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r37 | martin | 2008-12-24 15:08:00 +0900 (Wed, 24 Dec 2008) | 2 lines

Updated the documentation, including a table of optimal spaced seeds.

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r36 | martin | 2008-12-22 20:47:12 +0900 (Mon, 22 Dec 2008) | 2 lines

Made lastdb bucket-making code slightly simpler & faster.

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r35 | martin | 2008-12-22 16:11:32 +0900 (Mon, 22 Dec 2008) | 8 lines

Enabled reading & writing of huge files (at least on one system with
Linux-2.6.13/x86_64/gcc-4.0.2).

Made lastdb radix sort a bit faster, with the oracle array trick.

Allowed the mismatch score to be zero, due to a request.


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r34 | martin | 2008-12-09 16:02:40 +0900 (Tue, 09 Dec 2008) | 2 lines

Made gapped extension faster for short sequences (e.g. tag mapping).

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r33 | martin | 2008-12-08 20:42:07 +0900 (Mon, 08 Dec 2008) | 3 lines

Bugfix: the sequence names weren't printed correctly for
match-counting output (-j 0).

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r32 | martin | 2008-12-05 18:07:50 +0900 (Fri, 05 Dec 2008) | 2 lines

Fixed compiler warnings with gcc 4.3

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r31 | martin | 2008-11-06 09:02:28 +0900 (Thu, 06 Nov 2008) | 3 lines

Added "." after "svnversion" to support older versions of svn.
(Thanks: Nicolas Sierro)

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r30 | martin | 2008-11-04 18:50:21 +0900 (Tue, 04 Nov 2008) | 2 lines

Added unistd.h includes, for getopt, so it compiles more portably(?)

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r29 | martin | 2008-11-04 10:33:07 +0900 (Tue, 04 Nov 2008) | 2 lines

Refactor: replaced a magic number with a named constant (score matrix size).

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r28 | martin | 2008-11-01 16:06:03 +0900 (Sat, 01 Nov 2008) | 2 lines

Made last-dotplot.py work with older versions of Python (not tested).

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r27 | martin | 2008-10-31 18:08:41 +0900 (Fri, 31 Oct 2008) | 2 lines

Fixed the test script, which broke after moving HOXD70.

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r26 | martin | 2008-10-31 18:01:53 +0900 (Fri, 31 Oct 2008) | 2 lines

Added the examples directory.

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r25 | martin | 2008-10-29 15:59:28 +0900 (Wed, 29 Oct 2008) | 2 lines

Removed an obsolete comment.

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r24 | martin | 2008-10-29 15:56:52 +0900 (Wed, 29 Oct 2008) | 2 lines

Made lastal a bit faster, by using fewer bins in DiagonalTable.

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r23 | martin | 2008-10-25 21:16:09 +0900 (Sat, 25 Oct 2008) | 2 lines

Made the probability calculations slightly faster, by micro-optimization.

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r22 | martin | 2008-10-25 16:44:52 +0900 (Sat, 25 Oct 2008) | 6 lines

Made the probability calculations much faster, by using scaling
instead of log.

Added code to get expected counts of emissions and transitions, which
isn't used yet.

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r21 | martin | 2008-10-21 17:44:15 +0900 (Tue, 21 Oct 2008) | 4 lines

Changed how seeds for gapped alignments are derived from gapless
alignments, to prevent occasionally getting the same gapped alignment
more than once.

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r20 | martin | 2008-10-10 09:28:04 +0900 (Fri, 10 Oct 2008) | 3 lines

Removed malloc.h from nrutil.c, so it compiles on Mac OS X.
Small additions to the manual.

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r19 | martin | 2008-10-02 14:29:51 +0900 (Thu, 02 Oct 2008) | 2 lines

Added probabilistic & centroid alignment!

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r18 | martin | 2008-10-01 19:58:02 +0900 (Wed, 01 Oct 2008) | 2 lines

Made the MAF-reading scripts cope with an extra 'p' line (probabilities).

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r17 | martin | 2008-09-30 17:49:42 +0900 (Tue, 30 Sep 2008) | 2 lines

Minor comment changes.

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r16 | martin | 2008-09-30 17:38:13 +0900 (Tue, 30 Sep 2008) | 4 lines

!! Changed the lastal option letter for "output type" from -g to -j
(so that -g can be used for 'gamma' in gamma-centroid alignment).
Made the usage messages and documentation a bit nicer.

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r15 | martin | 2008-09-30 13:31:17 +0900 (Tue, 30 Sep 2008) | 2 lines

Made maf-swap.py work with Python 2.3.3.

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r14 | martin | 2008-09-18 11:42:08 +0900 (Thu, 18 Sep 2008) | 2 lines

Minor refactoring.

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r13 | martin | 2008-09-18 09:59:47 +0900 (Thu, 18 Sep 2008) | 3 lines

Refactor: templatized some XdropAligner functions.
This will be useful when probabilistic alignment gets added.

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r12 | martin | 2008-09-17 19:45:35 +0900 (Wed, 17 Sep 2008) | 2 lines

Refactored the conversion of gapped Xdrop extensions to alignments.

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r11 | martin | 2008-09-16 21:49:53 +0900 (Tue, 16 Sep 2008) | 2 lines

Added FAQ (just one entry so far).

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r10 | martin | 2008-09-16 18:20:11 +0900 (Tue, 16 Sep 2008) | 2 lines

Refactor: Made gapped alignments remember their seeds.

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r9 | martin | 2008-09-16 15:29:27 +0900 (Tue, 16 Sep 2008) | 2 lines

Added a minimal regression test.

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r8 | martin | 2008-09-11 15:42:18 +0900 (Thu, 11 Sep 2008) | 3 lines

Added some "#include"s so that it compiles on picky systems.  (Thanks:
Charles Plessy)

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r7 | martin | 2008-09-10 09:37:18 +0900 (Wed, 10 Sep 2008) | 2 lines

Added lastdbName to the header of the lastal output.

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r6 | martin | 2008-09-10 09:30:40 +0900 (Wed, 10 Sep 2008) | 2 lines

Added version to lastdb ".prj" file.

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r5 | martin | 2008-09-10 09:20:47 +0900 (Wed, 10 Sep 2008) | 2 lines

Tiny change to the header in lastal output.

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r4 | martin | 2008-09-09 19:00:59 +0900 (Tue, 09 Sep 2008) | 2 lines

Added Harada-san to credits.

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r3 | martin | 2008-09-08 17:06:55 +0900 (Mon, 08 Sep 2008) | 2 lines

Separated "make dist" from "make all".

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r2 | martin | 2008-09-08 17:00:46 +0900 (Mon, 08 Sep 2008) | 2 lines

Added Credits & Citation to last-manual.txt.

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r1 | martin | 2008-09-08 15:20:39 +0900 (Mon, 08 Sep 2008) | 2 lines

First commit!

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