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+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+------------------------------------------------------------------------
+r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.9rc1-2 (r1605)
+ * fixed a typo/bug in bwasw
+
+------------------------------------------------------------------------
+r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+
+a typo in the manual
+
+------------------------------------------------------------------------
+r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/utils.c
+   M /branches/prog/bwa/utils.h
+
+ * bwa-0.5.9rc1-1 (r1586)
+ * a few patches by John
+
+------------------------------------------------------------------------
+r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+
+documentation on specifying @RG
+
+------------------------------------------------------------------------
+r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.9rc1 (r1561)
+
+------------------------------------------------------------------------
+r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwaseqio.c
+   M /branches/prog/bwa/main.c
+
+ * fixed a small memory leak caused by the BAM reader
+ * fixed a memory violation, also in the BAM reader
+
+------------------------------------------------------------------------
+r1559 | lh3 | 2010-12-10 00:10:48 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/Makefile
+
+change Makefile gcc options
+
+------------------------------------------------------------------------
+r1558 | lh3 | 2010-12-10 00:09:22 -0500 (Fri, 10 Dec 2010) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.8-6 (r1557)
+ * added a little more comments to BWA-SW
+ * randomly choosing a mapping if there are more than one
+
+------------------------------------------------------------------------
+r1557 | lh3 | 2010-12-09 21:58:00 -0500 (Thu, 09 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+   M /branches/prog/bwa/bwtsw2_aux.c
+
+sometimes unmapped reads may not be printed...
+
+------------------------------------------------------------------------
+r1556 | lh3 | 2010-12-09 21:50:26 -0500 (Thu, 09 Dec 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+   M /branches/prog/bwa/bwtsw2_aux.c
+
+print unmapped reads
+
+------------------------------------------------------------------------
+r1555 | lh3 | 2010-12-09 21:17:20 -0500 (Thu, 09 Dec 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.8-5 (r1555)
+ * BAM input documentation
+
+------------------------------------------------------------------------
+r1544 | lh3 | 2010-11-23 11:01:41 -0500 (Tue, 23 Nov 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.8-4 (r1544)
+ * supporting adding RG tags and RG lines
+
+------------------------------------------------------------------------
+r1543 | lh3 | 2010-11-23 00:16:40 -0500 (Tue, 23 Nov 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.8-3 (r1543)
+ * fixed a memory leak
+
+------------------------------------------------------------------------
+r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.8-2 (r1542)
+ * fixed a long existing bug in random placement of reads
+
+------------------------------------------------------------------------
+r1541 | lh3 | 2010-11-22 23:27:29 -0500 (Mon, 22 Nov 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+   A /branches/prog/bwa/bamlite.c
+   A /branches/prog/bwa/bamlite.h
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwaseqio.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+
+preliminary BAM input support
+
+------------------------------------------------------------------------
+r1537 | lh3 | 2010-10-16 23:46:20 -0400 (Sat, 16 Oct 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/bwa.1
+
+change version number and ChangeLog
+
+------------------------------------------------------------------------
+r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.c
+
+ * fixed a bug in the scoring matrix
+ * release bwa-0.5.8c (r1536)
+
+------------------------------------------------------------------------
+r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+
+version change
+
+------------------------------------------------------------------------
+r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.c
+
+ * bwa-0.5.8b (r1450)
+ * fixed a bug in scoring matrix
+
+------------------------------------------------------------------------
+r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwape.c
+
+fixed a serious bug
+
+------------------------------------------------------------------------
+r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.8 (r1442)
+
+------------------------------------------------------------------------
+r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-r1440
+ * sorry, forget to remove a debugging line
+
+------------------------------------------------------------------------
+r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-r1439
+ * fixed a bug in bwasw caused by a recent modification
+ * throwing insane insert size when estimating isize
+
+------------------------------------------------------------------------
+r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.7-7 (r1425)
+ * fixed a minor bug in bwasw command-line parsing
+ * When band-width is not large enough, bwasw may find two highly
+   overlapping but not completely overlapping alignments. The old
+   version will filter out one of them, which leads to false
+   negatives. The current outputs both. This solution is obviously not
+   ideal. The ideal one would be to increase the band-width and redo the
+   alignment.
+
+
+------------------------------------------------------------------------
+r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.7-6 (r1399)
+ * fixed a typo/bug (by Vaughn Iverson)
+
+------------------------------------------------------------------------
+r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+small correction
+
+------------------------------------------------------------------------
+r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.7-4 (r1328)
+ * automatically adjust ap_prior based on alignment
+
+------------------------------------------------------------------------
+r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.c
+   M /branches/prog/bwa/stdaln.h
+
+ * bwa-0.5.7-3 (r1327)
+ * evaluate hits obtained from SW alignment in a more proper way.
+
+------------------------------------------------------------------------
+r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+
+fixed a potential out-of-boundary error. Need more testing.
+
+------------------------------------------------------------------------
+r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+
+insert size is `weird' if the 3rd quatile larger than 100,000bp
+
+------------------------------------------------------------------------
+r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.7-2 (r1318)
+ * in sampe, allow to disable insert size estimate
+
+------------------------------------------------------------------------
+r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/solid2fastq.pl
+
+ * bwa-0.5.7-1 (r1317)
+ * fixed a potential bug in solid2fastq.pl
+ * fixed a bug in calculating mapping quality (by Rodrigo Goya)
+ * fixed a very rare bug (if ever occur) about pairing
+
+------------------------------------------------------------------------
+r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.7
+
+------------------------------------------------------------------------
+r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.6-2 (r1309)
+ * fixed an unfixed bug (by Carol Scott)
+ * fixed some tiny formatting
+
+------------------------------------------------------------------------
+r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.6-1 (r1304)
+ * optionally write output to a file (by Tim Fennel)
+
+------------------------------------------------------------------------
+r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.6
+
+------------------------------------------------------------------------
+r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.5-10 (r1302)
+ * improve max insert size estimate (method suggested by Gerton Lunter)
+
+------------------------------------------------------------------------
+r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.5-9 (r1301)
+ * improve mapping quality calculation for abnomalous pairs
+ * fixed a bug in multiple hits
+ * SOLiD multiple hits should work now
+
+------------------------------------------------------------------------
+r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.5-8 (r1300)
+ * output kurtosis
+
+------------------------------------------------------------------------
+r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.5-7 (r1299)
+ * calculate skewness in sampe
+ * increase min_len in SW to 20
+ * perform more SW to fix discordant pairs
+
+------------------------------------------------------------------------
+r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/cs2nt.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.h
+
+ * bwa-0.5.5-6 (r1297)
+ * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya)
+
+------------------------------------------------------------------------
+r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/solid2fastq.pl
+
+the old fix seems not working!
+
+------------------------------------------------------------------------
+r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.5-5 (r1296)
+ * fixed a minor issue that the lower bound of insert size is not correctly set.
+
+------------------------------------------------------------------------
+r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwaseqio.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.5-4 (r1295)
+ * fixed a memory leak
+ * change the behaviour of -n (samse and sampe)
+ * change the default of -n
+
+------------------------------------------------------------------------
+r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwaseqio.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.5-3 (r1294)
+ * improved multi-hit report
+
+------------------------------------------------------------------------
+r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/cs2nt.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/solid2fastq.pl
+
+ * bwa-0.5.5-2 (r1293)
+ * bugfix: truncated quality string
+ * bugfix: quality -1 in solid->fastq conversion
+ * bugfix: color reads on the reverse strand is not complemented
+
+------------------------------------------------------------------------
+r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bntseq.c
+   M /branches/prog/bwa/bntseq.h
+   M /branches/prog/bwa/bwase.c
+   A /branches/prog/bwa/bwase.h
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.5-1 (r1279)
+ * incorporate changes from Matt Hanna for Java bindings.
+
+------------------------------------------------------------------------
+r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+
+update ChangeLog
+
+------------------------------------------------------------------------
+r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/main.c
+   A /branches/prog/bwa/qualfa2fq.pl
+
+Release bwa-0.5.5 (r1273)
+
+------------------------------------------------------------------------
+r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.4-3 (r1272)
+ * fixed another typo which may lead to incorrect single-end mapping quality
+
+------------------------------------------------------------------------
+r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.4-2 (r1271)
+ * fixed a serious typo/bug which does not hurt if we allow one gap open
+   and work with <200bp reads, but causes segfault for long reads.
+
+------------------------------------------------------------------------
+r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/cs2nt.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.4-1 (r1270)
+ * fixed a bug in color alignment
+
+------------------------------------------------------------------------
+r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwaseqio.c
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.4
+
+------------------------------------------------------------------------
+r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwaseqio.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.c
+
+ * bwa-0.5.3-4 (r1244)
+ * output the clipped length in XC:i: tag
+ * skip mate alignment when stdaln is buggy
+ * fixed a bug in NM:i: tag
+
+------------------------------------------------------------------------
+r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.3-3 (r1243)
+ * sampe: fixed a bug when a read sequence is identical its reverse complement.
+
+------------------------------------------------------------------------
+r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bntseq.c
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.3-2 (r1242)
+ * sampe: optionall preload the full index into memory
+ * aln: change the default seed length to 32bp
+
+------------------------------------------------------------------------
+r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/khash.h
+
+Improve portability of khash.h
+
+------------------------------------------------------------------------
+r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/main.c
+
+fixed a typo
+
+------------------------------------------------------------------------
+r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.3-1 (r1226)
+ * in dBWT-SW, optionall use hard clipping instead of soft clipping
+
+------------------------------------------------------------------------
+r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.3 (r1225)
+
+------------------------------------------------------------------------
+r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.2
+
+------------------------------------------------------------------------
+r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.1-5 (r1222)
+ * fixed a typo. No real change
+
+------------------------------------------------------------------------
+r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwaseqio.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.1-4 (r1221)
+ * trim reads before alignment
+
+------------------------------------------------------------------------
+r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.1-3 (r1216)
+ * fixed a bug about NM tags for gapped alignment
+ * print SAM header
+
+------------------------------------------------------------------------
+r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.1-2 (r1215)
+ * fixed a bug when read lengths vary (by John Marshall)
+
+------------------------------------------------------------------------
+r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.1-1 (r1213)
+ * change default -T to 30
+
+------------------------------------------------------------------------
+r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.1
+
+------------------------------------------------------------------------
+r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+
+ * ChangeLog
+
+------------------------------------------------------------------------
+r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.0-6 (r1206)
+ * fixed two bugs caused by previous modification
+
+------------------------------------------------------------------------
+r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.0-4 (r1205)
+ * reduce false coordinates and CIGAR when a query bridges two reference
+   sequences, although some very rare cases may fail bwa.
+
+------------------------------------------------------------------------
+r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.0-3 (r1204)
+ * choose one repetitive hit to extend
+
+------------------------------------------------------------------------
+r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.0-2 (r1203)
+ * dBWT-SW: change a parameter in calculating mapping quality
+ * fixed a bug in samse
+
+------------------------------------------------------------------------
+r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.5.0-1 (r1202)
+ * change default band width to 50
+ * improve mapping quality a bit
+
+------------------------------------------------------------------------
+r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.5.0 (r1200)
+
+------------------------------------------------------------------------
+r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/bwa.1
+
+Updated ChangeLog and the manual
+
+------------------------------------------------------------------------
+r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-36 (r1198)
+ * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse.
+
+------------------------------------------------------------------------
+r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+   M /branches/prog/bwa/bwtsw2_aux.c
+   A /branches/prog/bwa/bwtsw2_chain.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-35 (r1197)
+ * further heuristic acceleration for long queries
+
+------------------------------------------------------------------------
+r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-34 (r1196)
+ * updated the manual page
+ * output base quality if the input is fastq
+
+------------------------------------------------------------------------
+r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/simple_dp.c
+
+ * bwa-0.4.9-33 (r1191)
+ * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment
+ * in dbwtsw adjust -T and -c according to -a
+
+------------------------------------------------------------------------
+r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+
+update manual
+
+------------------------------------------------------------------------
+r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwtsw2_main.c
+
+update documentation
+
+------------------------------------------------------------------------
+r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-32 (r1190)
+ * only help messages are changed
+
+------------------------------------------------------------------------
+r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-31 (r1189)
+ * in bwape/bwase, print CIGAR "*" if the read is unmapped
+ * improved the calculation of mapping quality
+
+------------------------------------------------------------------------
+r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+
+fflush()
+
+------------------------------------------------------------------------
+r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-30 (r1180)
+ * fixed a memory problem
+ * multi-threading sometimes does not work...
+
+------------------------------------------------------------------------
+r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-29 (r1179)
+ * preliminary mutli-threading support in dbwtsw
+
+------------------------------------------------------------------------
+r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-28 (r1178)
+ * fixed a bug in printing repetitive hits
+
+------------------------------------------------------------------------
+r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-27 (r1177)
+ * bwtsw2: fixed a hidden memory leak
+
+------------------------------------------------------------------------
+r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-26
+ * change the way mapping quality is calculated
+
+------------------------------------------------------------------------
+r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-25
+ * code clean up
+ * automatically adjust ->t and ->is_rev based on input
+
+------------------------------------------------------------------------
+r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-24
+ * fixed a bug in printing the hits
+
+------------------------------------------------------------------------
+r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-23
+ * allow to skip reverse alignment
+ * increase opt->t to 37
+
+------------------------------------------------------------------------
+r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-22
+ * report if the hit is found in both directions
+
+------------------------------------------------------------------------
+r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-21
+ * dbwtsw: map to both forward and reverse BWT to reduce false alignment
+
+------------------------------------------------------------------------
+r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+save hits before cut_tail()
+
+------------------------------------------------------------------------
+r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.c
+   M /branches/prog/bwa/stdaln.h
+
+ * bwa-0.4.9-19
+ * use a global memory pool to reduce the CPU time spent on malloc/free().
+
+------------------------------------------------------------------------
+r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-18
+ * reduce unnecessary extension to the 5'-end
+ * allow to use different interval size for the 2 rounds
+ * change default parameters
+
+------------------------------------------------------------------------
+r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-17
+ * dbwtsw: fixed THE memory leak.
+
+------------------------------------------------------------------------
+r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.c
+
+ * bwa-0.4.9-16
+ * fixed a memory leak
+ * a small memory leak still occurs to bwtsw2_core(). I will work on that later.
+ * changed the default parameters
+
+------------------------------------------------------------------------
+r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.c
+
+ * bwa-0.4.9-15
+ * generate CIGAR right before output. This saves unnecessary computation.
+ * this version may be buggy as I have not tested it.
+
+------------------------------------------------------------------------
+r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/stdaln.c
+   M /branches/prog/bwa/stdaln.h
+
+ * bwa-0.4.9-14
+
+ * deplete unique hits in dbwtsw and postprocess them with standard sw
+
+ * in principle, this stratgy should be faster and more accurate, but I
+   have not tested this point. I may switch back to the old method if
+   this does not work.
+
+ * the code looks quite nasty now. it needs clean up...
+
+
+------------------------------------------------------------------------
+r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+
+change a default parameter
+
+------------------------------------------------------------------------
+r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-13
+ * dbwtsw: switch between small and large Z-best
+
+------------------------------------------------------------------------
+r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-12
+ * changed the default -z to 100
+ * heuristically speed up alignments for polyA reads
+
+------------------------------------------------------------------------
+r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-11
+
+ * dbwtsw potentially generates less false alignments, although in
+   practice, the modification brings no improvement.
+
+
+------------------------------------------------------------------------
+r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-10
+ * disabled debugging code
+ * add "BAM_FMU" if both ends are unmapped
+
+------------------------------------------------------------------------
+r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/main.c
+
+nothing, really
+
+------------------------------------------------------------------------
+r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-9
+ * bwtsw2: generate SAM output
+
+------------------------------------------------------------------------
+r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-8
+
+ * fixed a weird deadloop which only happens to icc -O3. Thanks John
+   Marshall for the fix.
+
+
+------------------------------------------------------------------------
+r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-7
+
+ * fixed a typo in bwtsw2 alignment. Now score from the standard SW
+   seems to agree with score from bwtsw2, except that in reporting
+   alignments, bwtsw2 may report non-optimal segments. This is expected,
+   though. I will improve in future.
+
+
+------------------------------------------------------------------------
+r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/stdaln.c
+   M /branches/prog/bwa/stdaln.h
+
+ * aln_left_core() seems to work properly
+ * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!!
+
+------------------------------------------------------------------------
+r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/stdaln.c
+
+removed debugging code...
+
+------------------------------------------------------------------------
+r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/stdaln.c
+
+ * radical changes failed...
+ * fixed a bug
+
+------------------------------------------------------------------------
+r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/stdaln.c
+
+temporary changes. Will apply some radical changes to this file...
+
+------------------------------------------------------------------------
+r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/stdaln.c
+
+fixed a long-existing bug in Smith-Waterman alignment
+
+------------------------------------------------------------------------
+r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/simple_dp.c
+   M /branches/prog/bwa/stdaln.c
+   M /branches/prog/bwa/stdaln.h
+
+ * bwa-0.4.9-6
+ * unexplained inconsistency still occurs, but the results largely look reasonable.
+
+------------------------------------------------------------------------
+r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/stdaln.c
+
+half DP
+
+------------------------------------------------------------------------
+r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/bwtsw2_main.c
+
+a bit code clean up
+
+------------------------------------------------------------------------
+r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-5
+ * fixed a bug in determining sub-optimal hits
+ * removed some debugging codes
+
+------------------------------------------------------------------------
+r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-4
+ * better cmd interface
+ * faster speed
+
+------------------------------------------------------------------------
+r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2.h
+   M /branches/prog/bwa/bwtsw2_aux.c
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+
+bwtsw2 (dBWT-SW) is working apparently...
+
+
+------------------------------------------------------------------------
+r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwtsw2_core.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.9-2
+ * bwtsw2: change cut_tail() such that it is faster but more likely to
+   miss true hits
+
+------------------------------------------------------------------------
+r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+   A /branches/prog/bwa/bwt_lite.c
+   A /branches/prog/bwa/bwt_lite.h
+   A /branches/prog/bwa/bwtsw2.h
+   A /branches/prog/bwa/bwtsw2_aux.c
+   A /branches/prog/bwa/bwtsw2_core.c
+   A /branches/prog/bwa/bwtsw2_main.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/main.h
+
+ * bwa-0.4.9-1
+ * added back bwtsw2
+
+------------------------------------------------------------------------
+r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.4.9
+
+------------------------------------------------------------------------
+r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.4.8
+
+------------------------------------------------------------------------
+r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.7-2
+ * change the default of "aln -R" to 30
+
+------------------------------------------------------------------------
+r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/bwtgap.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.7-1
+ * search for suboptimal hits if the top hit is not so repetitive
+
+------------------------------------------------------------------------
+r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.4.7
+
+------------------------------------------------------------------------
+r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.6-9
+ * fixed compiling errors on some Linux machines
+
+------------------------------------------------------------------------
+r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtaln.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.6-8
+ * avoid compilation error on some systems.
+
+------------------------------------------------------------------------
+r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.6-7
+ * fixed an integer overflow caused by previous modifications
+ * made insert size estimation more robust
+
+------------------------------------------------------------------------
+r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.6-5
+ * fixed a integer overflow problem which may cause seg fault in very rare cases
+ * made XN tags more accurate
+
+------------------------------------------------------------------------
+r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/simple_dp.c
+   M /branches/prog/bwa/stdaln.c
+   M /branches/prog/bwa/stdaln.h
+
+ * bwa-0.4.6-4
+ * heuristic rules to detect suboptimal alignment
+ * stdsw: support double-strand and protein alignment
+
+------------------------------------------------------------------------
+r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/simple_dp.c
+   M /branches/prog/bwa/stdaln.c
+   M /branches/prog/bwa/stdaln.h
+
+ * bwa-0.4.6-2
+ * improve the functionality of stdsw
+ * allow to add a threshold on SW alignment. Hope this does not incur new bugs...
+
+------------------------------------------------------------------------
+r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.6-1
+ * output SM and AM tag
+
+------------------------------------------------------------------------
+r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/NEWS
+   M /branches/prog/bwa/main.c
+
+Release bwa-0.4.6
+
+------------------------------------------------------------------------
+r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwa.1
+   M /branches/prog/bwa/bwape.c
+   A /branches/prog/bwa/solid2fastq.pl
+
+ * added notes to bwa
+ * added a script to convert SOLiD reads
+ * updated documentations
+
+------------------------------------------------------------------------
+r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/ChangeLog
+   M /branches/prog/bwa/kstring.c
+   M /branches/prog/bwa/main.c
+
+fixed a bug in kstring
+
+------------------------------------------------------------------------
+r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwtmisc.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.5-7
+ * fixed a bug in pac2cspac
+
+------------------------------------------------------------------------
+r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+
+disable debugging
+
+------------------------------------------------------------------------
+r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/cs2nt.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.5-6
+ * fixed problems with coordinates for color gapped alignment
+
+------------------------------------------------------------------------
+r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/cs2nt.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.5-5
+ * added support for gapped color alignment
+
+------------------------------------------------------------------------
+r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwase.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/cs2nt.c
+   M /branches/prog/bwa/main.c
+
+ * convert cs read to nt read (for ungapped alignment only)
+
+------------------------------------------------------------------------
+r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines
+Changed paths:
+   M /branches/prog/bwa/Makefile
+   M /branches/prog/bwa/bwase.c
+   A /branches/prog/bwa/cs2nt.c
+
+prepare to implement cs->nt conversion (have not yet...)
+
+------------------------------------------------------------------------
+r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bntseq.c
+   M /branches/prog/bwa/bntseq.h
+   M /branches/prog/bwa/bwtindex.c
+   M /branches/prog/bwa/bwtmisc.c
+   M /branches/prog/bwa/main.c
+   M /branches/prog/bwa/main.h
+
+ * bwa-0.4.5-3
+ * generate color index from nucleotide fasta reference
+
+------------------------------------------------------------------------
+r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/main.c
+
+ * bwa-0.4.5-2
+ * improved mapping quality a bit if one end falls in a tandem repeat
+   but the mate is unique.
+
+------------------------------------------------------------------------
+r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines
+Changed paths:
+   M /branches/prog/bwa/bwape.c
+   M /branches/prog/bwa/bwtaln.h
+   M /branches/prog/bwa/main.c