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1 parent fafeef9 commit 03fbda3906dcb734cad43ae29f06d9779e4cd2f7 langmead committed Dec 18, 2012
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Showing with 144 additions and 144 deletions.
  1. +1 −1 Makefile
  2. +1 −1 aligner_bt.cpp
  3. +1 −1 aligner_bt.h
  4. +1 −1 aligner_cache.cpp
  5. +1 −1 aligner_cache.h
  6. +1 −1 aligner_driver.cpp
  7. +1 −1 aligner_driver.h
  8. +1 −1 aligner_metrics.h
  9. +1 −1 aligner_report.h
  10. +1 −1 aligner_result.cpp
  11. +1 −1 aligner_result.h
  12. +1 −1 aligner_seed.cpp
  13. +1 −1 aligner_seed.h
  14. +1 −1 aligner_seed2.cpp
  15. +1 −1 aligner_seed2.h
  16. +1 −1 aligner_seed_policy.cpp
  17. +1 −1 aligner_seed_policy.h
  18. +1 −1 aligner_sw.cpp
  19. +1 −1 aligner_sw.h
  20. +1 −1 aligner_sw_common.h
  21. +1 −1 aligner_sw_driver.cpp
  22. +1 −1 aligner_sw_driver.h
  23. +1 −1 aligner_sw_nuc.h
  24. +1 −1 aligner_swsse.cpp
  25. +1 −1 aligner_swsse.h
  26. +1 −1 aligner_swsse_ee_i16.cpp
  27. +1 −1 aligner_swsse_ee_u8.cpp
  28. +1 −1 aligner_swsse_loc_i16.cpp
  29. +1 −1 aligner_swsse_loc_u8.cpp
  30. +1 −1 aln_sink.cpp
  31. +1 −1 aln_sink.h
  32. +1 −1 alphabet.cpp
  33. +1 −1 alphabet.h
  34. +1 −1 assert_helpers.h
  35. +1 −1 banded.cpp
  36. +1 −1 banded.h
  37. +1 −1 binary_sa_search.h
  38. +1 −1 bitpack.h
  39. +1 −1 blockwise_sa.h
  40. +1 −1 bowtie2
  41. +1 −1 bowtie_build_main.cpp
  42. +1 −1 bowtie_main.cpp
  43. +1 −1 bt2_build.cpp
  44. +1 −1 bt2_idx.cpp
  45. +1 −1 bt2_idx.h
  46. +1 −1 bt2_inspect.cpp
  47. +1 −1 bt2_io.cpp
  48. +1 −1 bt2_search.cpp
  49. +1 −1 bt2_util.cpp
  50. +1 −1 ccnt_lut.cpp
  51. +1 −1 diff_sample.cpp
  52. +1 −1 diff_sample.h
  53. +1 −1 doc/website/index.shtml
  54. +1 −1 dp_framer.cpp
  55. +1 −1 dp_framer.h
  56. +1 −1 ds.cpp
  57. +1 −1 ds.h
  58. +1 −1 edit.cpp
  59. +1 −1 edit.h
  60. +1 −1 endian_swap.h
  61. +1 −1 example/reads/simulate.pl
  62. +1 −1 filebuf.h
  63. +1 −1 formats.h
  64. +1 −1 group_walk.cpp
  65. +1 −1 group_walk.h
  66. +1 −1 ival_list.cpp
  67. +1 −1 ival_list.h
  68. +1 −1 limit.cpp
  69. +1 −1 limit.h
  70. +1 −1 ls.cpp
  71. +1 −1 ls.h
  72. +1 −1 mask.cpp
  73. +1 −1 mask.h
  74. +1 −1 mem_ids.h
  75. +1 −1 mm.h
  76. +1 −1 multikey_qsort.cpp
  77. +1 −1 multikey_qsort.h
  78. +1 −1 opts.h
  79. +1 −1 outq.cpp
  80. +1 −1 outq.h
  81. +1 −1 pat.cpp
  82. +1 −1 pat.h
  83. +1 −1 pe.cpp
  84. +1 −1 pe.h
  85. +1 −1 presets.cpp
  86. +1 −1 presets.h
  87. +1 −1 qual.cpp
  88. +1 −1 qual.h
  89. +1 −1 random_source.cpp
  90. +1 −1 random_source.h
  91. +1 −1 random_util.cpp
  92. +1 −1 random_util.h
  93. +1 −1 read.h
  94. +1 −1 read_qseq.cpp
  95. +1 −1 ref_coord.cpp
  96. +1 −1 ref_coord.h
  97. +1 −1 ref_read.cpp
  98. +1 −1 ref_read.h
  99. +1 −1 reference.cpp
  100. +1 −1 reference.h
  101. +1 −1 sam.cpp
  102. +1 −1 sam.h
  103. +1 −1 scoring.cpp
  104. +1 −1 scoring.h
  105. +1 −1 scripts/convert_quals.pl
  106. +1 −1 scripts/gen_2b_occ_lookup.pl
  107. +1 −1 scripts/gen_occ_lookup.pl
  108. +1 −1 scripts/gen_solqual_lookup.pl
  109. +1 −1 scripts/infer_fraglen.pl
  110. +1 −1 scripts/sim/AlignmentCheck.pm
  111. +1 −1 scripts/sim/DNA.pm
  112. +1 −1 scripts/sim/Mutate.pm
  113. +1 −1 scripts/sim/RandDNA.pm
  114. +1 −1 scripts/sim/SampleRead.pm
  115. +1 −1 scripts/sim/Sim.pm
  116. +1 −1 scripts/sim/Test.pm
  117. +1 −1 scripts/sim/run.pl
  118. +1 −1 scripts/sim/run.sh
  119. +1 −1 scripts/sim/unit.sh
  120. +1 −1 scripts/test/DNA.pm
  121. +1 −1 scripts/test/Read.pm
  122. +1 −1 scripts/test/args.pl
  123. +1 −1 scripts/test/simple_tests.pl
  124. +1 −1 scripts/test/simple_tests.sh
  125. +1 −1 search_globals.h
  126. +1 −1 sequence_io.h
  127. +1 −1 shmem.cpp
  128. +1 −1 shmem.h
  129. +1 −1 simple_func.cpp
  130. +1 −1 simple_func.h
  131. +1 −1 spinlock.h
  132. +1 −1 sse_util.cpp
  133. +1 −1 sse_util.h
  134. +1 −1 sstring.cpp
  135. +1 −1 sstring.h
  136. +1 −1 str_util.h
  137. +1 −1 threading.h
  138. +1 −1 timer.h
  139. +1 −1 tokenize.h
  140. +1 −1 unique.cpp
  141. +1 −1 unique.h
  142. +1 −1 util.h
  143. +1 −1 word_io.h
  144. +1 −1 zbox.h
View
2 Makefile
@@ -1,5 +1,5 @@
#
-# Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
View
2 aligner_bt.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_bt.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_cache.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_cache.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_driver.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2012, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2012, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_driver.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2012, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2012, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_metrics.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_report.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_result.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_result.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_seed.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_seed.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_seed2.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_seed2.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_seed_policy.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_seed_policy.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_sw.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_sw.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_sw_common.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_sw_driver.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_sw_driver.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_sw_nuc.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_swsse.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_swsse.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_swsse_ee_i16.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_swsse_ee_u8.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_swsse_loc_i16.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aligner_swsse_loc_u8.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aln_sink.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 aln_sink.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 alphabet.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 alphabet.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 assert_helpers.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 banded.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 banded.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 binary_sa_search.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bitpack.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 blockwise_sa.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bowtie2
@@ -1,7 +1,7 @@
#!/usr/bin/env perl
#
-# Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
View
2 bowtie_build_main.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bowtie_main.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bt2_build.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bt2_idx.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bt2_idx.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bt2_inspect.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bt2_io.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bt2_search.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 bt2_util.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 ccnt_lut.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 diff_sample.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 diff_sample.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 doc/website/index.shtml
@@ -36,7 +36,7 @@ gapped, local, and paired-end alignment modes.
<table width="100%"><tr><td>
This research was supported in part by NIH grants R01-HG006102 and R01-GM083873 and AWS in Education research grants.
</td><td align="right">
- Administrator: <a href="mailto:blangmea@jhsph.edu">Ben Langmead</a>. Design by <a href="http://www.free-css-templates.com" title="Design by David Herreman">David Herreman</a>
+ Administrator: <a href="mailto:langmea@cs.jhu.edu">Ben Langmead</a>. Design by <a href="http://www.free-css-templates.com" title="Design by David Herreman">David Herreman</a>
</td></tr>
</table>
<div style="text-align:center">
View
2 dp_framer.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 dp_framer.h
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
View
2 ds.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
+ * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
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