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r58 | martin | 2009-06-14 19:20:30 +0900 (Sun, 14 Jun 2009) | 1 line

Made lastal able to use sequence quality scores!
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r57 | martin | 2009-06-14 16:29:11 +0900 (Sun, 14 Jun 2009) | 8 lines

Made gapped alignments more reproducible, by breaking ties when
sorting gapless alignments.  Now, the query batch size should really
have no effect on the results.

Rewrote the tag mapping document.

Minor code improvements.

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r56 | martin | 2009-06-08 15:20:23 +0900 (Mon, 08 Jun 2009) | 5 lines

Made lastal match-counting (-j 0) much faster, for short queries with
a large minimum-depth option (-l).

Refactor: neatened the setting of default option values for lastal.

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r55 | martin | 2009-06-07 17:53:18 +0900 (Sun, 07 Jun 2009) | 1 line

Minor code re-organization.
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r54 | martin | 2009-05-30 17:23:18 +0900 (Sat, 30 May 2009) | 5 lines

Bugfix: the lastdb volume size option (-s) wasn't always respected.
Made lastal not needlessly re-read a single-volume lastdb database.
Added a test (of database volumes & query batches).
Some minor refactoring.

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r53 | martin | 2009-05-27 15:40:19 +0900 (Wed, 27 May 2009) | 3 lines

Added a FAQ item.
Refactor: reduced parameter-passing in lastal.cc.

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r52 | martin | 2009-05-08 15:52:49 +0900 (Fri, 08 May 2009) | 3 lines

Added maf2html.py: converts MAF-format alignments to coloured HTML format.
Disguised the email address in last-manual.txt.

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r51 | martin | 2009-05-02 18:16:05 +0900 (Sat, 02 May 2009) | 3 lines

Made lastal gapped extension faster, by removing an assert (surprising).
Bugfix: made last-dotplot.py not crash on small sequences.

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r50 | martin | 2009-04-08 19:55:08 +0900 (Wed, 08 Apr 2009) | 1 line

Minor code cleaning: variable name, comments.
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r49 | martin | 2009-04-02 12:04:52 +0900 (Thu, 02 Apr 2009) | 3 lines

Updated examples/myalns.maf to reflect the new default score parameters.
Minor changes to last-manual.txt.

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r48 | martin | 2009-04-01 19:32:28 +0900 (Wed, 01 Apr 2009) | 1 line

Removed unnecessary robustness from maf-sort.sh, to avoid bugs in unix sort(!)
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r47 | martin | 2009-04-01 18:02:45 +0900 (Wed, 01 Apr 2009) | 8 lines

Added maf-join.py: joins pairwise alignments into multiple alignments!
Added example files to illustrate usage of maf-join.py.
Changed lastal default gap existence cost for DNA to 7.
Changed lastal default gapped score threshold for DNA to 40.
Added TiTv212 scoring matrix to examples.
maf-swap.py: Added -n option to move any sequence to the top.
Updated the documents.

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r46 | martin | 2009-03-31 17:53:41 +0900 (Tue, 31 Mar 2009) | 1 line

Made last-remove-dominated.py faster.
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r45 | martin | 2009-03-30 19:16:01 +0900 (Mon, 30 Mar 2009) | 4 lines

Added gaps to MAF probability lines: easier to parse.
Made maf-sort.sh more robust.
Improved the documents a bit.

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r44 | martin | 2009-03-18 18:37:15 +0900 (Wed, 18 Mar 2009) | 1 line

Allow suffixes K(ibibyte), M(ebibyte), and G(ibibyte) for sizes.
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r43 | martin | 2009-03-06 11:19:28 +0900 (Fri, 06 Mar 2009) | 1 line

Simplified the probability & centroid code.  (Thanks: Hamada-san)
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r42 | martin | 2009-03-03 19:35:53 +0900 (Tue, 03 Mar 2009) | 1 line

Bugfix: overflow error made lastal discard some gapped alignments.
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r41 | martin | 2009-02-28 18:22:53 +0900 (Sat, 28 Feb 2009) | 1 line

Allow lastal options to be set in the score-matrix file.
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r40 | martin | 2009-02-28 15:30:37 +0900 (Sat, 28 Feb 2009) | 1 line

Minor refactoring.
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r39 | martin | 2009-01-30 18:43:28 +0900 (Fri, 30 Jan 2009) | 3 lines

Bugfix: for protein alignments, tyrosine was forbidden in initial matches.
!! Old lastdb protein databases won't work properly: you need to re-run lastdb.

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r38 | martin | 2008-12-30 22:51:28 +0900 (Tue, 30 Dec 2008) | 1 line

Refactor: removed some namespace tedium from the code.
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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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