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r199 | martin | 2012-05-07 17:23:51 +0900 (Mon, 07 May 2012) | 1 line

Improved the makefile.
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r198 | martin | 2012-03-30 14:06:38 +0900 (Fri, 30 Mar 2012) | 1 line

Turned compile warnings off in the top makefile, on in the src makefile.
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r197 | martin | 2012-03-30 13:31:10 +0900 (Fri, 30 Mar 2012) | 1 line

Fixed compile error with clang++.
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r196 | martin | 2012-03-13 17:19:12 +0900 (Tue, 13 Mar 2012) | 1 line

Added automatic installation by "make install".
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r195 | martin | 2012-01-06 20:06:59 +0900 (Fri, 06 Jan 2012) | 1 line

Fully enabled fastq-versus-fastq alignment!
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r194 | martin | 2012-01-06 16:12:56 +0900 (Fri, 06 Jan 2012) | 1 line

Clarified something in the bisulfite doc.
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r193 | martin | 2011-12-20 17:27:40 +0900 (Tue, 20 Dec 2011) | 3 lines

Bisulfite doc: explained biased methylation estimates & how to avoid them.
Changed the bisulfite seeds to ones that work a bit better in some tests.

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r192 | martin | 2011-11-13 19:06:31 +0900 (Sun, 13 Nov 2011) | 7 lines

Switched to new gapped-alignment code: faster and simpler.

! The placement of frameshifts is different (probably better).

! Near ends of sequences: column ambiguity estimates (and thus
  gamma-centroid and LAMA alignments) are slightly different.

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r191 | martin | 2011-11-13 16:31:39 +0900 (Sun, 13 Nov 2011) | 1 line

Refactor: preparing to remove the old gapped-alignment code.
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r190 | martin | 2011-11-12 14:24:26 +0900 (Sat, 12 Nov 2011) | 1 line

Made the C++ more strictly correct and portable.  (Thanks: Fabien Campagne)
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r189 | martin | 2011-10-19 17:38:54 +0900 (Wed, 19 Oct 2011) | 1 line

Bugfix: lastal -j0 crashed with fastq input.  (Thanks: Fabien Campagne)
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r188 | martin | 2011-10-15 21:46:49 +0900 (Sat, 15 Oct 2011) | 1 line

Made lastdb faster in some cases, e.g. bisulfite alignment.
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r187 | martin | 2011-09-20 21:10:51 +0900 (Tue, 20 Sep 2011) | 1 line

Just fixed a comment that was wrong.
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r186 | martin | 2011-08-17 12:27:54 +0900 (Wed, 17 Aug 2011) | 1 line

Added comments explaining the new gapped X-drop algorithms in more detail.
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r185 | martin | 2011-08-15 12:25:12 +0900 (Mon, 15 Aug 2011) | 1 line

Added new gapped x-drop alignment code (not used yet).
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r184 | martin | 2011-08-03 20:25:44 +0900 (Wed, 03 Aug 2011) | 1 line

Added bisulfite doc, and a script that it refers to.
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r183 | martin | 2011-07-28 20:19:13 +0900 (Thu, 28 Jul 2011) | 1 line

Added bisulfite example files, and renamed score-matrix files.
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r182 | martin | 2011-07-28 19:05:34 +0900 (Thu, 28 Jul 2011) | 1 line

Fixed error in test output, in the previous commit.
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r181 | martin | 2011-07-28 19:00:38 +0900 (Thu, 28 Jul 2011) | 1 line

Added a test of probabilistic alignment with quality scores.
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r180 | martin | 2011-07-28 18:31:15 +0900 (Thu, 28 Jul 2011) | 1 line

Changed how last-pair-probs interprets read names to recognize paired reads.
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r179 | martin | 2011-07-15 20:56:47 +0900 (Fri, 15 Jul 2011) | 1 line

Just fixed a citation.
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r178 | martin | 2011-06-07 16:27:57 +0900 (Tue, 07 Jun 2011) | 1 line

Fixed lastex crashing on some systems.  (Thanks: Edward Wijaya)
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r177 | martin | 2011-06-03 20:35:26 +0900 (Fri, 03 Jun 2011) | 4 lines

! Changed column probabilities in lastal output, from numbers to ASCII codes.
! Changed some scripts to read the new format, but not the old.
Added documentation for probabilistic alignment.

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r176 | martin | 2011-05-30 07:07:50 +0900 (Mon, 30 May 2011) | 1 line

Fixed lastal slowness when self-comparing many short sequences.
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r175 | martin | 2011-05-25 19:42:57 +0900 (Wed, 25 May 2011) | 1 line

Fixed a compile error with some compilers.
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r174 | martin | 2011-05-25 14:52:56 +0900 (Wed, 25 May 2011) | 3 lines

Enabled probabilistic alignment with sequence quality data, and LAMA
(not documented yet).

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r173 | martin | 2011-05-19 18:24:11 +0900 (Thu, 19 May 2011) | 1 line

Made lastal's gapless extensions a bit faster.
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r172 | martin | 2011-05-19 15:20:25 +0900 (Thu, 19 May 2011) | 1 line

Write reference size in the lastal output header.
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r171 | martin | 2011-05-10 20:22:26 +0900 (Tue, 10 May 2011) | 4 lines

Added some clarifications to the docs.
Made the C++ compile more portably.  (Thanks: Andreas Tille)
Fixed alignment spacing in maf-convert HTML output, for some evil browsers.

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r170 | martin | 2011-04-20 14:26:16 +0900 (Wed, 20 Apr 2011) | 1 line

Enable lastal to read quality data written by lastdb (not useful yet).
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r169 | martin | 2011-04-20 11:51:28 +0900 (Wed, 20 Apr 2011) | 1 line

Enabled lastdb to read fastq data (not yet useful).
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r168 | martin | 2011-04-20 10:03:14 +0900 (Wed, 20 Apr 2011) | 1 line

Refactor: extracted an enum.
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r167 | martin | 2011-04-19 18:03:17 +0900 (Tue, 19 Apr 2011) | 1 line

Refactor: made the quality data mmap-able.
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r166 | martin | 2011-04-19 17:43:02 +0900 (Tue, 19 Apr 2011) | 1 line

Enable writing of qualities for both sequences in maf output.
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r165 | martin | 2011-04-19 16:58:33 +0900 (Tue, 19 Apr 2011) | 1 line

Minor code enhancements.
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r164 | martin | 2011-04-15 13:54:11 +0900 (Fri, 15 Apr 2011) | 9 lines

! Use more "gentle" substitution costs when masking lowercase letters.

Made fastq probabilities and scores depend on the background letter
frequencies of the score matrix.

Made alignment scores with quality data ignore the lastal -t option.

Made alignment scores for non-ACGT letters always ignore quality data.

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r163 | martin | 2011-04-14 17:41:38 +0900 (Thu, 14 Apr 2011) | 1 line

Added a test for sequence quality data in prb format.
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r162 | martin | 2011-03-29 10:47:12 +0900 (Tue, 29 Mar 2011) | 1 line

Added --rna option to last-pair-probs.
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r161 | martin | 2011-03-28 09:25:23 +0900 (Mon, 28 Mar 2011) | 1 line

!! Bugfix: the DNA-vs-protein gapped extension was losing some good alignments.
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r160 | martin | 2011-03-22 18:22:25 +0900 (Tue, 22 Mar 2011) | 3 lines

Made last-map-probs read its input just once, to avoid huge temp files.
Tried to clarify the last-map-probs document.

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r159 | martin | 2011-02-14 18:15:39 +0900 (Mon, 14 Feb 2011) | 4 lines

Added last-pair-probs script and document.
Allow "." in sequences (appears in some fastq files).
Made maf-sort more efficient.

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r158 | martin | 2011-02-08 10:37:42 +0900 (Tue, 08 Feb 2011) | 3 lines

Bugfix: maf-sort mangled alignment data containing "#".
Added maf-sort option to sort by sequences other than the top one.

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r157 | martin | 2011-01-31 17:47:52 +0900 (Mon, 31 Jan 2011) | 4 lines

Made the documentation for last-map-probs actually usable.
Bugfix: maf-convert was spuriously deleting seq quality codes in sam output.
Bugfix: lastal with PSSM input could find inferior gapped alignments.

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r156 | martin | 2011-01-20 08:53:10 +0900 (Thu, 20 Jan 2011) | 1 line

Bugfix: sam headers should be tab-delimited.
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r155 | martin | 2011-01-08 18:31:48 +0900 (Sat, 08 Jan 2011) | 1 line

Added sam header option to maf-convert.
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r154 | martin | 2011-01-07 19:50:39 +0900 (Fri, 07 Jan 2011) | 1 line

Removed discussion of repeats from docs.
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r153 | martin | 2010-12-29 14:03:05 +0900 (Wed, 29 Dec 2010) | 1 line

Allow all types of lowercase masking when using sequence quality data.
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r152 | martin | 2010-12-28 16:58:12 +0900 (Tue, 28 Dec 2010) | 1 line

Improved the documents (thanks: Hamada-san, Terai-san.
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r151 | martin | 2010-12-09 18:52:46 +0900 (Thu, 09 Dec 2010) | 1 line

Rewrote much of the documentation: separated tutorial from reference.
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r150 | martin | 2010-12-09 16:57:39 +0900 (Thu, 09 Dec 2010) | 1 line

Bugfix: made maf-convert not crash for blast output format!
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r149 | martin | 2010-11-26 11:01:23 +0900 (Fri, 26 Nov 2010) | 1 line

Minor enhancements.
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r148 | martin | 2010-11-25 16:24:01 +0900 (Thu, 25 Nov 2010) | 7 lines

! Made last-map-probs write *mismap* probabilities.
Gave last-map-probs options to omit alignments with lo score or hi mismap-prob.
Made last-map-probs work on MAF, and improved its UI a bit.
Added SAM output format to maf-convert.
Made maf-convert count psl matches correctly, and added -p (protein) option.
Added documents for last-map-probs and maf-convert.

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r147 | martin | 2010-11-25 10:04:36 +0900 (Thu, 25 Nov 2010) | 1 line

Made maf-swap keep q lines with s lines.
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r146 | martin | 2010-11-18 19:10:28 +0900 (Thu, 18 Nov 2010) | 1 line

Added a partial check for wrong FASTQ format.
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r145 | martin | 2010-11-12 17:39:20 +0900 (Fri, 12 Nov 2010) | 1 line

Added alignment-culling script.
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r144 | martin | 2010-11-12 17:28:09 +0900 (Fri, 12 Nov 2010) | 4 lines

Made maf-sort.sh consider the strand of the top sequence.
Rewrote maf-convert.py: nicer spacing, nicer error messages, and
doesn't try to flip strands for translated DNA.

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r143 | martin | 2010-11-08 14:57:08 +0900 (Mon, 08 Nov 2010) | 1 line

Added a new test file (forgotten in the previous commit).
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r142 | martin | 2010-11-08 14:39:06 +0900 (Mon, 08 Nov 2010) | 1 line

! Changed the interpretation of lastal -Q, to add FASTQ-Illumina input format.
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r141 | martin | 2010-11-08 11:31:49 +0900 (Mon, 08 Nov 2010) | 1 line

Refactor: use an enum instead of obscure int values.
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r140 | martin | 2010-11-02 16:21:58 +0900 (Tue, 02 Nov 2010) | 4 lines

Added psl and blast-like outputs to maf-convert.py.
Merged maf2html.py into maf-convert.py.
Bugfix: the html coordinates were wrong for translated alignments.

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r139 | martin | 2010-10-13 09:48:14 +0900 (Wed, 13 Oct 2010) | 1 line

Fixed last-map-probs.py crashing (math overflow) on large alignments.
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r138 | martin | 2010-10-12 18:01:14 +0900 (Tue, 12 Oct 2010) | 1 line

Made lastdb's default volume size (-s) unlimited, to simplify typical usage.
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r137 | martin | 2010-10-12 16:09:55 +0900 (Tue, 12 Oct 2010) | 1 line

Changed the default setting of lastal -u: made it depend on lastdb -c.
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r136 | martin | 2010-10-12 14:48:22 +0900 (Tue, 12 Oct 2010) | 1 line

Added lastal -z option: maximum score drop for final gapped alignments.
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r135 | martin | 2010-10-12 12:20:49 +0900 (Tue, 12 Oct 2010) | 3 lines

! Changed lastal -u: new option to mask lowercase during gapped
extensions but not "final" extensions (i.e. do gapped extensions twice).

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r134 | martin | 2010-10-12 10:05:56 +0900 (Tue, 12 Oct 2010) | 1 line

Added colour options to the dotplot script.
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r133 | martin | 2010-08-20 11:48:16 +0900 (Fri, 20 Aug 2010) | 3 lines

Reorganized code for gapless & gapped extensions.  Results should be
identical, provided that max gapped dropoff >= max gapless dropoff.

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r132 | martin | 2010-08-20 10:33:34 +0900 (Fri, 20 Aug 2010) | 1 line

Minor refactoring.
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r131 | martin | 2010-08-19 11:13:32 +0900 (Thu, 19 Aug 2010) | 1 line

Made lastex check for bad input more carefully.
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r130 | martin | 2010-08-04 11:54:59 +0900 (Wed, 04 Aug 2010) | 1 line

Bugfix: made lastdb allow non-alphabetic symbols in user-defined alphabets.
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r129 | martin | 2010-08-03 11:06:58 +0900 (Tue, 03 Aug 2010) | 3 lines

Bugfix: stopped lastal from freezing with some score matrices, e.g. PAM70.
Made "lastdb -x" less likely to run out of memory.  (Thanks: Junko Tsuji)

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r128 | martin | 2010-06-28 13:27:29 +0900 (Mon, 28 Jun 2010) | 3 lines

Bugfix: made last-dotplot.pl check for no alignments, instead of crashing.
Made lastdb and lastal check for '>' in FASTA and '@' in FASTQ.

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r127 | martin | 2010-06-24 20:03:55 +0900 (Thu, 24 Jun 2010) | 1 line

Made lastex results more reproducible, by removing time limits.
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r126 | martin | 2010-06-21 08:53:05 +0900 (Mon, 21 Jun 2010) | 1 line

Read PSSM names; ensure lastal doesn't try to use non-existent PSSMs.
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r125 | martin | 2010-06-18 15:21:44 +0900 (Fri, 18 Jun 2010) | 1 line

Clarified the default values of some lastal options.
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r124 | martin | 2010-06-18 14:33:51 +0900 (Fri, 18 Jun 2010) | 1 line

Bugfix: the PSSM reverse-complementation routine was wrong.
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r123 | martin | 2010-06-18 14:07:55 +0900 (Fri, 18 Jun 2010) | 1 line

Allow PSSMs as queries for lastal!
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r122 | martin | 2010-06-17 14:54:19 +0900 (Thu, 17 Jun 2010) | 1 line

Made lastex sensibly handle a both-strand translated alignments file.
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r121 | martin | 2010-06-17 12:03:29 +0900 (Thu, 17 Jun 2010) | 3 lines

Bugfix: made lastex work with weird letter frequencies (asymmetric with zeros).
Improved some error messages & other minor code improvements.

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r120 | martin | 2010-06-02 12:05:16 +0900 (Wed, 02 Jun 2010) | 1 line

Made maf-convert.py write expect values in tab output, if present in the input.
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r119 | martin | 2010-05-18 07:59:22 +0900 (Tue, 18 May 2010) | 1 line

Fixed compilation error & warning that occurred on some systems.
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r118 | martin | 2010-05-14 15:49:43 +0900 (Fri, 14 May 2010) | 1 line

Tried to make the C++ more strictly correct and portable.
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r117 | martin | 2010-05-12 18:37:28 +0900 (Wed, 12 May 2010) | 1 line

Try to put the correct version number in lastex's output.
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r116 | martin | 2010-05-12 18:33:17 +0900 (Wed, 12 May 2010) | 3 lines

Write the version number in lastex's output.
Exclude executable files from the distribution.

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r115 | martin | 2010-05-12 17:53:13 +0900 (Wed, 12 May 2010) | 1 line

Added lastex: expected numbers of alignments for random sequences!
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r114 | martin | 2010-05-12 16:08:39 +0900 (Wed, 12 May 2010) | 3 lines

Changed the prefix for options in the matrix file, from "#lastal" to
just "#last".  ("#lastal" still works.)

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r113 | martin | 2010-05-12 11:35:07 +0900 (Wed, 12 May 2010) | 1 line

Added lastdb warning if the input doesn't look like DNA.
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r112 | martin | 2010-05-10 11:42:33 +0900 (Mon, 10 May 2010) | 1 line

Gave lastdb an option to just count sequences & letters.
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r111 | martin | 2010-05-10 11:15:29 +0900 (Mon, 10 May 2010) | 1 line

Made lastdb count sequences & letters (not used yet).
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r110 | martin | 2010-05-10 10:14:29 +0900 (Mon, 10 May 2010) | 1 line

Made FASTA-reading faster.
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r109 | martin | 2010-05-08 19:39:44 +0900 (Sat, 08 May 2010) | 1 line

Made yass.seed the default for DNA only.
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r108 | martin | 2010-04-08 16:47:42 +0900 (Thu, 08 Apr 2010) | 1 line

Rewrote some code for getting probabilities from a scoring matrix.
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r107 | martin | 2010-04-08 15:35:39 +0900 (Thu, 08 Apr 2010) | 1 line

Added a test with an asymmetric scoring matrix.
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r106 | martin | 2010-04-08 15:12:32 +0900 (Thu, 08 Apr 2010) | 1 line

Made centroid alignment report the score of the ordinary gapped alignment.
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r105 | martin | 2010-04-08 14:07:59 +0900 (Thu, 08 Apr 2010) | 1 line

Minor refactoring.
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r104 | martin | 2010-04-08 13:48:04 +0900 (Thu, 08 Apr 2010) | 1 line

Made file I/O error messages a bit more specific; minor refactoring.
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r103 | martin | 2010-04-02 12:00:24 +0900 (Fri, 02 Apr 2010) | 3 lines

Made yass.seed the default seed pattern.
Greatly improved the documents & LAST recipes: please re-read them!

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r102 | martin | 2010-03-23 18:43:25 +0900 (Tue, 23 Mar 2010) | 3 lines

Made maf-convert.py work with older versions of python.
Avoided some warnings with some compilers.

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r101 | martin | 2010-03-23 10:48:33 +0900 (Tue, 23 Mar 2010) | 3 lines

Bugfix: maf2tab didn't work on translated alignments.
Replaced it with maf-convert.py (can also write AXT format).

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r100 | martin | 2010-03-18 20:24:43 +0900 (Thu, 18 Mar 2010) | 1 line

Bugfix: fixed errors related to volumes and batches >~4 gigabytes.
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r99 | martin | 2010-03-06 14:05:21 +0900 (Sat, 06 Mar 2010) | 3 lines

Made lastal write a comment line between query batches: might help parsers.
Made maf2tab.py preserve comment lines (but it might move them).

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r98 | martin | 2010-02-27 18:31:56 +0900 (Sat, 27 Feb 2010) | 1 line

Added lastal -n option to limit gapless alignments.
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r97 | martin | 2010-02-16 10:35:02 +0900 (Tue, 16 Feb 2010) | 1 line

Made lastdb and lastal require at least one sequence file.
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r96 | martin | 2010-02-02 19:20:22 +0900 (Tue, 02 Feb 2010) | 1 line

Enabled memory sharing by parallel lastal runs.
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r95 | martin | 2010-02-01 17:09:02 +0900 (Mon, 01 Feb 2010) | 1 line

Enable dotplots to have zero margins.
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r94 | martin | 2010-02-01 08:45:36 +0900 (Mon, 01 Feb 2010) | 7 lines

Bugfix: made maf-sort.sh (and thus last-reduce-alignments.sh) work on
Mac OS X, by not using "uniq".

Stopped spurious error messages from python scripts.

Slight FAQ re-wording.

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r93 | martin | 2010-01-18 22:48:11 +0900 (Mon, 18 Jan 2010) | 1 line

Fixed build error & warning that occurred on some platforms.
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r92 | martin | 2010-01-18 22:03:20 +0900 (Mon, 18 Jan 2010) | 1 line

Added citations & FAQs to the docs.
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r91 | martin | 2010-01-18 20:29:14 +0900 (Mon, 18 Jan 2010) | 1 line

Refactor: finished encapsulating the sequence data.
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r90 | martin | 2010-01-15 11:50:15 +0900 (Fri, 15 Jan 2010) | 1 line

Refactor: further reduced direct access to the seqeunce data...
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r89 | martin | 2010-01-14 18:30:16 +0900 (Thu, 14 Jan 2010) | 1 line

Refactor: reduce direct access to the seqeunce data (aim to encapsulate it).
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r88 | martin | 2010-01-14 15:48:15 +0900 (Thu, 14 Jan 2010) | 1 line

Refactor: simplified some code.
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r87 | martin | 2009-10-30 15:05:26 +0900 (Fri, 30 Oct 2009) | 7 lines

Bugfix: made lastal not crash when there are no identical matches to
initiate gapped extensions (can happen with subset seeds).

Improved & updated the documents.

Made lastal frameshifting gapped extension a bit faster.

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r86 | martin | 2009-10-29 17:07:12 +0900 (Thu, 29 Oct 2009) | 1 line

Made lastal gapped extension a fair bit faster.  (I don't understand why.)
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r85 | martin | 2009-10-29 12:27:09 +0900 (Thu, 29 Oct 2009) | 3 lines

Made lastal gapped extension a bit faster.
Made lastal -v write the count of initial matches.

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r84 | martin | 2009-10-26 18:14:09 +0900 (Mon, 26 Oct 2009) | 1 line

Explain lowercase & repeats a bit in the manual.
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r83 | martin | 2009-10-26 10:18:19 +0900 (Mon, 26 Oct 2009) | 1 line

Made lastal match-finding slightly faster.
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r82 | martin | 2009-10-23 15:27:51 +0900 (Fri, 23 Oct 2009) | 5 lines

! Lastdb and lastal no longer convert sequences to uppercase on reading.
! Lastdb -c now means: forbid lowercase in initial matches (in both sequences).
! Lastal -u numbers have changed (lowercase masking for extensions only).
Simplified the documentation by de-emphasizing lastal -u.

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r81 | martin | 2009-10-22 18:56:39 +0900 (Thu, 22 Oct 2009) | 1 line

Added a test of subset seeds; a few cosmetic changes.
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r80 | martin | 2009-10-22 18:17:28 +0900 (Thu, 22 Oct 2009) | 6 lines

Implemented subset seeds!
This makes lastdb and lastal a bit slower :-(
! The meaning of lastal -l has changed: it includes skipped positions now.
! The meaning of match-count output (lastal -j0) has changed in the same way.
! Skipped positions no longer tolerate lowercase or non-alphabet letters.

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r79 | martin | 2009-10-21 17:02:04 +0900 (Wed, 21 Oct 2009) | 3 lines

Just re-organized some calculations.
Lastal will now refuse to read older lastdb databases if the bucket depth = 0.

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r78 | martin | 2009-10-16 17:24:13 +0900 (Fri, 16 Oct 2009) | 1 line

Trivially re-organised the suffix sorting code.
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r77 | martin | 2009-10-16 16:19:55 +0900 (Fri, 16 Oct 2009) | 1 line

Refactored the suffix array code yet more (removed the constructor)...
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r76 | martin | 2009-10-16 13:25:07 +0900 (Fri, 16 Oct 2009) | 1 line

Refactored the suffix array code some more (removed reference members)...
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r75 | martin | 2009-10-16 10:46:23 +0900 (Fri, 16 Oct 2009) | 1 line

Refactored suffix sorting a bit.
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r74 | martin | 2009-10-13 15:35:48 +0900 (Tue, 13 Oct 2009) | 1 line

Added missing FASTQ test data!
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r73 | martin | 2009-10-13 15:30:38 +0900 (Tue, 13 Oct 2009) | 1 line

Minor refactoring.
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r72 | martin | 2009-10-13 14:13:29 +0900 (Tue, 13 Oct 2009) | 1 line

Code reorganization.
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r71 | martin | 2009-10-13 10:13:30 +0900 (Tue, 13 Oct 2009) | 1 line

Minor code cleaning.
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r70 | martin | 2009-10-05 12:22:04 +0900 (Mon, 05 Oct 2009) | 1 line

Added a test with FASTQ sequence quality data.
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r69 | martin | 2009-10-05 08:47:39 +0900 (Mon, 05 Oct 2009) | 3 lines

Changed the default "maximum score dropoff for gapless extensions"
(lastal -y): made it adapt better to the scoring matrix.

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r68 | martin | 2009-10-05 08:31:12 +0900 (Mon, 05 Oct 2009) | 1 line

Added frameshifting alignment!
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r67 | martin | 2009-10-02 09:24:02 +0900 (Fri, 02 Oct 2009) | 6 lines

Improved Debian/GNU conformance of progam help messages.  (Thanks:
Andreas Tille)

Bugfix: made last-reduce-alignments.sh better able to find the scripts
that it calls.

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r66 | martin | 2009-09-30 12:08:32 +0900 (Wed, 30 Sep 2009) | 1 line

Generalized some of the code in preparation for frameshifts.
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r65 | martin | 2009-09-28 15:07:10 +0900 (Mon, 28 Sep 2009) | 1 line

Added translated alignment (but without frameshifts for now)!
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r64 | martin | 2009-09-28 12:01:38 +0900 (Mon, 28 Sep 2009) | 9 lines

!! Changed the lastal option letter for query input format from -F to -Q
(so that -F can be used for frameshift cost).

Bugfix: fixed crash when bucket depth = 0.

Removed spurious message "no sensible solution in the plausible x range..."

Minor code cleaning.

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r63 | martin | 2009-09-24 14:35:39 +0900 (Thu, 24 Sep 2009) | 10 lines

Changed the bucket data structure.
  Advantages:
  * Uses only 80% as much memory, for a given bucket depth
  * Simpler code
  * Slightly faster construction (lastdb)
  Disadvantages:
  * Slightly slower scanning (lastal), for a given bucket depth
  * Changed database format
!! Lastal now refuses to read older lastdb databases.

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r62 | martin | 2009-09-16 08:25:30 +0900 (Wed, 16 Sep 2009) | 7 lines

Bugfix: lastal match counts (-j 0) were not reset between query
batches, so they were wrong for all but the first batch.

Added a test for match counting.

Improved the tag mapping documentation.

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r61 | martin | 2009-09-01 02:00:16 +0900 (Tue, 01 Sep 2009) | 3 lines

Added a script to calculate mapping probabilities (& minimal documentation).
Made lastal always try to calculate lambda (hence default temperature).

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r60 | martin | 2009-08-22 19:40:12 +0900 (Sat, 22 Aug 2009) | 1 line

Made lastdb faster for DNA, with a specialized 4-letter radix sort.
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r59 | martin | 2009-08-22 17:01:15 +0900 (Sat, 22 Aug 2009) | 4 lines

Fixed underflow error with phred score=0 and huge mismatch cost.
Friendlier out-of-memory message.
Improved the documentation a bit.

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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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