.cpp +++ b/aligner_bt.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_bt.h b/aligner_bt.h index 2043d46d..8056b7ab 100644 --- a/aligner_bt.h +++ b/aligner_bt.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_cache.cpp b/aligner_cache.cpp index 0023b86b..2bec5e01 100644 --- a/aligner_cache.cpp +++ b/aligner_cache.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_cache.h b/aligner_cache.h index 30df0c7e..e29d3555 100644 --- a/aligner_cache.h +++ b/aligner_cache.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_driver.cpp b/aligner_driver.cpp index 24bfca29..e4227d67 100644 --- a/aligner_driver.cpp +++ b/aligner_driver.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2012, Ben Langmead + * Copyright 2012, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_driver.h b/aligner_driver.h index 25ebfe47..4dd73451 100644 --- a/aligner_driver.h +++ b/aligner_driver.h @@ -1,5 +1,5 @@ /* - * Copyright 2012, Ben Langmead + * Copyright 2012, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_metrics.h b/aligner_metrics.h index 9bd8bb7a..c0b01823 100644 --- a/aligner_metrics.h +++ b/aligner_metrics.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_report.h b/aligner_report.h index 73dccc02..6262f46f 100644 --- a/aligner_report.h +++ b/aligner_report.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_result.cpp b/aligner_result.cpp index 49f9a81e..a03abb64 100644 --- a/aligner_result.cpp +++ b/aligner_result.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_result.h b/aligner_result.h index 74455b17..a5b08ab5 100644 --- a/aligner_result.h +++ b/aligner_result.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_seed.cpp b/aligner_seed.cpp index e628f2eb..5dd122ed 100644 --- a/aligner_seed.cpp +++ b/aligner_seed.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_seed.h b/aligner_seed.h index baf7cd5c..1baaad6e 100644 --- a/aligner_seed.h +++ b/aligner_seed.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_seed2.cpp b/aligner_seed2.cpp index 4e546b69..58415bcd 100644 --- a/aligner_seed2.cpp +++ b/aligner_seed2.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_seed2.h b/aligner_seed2.h index cde3e4c4..0b095ca5 100644 --- a/aligner_seed2.h +++ b/aligner_seed2.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_seed_policy.cpp b/aligner_seed_policy.cpp index df7d6606..1f6c51fa 100644 --- a/aligner_seed_policy.cpp +++ b/aligner_seed_policy.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_seed_policy.h b/aligner_seed_policy.h index 4287e881..7bdaab7d 100644 --- a/aligner_seed_policy.h +++ b/aligner_seed_policy.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_sw.cpp b/aligner_sw.cpp index 5747b3de..ea3b1781 100644 --- a/aligner_sw.cpp +++ b/aligner_sw.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_sw.h b/aligner_sw.h index 0d1a484b..1e2c48fa 100644 --- a/aligner_sw.h +++ b/aligner_sw.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_sw_common.h b/aligner_sw_common.h index c0d9bd3f..14582bc3 100644 --- a/aligner_sw_common.h +++ b/aligner_sw_common.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_sw_driver.cpp b/aligner_sw_driver.cpp index d194398c..2d0c7b0c 100644 --- a/aligner_sw_driver.cpp +++ b/aligner_sw_driver.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_sw_driver.h b/aligner_sw_driver.h index 2c09cdd7..ad9438b8 100644 --- a/aligner_sw_driver.h +++ b/aligner_sw_driver.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_sw_nuc.h b/aligner_sw_nuc.h index ecca06c0..6bec1de8 100644 --- a/aligner_sw_nuc.h +++ b/aligner_sw_nuc.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_swsse.cpp b/aligner_swsse.cpp index 702ca363..d4f7d782 100644 --- a/aligner_swsse.cpp +++ b/aligner_swsse.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_swsse.h b/aligner_swsse.h index 6e17a6cf..f99f97f9 100644 --- a/aligner_swsse.h +++ b/aligner_swsse.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_swsse_ee_i16.cpp b/aligner_swsse_ee_i16.cpp index 6afaae03..f5796a47 100644 --- a/aligner_swsse_ee_i16.cpp +++ b/aligner_swsse_ee_i16.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_swsse_ee_u8.cpp b/aligner_swsse_ee_u8.cpp index 91467928..0060a3d8 100644 --- a/aligner_swsse_ee_u8.cpp +++ b/aligner_swsse_ee_u8.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_swsse_loc_i16.cpp b/aligner_swsse_loc_i16.cpp index eddf28bb..1887bd55 100644 --- a/aligner_swsse_loc_i16.cpp +++ b/aligner_swsse_loc_i16.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aligner_swsse_loc_u8.cpp b/aligner_swsse_loc_u8.cpp index 5d81501b..71da4ec7 100644 --- a/aligner_swsse_loc_u8.cpp +++ b/aligner_swsse_loc_u8.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aln_sink.cpp b/aln_sink.cpp index b256ae76..3af86d12 100644 --- a/aln_sink.cpp +++ b/aln_sink.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/aln_sink.h b/aln_sink.h index 9d942079..dacf1d0b 100644 --- a/aln_sink.h +++ b/aln_sink.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/alphabet.cpp b/alphabet.cpp index 23b5fc22..7613557e 100644 --- a/alphabet.cpp +++ b/alphabet.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/alphabet.h b/alphabet.h index e277f609..340942eb 100644 --- a/alphabet.h +++ b/alphabet.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/assert_helpers.h b/assert_helpers.h index 6b3ce959..688181a0 100644 --- a/assert_helpers.h +++ b/assert_helpers.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/banded.cpp b/banded.cpp index 3edae4fd..e88f7caf 100644 --- a/banded.cpp +++ b/banded.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/banded.h b/banded.h index f4988e4e..edf53939 100644 --- a/banded.h +++ b/banded.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/binary_sa_search.h b/binary_sa_search.h index 18329328..25ceea0a 100644 --- a/binary_sa_search.h +++ b/binary_sa_search.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bitpack.h b/bitpack.h index 0134415a..b6a7cf4f 100644 --- a/bitpack.h +++ b/bitpack.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/blockwise_sa.h b/blockwise_sa.h index 0c2bf9a6..c68ce622 100644 --- a/blockwise_sa.h +++ b/blockwise_sa.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bowtie2 b/bowtie2 index 0aef2da6..6d2f3b2a 100755 --- a/bowtie2 +++ b/bowtie2 @@ -1,7 +1,7 @@ #!/usr/bin/env perl # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/bowtie_build_main.cpp b/bowtie_build_main.cpp index 6a15baeb..03228c7d 100644 --- a/bowtie_build_main.cpp +++ b/bowtie_build_main.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bowtie_main.cpp b/bowtie_main.cpp index fa4f8c45..844c8ca4 100644 --- a/bowtie_main.cpp +++ b/bowtie_main.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bt2_build.cpp b/bt2_build.cpp index e360987a..0b322e16 100644 --- a/bt2_build.cpp +++ b/bt2_build.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bt2_idx.cpp b/bt2_idx.cpp index 80ba7f43..0ec626a1 100644 --- a/bt2_idx.cpp +++ b/bt2_idx.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bt2_idx.h b/bt2_idx.h index 41f01af5..af5db200 100644 --- a/bt2_idx.h +++ b/bt2_idx.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bt2_inspect.cpp b/bt2_inspect.cpp index c74540a2..54ecf7bd 100644 --- a/bt2_inspect.cpp +++ b/bt2_inspect.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bt2_io.cpp b/bt2_io.cpp index 25a0c822..4a54f60d 100644 --- a/bt2_io.cpp +++ b/bt2_io.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bt2_search.cpp b/bt2_search.cpp index c2a3dc32..16b1d651 100644 --- a/bt2_search.cpp +++ b/bt2_search.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/bt2_util.cpp b/bt2_util.cpp index e421d5dc..51327d76 100644 --- a/bt2_util.cpp +++ b/bt2_util.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ccnt_lut.cpp b/ccnt_lut.cpp index 6141fd8f..9422449c 100644 --- a/ccnt_lut.cpp +++ b/ccnt_lut.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/diff_sample.cpp b/diff_sample.cpp index 91a7ad03..b7227026 100644 --- a/diff_sample.cpp +++ b/diff_sample.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/diff_sample.h b/diff_sample.h index c057e373..31b345c2 100644 --- a/diff_sample.h +++ b/diff_sample.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/doc/website/index.shtml b/doc/website/index.shtml index 1c3e6f22..a05e7934 100644 --- a/doc/website/index.shtml +++ b/doc/website/index.shtml @@ -36,7 +36,7 @@ gapped, local, and paired-end alignment modes.
This research was supported in part by NIH grants R01-HG006102 and R01-GM083873 and AWS in Education research grants. - Administrator: Ben Langmead. Design by David Herreman + Administrator: Ben Langmead. Design by David Herreman
diff --git a/dp_framer.cpp b/dp_framer.cpp index eee67f43..d7e359a5 100644 --- a/dp_framer.cpp +++ b/dp_framer.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/dp_framer.h b/dp_framer.h index 045da01d..4209f41f 100644 --- a/dp_framer.h +++ b/dp_framer.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ds.cpp b/ds.cpp index 1f440d3a..4cff2a5f 100644 --- a/ds.cpp +++ b/ds.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ds.h b/ds.h index a91e7037..ac5cf596 100644 --- a/ds.h +++ b/ds.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/edit.cpp b/edit.cpp index 8a806226..906b6928 100644 --- a/edit.cpp +++ b/edit.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/edit.h b/edit.h index 1ec1d006..f9f85d12 100644 --- a/edit.h +++ b/edit.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/endian_swap.h b/endian_swap.h index f7039be4..e5626ff8 100644 --- a/endian_swap.h +++ b/endian_swap.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/example/reads/simulate.pl b/example/reads/simulate.pl index 53294e97..0f09f32b 100644 --- a/example/reads/simulate.pl +++ b/example/reads/simulate.pl @@ -1,7 +1,7 @@ #!/usr/bin/env perl ## -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/filebuf.h b/filebuf.h index 5108c6e6..2494e976 100644 --- a/filebuf.h +++ b/filebuf.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/formats.h b/formats.h index d15de45d..76278272 100644 --- a/formats.h +++ b/formats.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/group_walk.cpp b/group_walk.cpp index e50f865a..4abb1de2 100644 --- a/group_walk.cpp +++ b/group_walk.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/group_walk.h b/group_walk.h index d8cfe401..fc215fb5 100644 --- a/group_walk.h +++ b/group_walk.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ival_list.cpp b/ival_list.cpp index 18ccf086..acbe4604 100644 --- a/ival_list.cpp +++ b/ival_list.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ival_list.h b/ival_list.h index e8dff176..354e5855 100644 --- a/ival_list.h +++ b/ival_list.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/limit.cpp b/limit.cpp index a577f913..11460907 100644 --- a/limit.cpp +++ b/limit.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/limit.h b/limit.h index b963dc62..06ea0725 100644 --- a/limit.h +++ b/limit.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ls.cpp b/ls.cpp index bd276596..96c28c0e 100644 --- a/ls.cpp +++ b/ls.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ls.h b/ls.h index d907d3e2..9b0bc889 100644 --- a/ls.h +++ b/ls.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/mask.cpp b/mask.cpp index 9b76d9dd..ffefdc7e 100644 --- a/mask.cpp +++ b/mask.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/mask.h b/mask.h index fc5e20c1..e00c1942 100644 --- a/mask.h +++ b/mask.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/mem_ids.h b/mem_ids.h index b1b76a54..352817be 100644 --- a/mem_ids.h +++ b/mem_ids.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/mm.h b/mm.h index 64fe8fb5..c192cc5b 100644 --- a/mm.h +++ b/mm.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/multikey_qsort.cpp b/multikey_qsort.cpp index 9ff1f242..36fdd7d6 100644 --- a/multikey_qsort.cpp +++ b/multikey_qsort.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/multikey_qsort.h b/multikey_qsort.h index 45668201..4b69942d 100644 --- a/multikey_qsort.h +++ b/multikey_qsort.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/opts.h b/opts.h index b52bcb96..27a14aa1 100644 --- a/opts.h +++ b/opts.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/outq.cpp b/outq.cpp index b29f6f40..f5687ab2 100644 --- a/outq.cpp +++ b/outq.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/outq.h b/outq.h index 2143e900..30905fc9 100644 --- a/outq.h +++ b/outq.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/pat.cpp b/pat.cpp index fb53776b..7e5b9ccd 100644 --- a/pat.cpp +++ b/pat.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/pat.h b/pat.h index 926c8278..ddb3e7b1 100644 --- a/pat.h +++ b/pat.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/pe.cpp b/pe.cpp index 3d16176a..8eea8c3f 100644 --- a/pe.cpp +++ b/pe.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/pe.h b/pe.h index 3c601a07..8dd46a4c 100644 --- a/pe.h +++ b/pe.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/presets.cpp b/presets.cpp index 55073958..c36309fb 100644 --- a/presets.cpp +++ b/presets.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/presets.h b/presets.h index 4701e0b9..dfcec413 100644 --- a/presets.h +++ b/presets.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/qual.cpp b/qual.cpp index 43e30f83..f62fbc7c 100644 --- a/qual.cpp +++ b/qual.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/qual.h b/qual.h index 2542b8f9..089080bd 100644 --- a/qual.h +++ b/qual.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/random_source.cpp b/random_source.cpp index c5eb0f3f..0311f918 100644 --- a/random_source.cpp +++ b/random_source.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/random_source.h b/random_source.h index 755fcce3..9304d983 100644 --- a/random_source.h +++ b/random_source.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/random_util.cpp b/random_util.cpp index 808d22c1..2c5ed7d7 100644 --- a/random_util.cpp +++ b/random_util.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/random_util.h b/random_util.h index 4fe4a9b9..39f8c046 100644 --- a/random_util.h +++ b/random_util.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/read.h b/read.h index 7fa56d8b..f7e6f98d 100644 --- a/read.h +++ b/read.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/read_qseq.cpp b/read_qseq.cpp index bc8bf7bc..ced6c68e 100644 --- a/read_qseq.cpp +++ b/read_qseq.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ref_coord.cpp b/ref_coord.cpp index c5f3b1c4..738c6fa1 100644 --- a/ref_coord.cpp +++ b/ref_coord.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ref_coord.h b/ref_coord.h index 060f1ae7..4cd140ec 100644 --- a/ref_coord.h +++ b/ref_coord.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ref_read.cpp b/ref_read.cpp index 1e2b12e1..2b979860 100644 --- a/ref_read.cpp +++ b/ref_read.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/ref_read.h b/ref_read.h index a7fffb8e..a6654ffb 100644 --- a/ref_read.h +++ b/ref_read.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/reference.cpp b/reference.cpp index 97a74ba4..38da72dd 100644 --- a/reference.cpp +++ b/reference.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/reference.h b/reference.h index 07b016b7..711cff30 100644 --- a/reference.h +++ b/reference.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/sam.cpp b/sam.cpp index 549e0a2e..ac6e69c2 100644 --- a/sam.cpp +++ b/sam.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/sam.h b/sam.h index 5dfce929..eb0ecfd1 100644 --- a/sam.h +++ b/sam.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/scoring.cpp b/scoring.cpp index 0f80338a..13488219 100644 --- a/scoring.cpp +++ b/scoring.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/scoring.h b/scoring.h index 7944ffcf..55f4893d 100644 --- a/scoring.h +++ b/scoring.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/scripts/convert_quals.pl b/scripts/convert_quals.pl index ba73439a..abf344b1 100755 --- a/scripts/convert_quals.pl +++ b/scripts/convert_quals.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/gen_2b_occ_lookup.pl b/scripts/gen_2b_occ_lookup.pl index c9303a26..a6e8ff59 100755 --- a/scripts/gen_2b_occ_lookup.pl +++ b/scripts/gen_2b_occ_lookup.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/gen_occ_lookup.pl b/scripts/gen_occ_lookup.pl index af6296f3..daba33f7 100755 --- a/scripts/gen_occ_lookup.pl +++ b/scripts/gen_occ_lookup.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/gen_solqual_lookup.pl b/scripts/gen_solqual_lookup.pl index 218d3642..a1d5cd14 100755 --- a/scripts/gen_solqual_lookup.pl +++ b/scripts/gen_solqual_lookup.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/infer_fraglen.pl b/scripts/infer_fraglen.pl index 535e84e7..65ebe86c 100644 --- a/scripts/infer_fraglen.pl +++ b/scripts/infer_fraglen.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/AlignmentCheck.pm b/scripts/sim/AlignmentCheck.pm index ac727971..fb259c48 100644 --- a/scripts/sim/AlignmentCheck.pm +++ b/scripts/sim/AlignmentCheck.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/DNA.pm b/scripts/sim/DNA.pm index 91b2eab6..bf6b4e25 100644 --- a/scripts/sim/DNA.pm +++ b/scripts/sim/DNA.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/Mutate.pm b/scripts/sim/Mutate.pm index 00ed46dc..2157f73c 100644 --- a/scripts/sim/Mutate.pm +++ b/scripts/sim/Mutate.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/RandDNA.pm b/scripts/sim/RandDNA.pm index d93ca330..a924992d 100644 --- a/scripts/sim/RandDNA.pm +++ b/scripts/sim/RandDNA.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/SampleRead.pm b/scripts/sim/SampleRead.pm index 4a58a885..1defeed2 100644 --- a/scripts/sim/SampleRead.pm +++ b/scripts/sim/SampleRead.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/Sim.pm b/scripts/sim/Sim.pm index 21b5709d..458e8676 100644 --- a/scripts/sim/Sim.pm +++ b/scripts/sim/Sim.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/Test.pm b/scripts/sim/Test.pm index f3b1c1dc..82b37936 100644 --- a/scripts/sim/Test.pm +++ b/scripts/sim/Test.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/run.pl b/scripts/sim/run.pl index a75cb40d..02bf282a 100644 --- a/scripts/sim/run.pl +++ b/scripts/sim/run.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/run.sh b/scripts/sim/run.sh index da605558..6e6c2aeb 100644 --- a/scripts/sim/run.sh +++ b/scripts/sim/run.sh @@ -1,7 +1,7 @@ #!/bin/sh # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/sim/unit.sh b/scripts/sim/unit.sh index 6d359f98..f4fdcf83 100644 --- a/scripts/sim/unit.sh +++ b/scripts/sim/unit.sh @@ -1,7 +1,7 @@ #!/bin/sh # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/test/DNA.pm b/scripts/test/DNA.pm index bd185d38..06a6ec7c 100644 --- a/scripts/test/DNA.pm +++ b/scripts/test/DNA.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/test/Read.pm b/scripts/test/Read.pm index 0a602695..819a0778 100644 --- a/scripts/test/Read.pm +++ b/scripts/test/Read.pm @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/test/args.pl b/scripts/test/args.pl index 660c0537..15740f9d 100644 --- a/scripts/test/args.pl +++ b/scripts/test/args.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/test/simple_tests.pl b/scripts/test/simple_tests.pl index df8c657d..2bae3def 100644 --- a/scripts/test/simple_tests.pl +++ b/scripts/test/simple_tests.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl -w # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/scripts/test/simple_tests.sh b/scripts/test/simple_tests.sh index 9959ddf2..0ba1cb04 100644 --- a/scripts/test/simple_tests.sh +++ b/scripts/test/simple_tests.sh @@ -1,7 +1,7 @@ #!/bin/sh # -# Copyright 2011, Ben Langmead +# Copyright 2011, Ben Langmead # # This file is part of Bowtie 2. # diff --git a/search_globals.h b/search_globals.h index fbcbb1e7..bd2704fa 100644 --- a/search_globals.h +++ b/search_globals.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/sequence_io.h b/sequence_io.h index c1129d33..5a2cd6f3 100644 --- a/sequence_io.h +++ b/sequence_io.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/shmem.cpp b/shmem.cpp index 271baa1a..a4853e7c 100644 --- a/shmem.cpp +++ b/shmem.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/shmem.h b/shmem.h index 784861f6..374ee0c5 100644 --- a/shmem.h +++ b/shmem.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/simple_func.cpp b/simple_func.cpp index c1edd890..51df8fea 100644 --- a/simple_func.cpp +++ b/simple_func.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/simple_func.h b/simple_func.h index a69f0a3e..ca768693 100644 --- a/simple_func.h +++ b/simple_func.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/spinlock.h b/spinlock.h index f99b7fa2..eedf8e0b 100644 --- a/spinlock.h +++ b/spinlock.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/sse_util.cpp b/sse_util.cpp index 7e1aa824..d6310cf7 100644 --- a/sse_util.cpp +++ b/sse_util.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/sse_util.h b/sse_util.h index 8f98b3fb..c0174497 100644 --- a/sse_util.h +++ b/sse_util.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/sstring.cpp b/sstring.cpp index 7b461c19..3b265878 100644 --- a/sstring.cpp +++ b/sstring.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/sstring.h b/sstring.h index ac16adf8..c06bbc60 100644 --- a/sstring.h +++ b/sstring.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/str_util.h b/str_util.h index 5547aaf1..48dae171 100644 --- a/str_util.h +++ b/str_util.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/threading.h b/threading.h index ce6693b4..8890b75a 100644 --- a/threading.h +++ b/threading.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/timer.h b/timer.h index 25242aa2..b8a10977 100644 --- a/timer.h +++ b/timer.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/tokenize.h b/tokenize.h index b597a298..aba28a86 100644 --- a/tokenize.h +++ b/tokenize.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/unique.cpp b/unique.cpp index 07dbe1e2..c4704736 100644 --- a/unique.cpp +++ b/unique.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/unique.h b/unique.h index 88343834..7fccc565 100644 --- a/unique.h +++ b/unique.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/util.h b/util.h index 3b947ec1..b13a0b68 100644 --- a/util.h +++ b/util.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/word_io.h b/word_io.h index 681fb304..345073a5 100644 --- a/word_io.h +++ b/word_io.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. * diff --git a/zbox.h b/zbox.h index 58420871..63de7845 100644 --- a/zbox.h +++ b/zbox.h @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead + * Copyright 2011, Ben Langmead * * This file is part of Bowtie 2. *