------------------------------------------------------------------------ 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). ------------------------------------------------------------------------ r98 | martin | 2010-02-27 18:31:56 +0900 (Sat, 27 Feb 2010) | 1 line Added lastal -n option to limit gapless alignments. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r96 | martin | 2010-02-02 19:20:22 +0900 (Tue, 02 Feb 2010) | 1 line Enabled memory sharing by parallel lastal runs. ------------------------------------------------------------------------ r95 | martin | 2010-02-01 17:09:02 +0900 (Mon, 01 Feb 2010) | 1 line Enable dotplots to have zero margins. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r93 | martin | 2010-01-18 22:48:11 +0900 (Mon, 18 Jan 2010) | 1 line Fixed build error & warning that occurred on some platforms. ------------------------------------------------------------------------ r92 | martin | 2010-01-18 22:03:20 +0900 (Mon, 18 Jan 2010) | 1 line Added citations & FAQs to the docs. ------------------------------------------------------------------------ r91 | martin | 2010-01-18 20:29:14 +0900 (Mon, 18 Jan 2010) | 1 line Refactor: finished encapsulating the sequence data. ------------------------------------------------------------------------ r90 | martin | 2010-01-15 11:50:15 +0900 (Fri, 15 Jan 2010) | 1 line Refactor: further reduced direct access to the seqeunce data... ------------------------------------------------------------------------ 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). ------------------------------------------------------------------------ r88 | martin | 2010-01-14 15:48:15 +0900 (Thu, 14 Jan 2010) | 1 line Refactor: simplified some code. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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.) ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r84 | martin | 2009-10-26 18:14:09 +0900 (Mon, 26 Oct 2009) | 1 line Explain lowercase & repeats a bit in the manual. ------------------------------------------------------------------------ r83 | martin | 2009-10-26 10:18:19 +0900 (Mon, 26 Oct 2009) | 1 line Made lastal match-finding slightly faster. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r78 | martin | 2009-10-16 17:24:13 +0900 (Fri, 16 Oct 2009) | 1 line Trivially re-organised the suffix sorting code. ------------------------------------------------------------------------ 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)... ------------------------------------------------------------------------ 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)... ------------------------------------------------------------------------ r75 | martin | 2009-10-16 10:46:23 +0900 (Fri, 16 Oct 2009) | 1 line Refactored suffix sorting a bit. ------------------------------------------------------------------------ r74 | martin | 2009-10-13 15:35:48 +0900 (Tue, 13 Oct 2009) | 1 line Added missing FASTQ test data! ------------------------------------------------------------------------ r73 | martin | 2009-10-13 15:30:38 +0900 (Tue, 13 Oct 2009) | 1 line Minor refactoring. ------------------------------------------------------------------------ r72 | martin | 2009-10-13 14:13:29 +0900 (Tue, 13 Oct 2009) | 1 line Code reorganization. ------------------------------------------------------------------------ r71 | martin | 2009-10-13 10:13:30 +0900 (Tue, 13 Oct 2009) | 1 line Minor code cleaning. ------------------------------------------------------------------------ r70 | martin | 2009-10-05 12:22:04 +0900 (Mon, 05 Oct 2009) | 1 line Added a test with FASTQ sequence quality data. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r68 | martin | 2009-10-05 08:31:12 +0900 (Mon, 05 Oct 2009) | 1 line Added frameshifting alignment! ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r66 | martin | 2009-09-30 12:08:32 +0900 (Wed, 30 Sep 2009) | 1 line Generalized some of the code in preparation for frameshifts. ------------------------------------------------------------------------ r65 | martin | 2009-09-28 15:07:10 +0900 (Mon, 28 Sep 2009) | 1 line Added translated alignment (but without frameshifts for now)! ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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). ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r58 | martin | 2009-06-14 19:20:30 +0900 (Sun, 14 Jun 2009) | 1 line Made lastal able to use sequence quality scores! ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r55 | martin | 2009-06-07 17:53:18 +0900 (Sun, 07 Jun 2009) | 1 line Minor code re-organization. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r50 | martin | 2009-04-08 19:55:08 +0900 (Wed, 08 Apr 2009) | 1 line Minor code cleaning: variable name, comments. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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(!) ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r46 | martin | 2009-03-31 17:53:41 +0900 (Tue, 31 Mar 2009) | 1 line Made last-remove-dominated.py faster. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r43 | martin | 2009-03-06 11:19:28 +0900 (Fri, 06 Mar 2009) | 1 line Simplified the probability & centroid code. (Thanks: Hamada-san) ------------------------------------------------------------------------ r42 | martin | 2009-03-03 19:35:53 +0900 (Tue, 03 Mar 2009) | 1 line Bugfix: overflow error made lastal discard some gapped alignments. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r40 | martin | 2009-02-28 15:30:37 +0900 (Sat, 28 Feb 2009) | 1 line Minor refactoring. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r38 | martin | 2008-12-30 22:51:28 +0900 (Tue, 30 Dec 2008) | 1 line Refactor: removed some namespace tedium from the code. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r36 | martin | 2008-12-22 20:47:12 +0900 (Mon, 22 Dec 2008) | 2 lines Made lastdb bucket-making code slightly simpler & faster. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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). ------------------------------------------------------------------------ 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). ------------------------------------------------------------------------ r32 | martin | 2008-12-05 18:07:50 +0900 (Fri, 05 Dec 2008) | 2 lines Fixed compiler warnings with gcc 4.3 ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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(?) ------------------------------------------------------------------------ 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). ------------------------------------------------------------------------ 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). ------------------------------------------------------------------------ r27 | martin | 2008-10-31 18:08:41 +0900 (Fri, 31 Oct 2008) | 2 lines Fixed the test script, which broke after moving HOXD70. ------------------------------------------------------------------------ r26 | martin | 2008-10-31 18:01:53 +0900 (Fri, 31 Oct 2008) | 2 lines Added the examples directory. ------------------------------------------------------------------------ r25 | martin | 2008-10-29 15:59:28 +0900 (Wed, 29 Oct 2008) | 2 lines Removed an obsolete comment. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r23 | martin | 2008-10-25 21:16:09 +0900 (Sat, 25 Oct 2008) | 2 lines Made the probability calculations slightly faster, by micro-optimization. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r19 | martin | 2008-10-02 14:29:51 +0900 (Thu, 02 Oct 2008) | 2 lines Added probabilistic & centroid alignment! ------------------------------------------------------------------------ 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). ------------------------------------------------------------------------ r17 | martin | 2008-09-30 17:49:42 +0900 (Tue, 30 Sep 2008) | 2 lines Minor comment changes. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r14 | martin | 2008-09-18 11:42:08 +0900 (Thu, 18 Sep 2008) | 2 lines Minor refactoring. ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ r12 | martin | 2008-09-17 19:45:35 +0900 (Wed, 17 Sep 2008) | 2 lines Refactored the conversion of gapped Xdrop extensions to alignments. ------------------------------------------------------------------------ r11 | martin | 2008-09-16 21:49:53 +0900 (Tue, 16 Sep 2008) | 2 lines Added FAQ (just one entry so far). ------------------------------------------------------------------------ r10 | martin | 2008-09-16 18:20:11 +0900 (Tue, 16 Sep 2008) | 2 lines Refactor: Made gapped alignments remember their seeds. ------------------------------------------------------------------------ r9 | martin | 2008-09-16 15:29:27 +0900 (Tue, 16 Sep 2008) | 2 lines Added a minimal regression test. ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ r7 | martin | 2008-09-10 09:37:18 +0900 (Wed, 10 Sep 2008) | 2 lines Added lastdbName to the header of the lastal output. ------------------------------------------------------------------------ r6 | martin | 2008-09-10 09:30:40 +0900 (Wed, 10 Sep 2008) | 2 lines Added version to lastdb ".prj" file. ------------------------------------------------------------------------ r5 | martin | 2008-09-10 09:20:47 +0900 (Wed, 10 Sep 2008) | 2 lines Tiny change to the header in lastal output. ------------------------------------------------------------------------ r4 | martin | 2008-09-09 19:00:59 +0900 (Tue, 09 Sep 2008) | 2 lines Added Harada-san to credits. ------------------------------------------------------------------------ r3 | martin | 2008-09-08 17:06:55 +0900 (Mon, 08 Sep 2008) | 2 lines Separated "make dist" from "make all". ------------------------------------------------------------------------ r2 | martin | 2008-09-08 17:00:46 +0900 (Mon, 08 Sep 2008) | 2 lines Added Credits & Citation to last-manual.txt. ------------------------------------------------------------------------ r1 | martin | 2008-09-08 15:20:39 +0900 (Mon, 08 Sep 2008) | 2 lines First commit! ------------------------------------------------------------------------