2013-10-04  Martin C. Frith  <Martin C. Frith>

	* makefile:
	Added last-split to "make install"
	[d6323081a217] [tip]

	* doc/Makefile, doc/last-split-probs.txt, doc/last-split.txt, scripts
	/last-split-probs.py, src/makefile, src/split/cbrc_linalg.cc,
	src/split/cbrc_linalg.hh, src/split/cbrc_split_aligner.cc,
	src/split/cbrc_split_aligner.hh,
	src/split/cbrc_unsplit_alignment.cc,
	src/split/cbrc_unsplit_alignment.hh, src/split/last-split-main.cc,
	src/split/last-split.cc, src/split/last-split.hh,
	test/SRR359290-1k.maf, test/last-split-test.out, test/last-split-
	test.sh:
	Replaced last-split-probs with last-split !
	[bc5801666fb2]

2013-10-02  Martin C. Frith  <Martin C. Frith>

	* examples/lastal-bisulfite-paired.sh, src/Alphabet.hh,
	src/Centroid.hh:
	Very minor code tweaks
	[7add737275da]

2013-09-02  Martin C. Frith  <Martin C. Frith>

	* test/last-test.out, test/last-test.sh:
	Added a test.
	[b2417b896e40]

2013-09-01  Martin C. Frith  <Martin C. Frith>

	* src/Centroid.cc, src/Centroid.hh:
	Made the probabilistic dynamic-programming similar to the non-
	probabilistic DP.
	[54f9d38e78a8]

	* src/Centroid.cc:
	Fixed some code that's probably never used anyway.
	[ecf35f1babbb]

	* src/Centroid.cc, src/Centroid.hh:
	Simplified the probabilistic alignment with a cunning trick.
	[66169fb0dc4b]

2013-08-31  Martin C. Frith  <Martin C. Frith>

	* src/Centroid.cc, test/last-test.out, test/last-test.sh:
	Refactoring & added a test.
	[b14f98bb0aaf]

2013-08-29  Martin C. Frith  <Martin C. Frith>

	* src/Centroid.cc:
	Very minor refactoring.
	[da5103b17109]

	* src/Centroid.cc:
	Very minor refactoring.
	[e19ac83cdf39]

	* src/Centroid.cc:
	Refactoring.
	[4afc604780f8]

	* src/Centroid.cc:
	Refactoring.
	[045d538073b5]

	* src/Centroid.cc, src/Centroid.hh:
	Refactoring.
	[a4c602f1974f]

	* src/Centroid.cc:
	Refactoring.
	[28b33aa17b79]

	* src/Centroid.cc:
	Refactoring.
	[76d3f93bab3c]

	* src/Centroid.cc:
	Refactoring (just renamed a variable).
	[308b26210a2a]

	* src/Alignment.cc, src/Alignment.hh:
	Refactoring.
	[9a8f96fcc9e1]

	* src/Centroid.cc, src/Centroid.hh:
	Increased robustness to integer overflow (maybe).
	[ccc85569d01c]

	* src/Centroid.cc, src/Centroid.hh:
	Refactoring.
	[4e33c00a4a1b]

	* src/Centroid.cc, src/Centroid.hh:
	Refactoring.
	[d6c67ba4c15b]

	* src/Centroid.cc:
	Refactoring.
	[8c5ba2c1fcd5]

2013-08-28  Martin C. Frith  <Martin C. Frith>

	* src/Centroid.cc:
	Refactoring.
	[d598fe33632b]

	* src/Centroid.cc:
	Refactoring.
	[7817575bf345]

	* src/Centroid.cc:
	Refactoring.
	[8d6e98549602]

	* src/Centroid.cc:
	Refactoring.
	[3e6bfbaccc08]

	* src/Centroid.cc, src/Centroid.hh, src/lastal.cc:
	Removed trailing whitespace.
	[df07ac99d269]

	* src/Centroid.cc:
	Refactoring.
	[6482c7a4300a]

	* src/Centroid.cc:
	Refactoring.
	[32751b1d8a1f]

	* src/Alignment.cc, src/Centroid.cc, src/Centroid.hh:
	Added probabilistic overlap alignment (thanks: Toshiyuki Sato).
	[a6c02431602e]

	* src/Centroid.cc:
	Minor refactoring.
	[7e46c96be97f]

2013-08-26  Martin C. Frith  <Martin C. Frith>

	* doc/lastal.txt, test/last-test.out, test/last-test.sh:
	Added doc & test for overlap alignment.
	[62ec547050d0]

	* src/Alignment.cc, src/Alignment.hh, src/LastalArguments.cc,
	src/LastalArguments.hh, src/lastal.cc:
	Added overlap alignment! (Thanks: Toshiyuki Sato)
	[2ae0f4be8ea4]

	* src/Alignment.cc, src/GappedXdropAligner.cc,
	src/GappedXdropAligner.hh, src/GappedXdropAligner2qual.cc,
	src/GappedXdropAlignerInl.hh, src/GappedXdropAlignerPssm.cc:
	Started to add overlap alignment (thanks: Toshiyuki Sato).
	[16d72fa5320b]

	* src/Alignment.cc:
	Minor refactoring.
	[405438cd37ea]

2013-08-25  Martin C. Frith  <Martin C. Frith>

	* src/AlignmentWrite.cc:
	Generalized tabular-output-writing so it handles alignments ending
	with gaps.
	[7692523417d0]

	* src/GappedXdropAligner.cc:
	Generalized the traceback so it handles alignments ending with gaps.
	[4f46d830e949]

2013-08-23  Martin C. Frith  <Martin C. Frith>

	* doc/bisulfite.txt, examples/lastal-bisulfite-paired.sh:
	Added a script for aligning paired bisulfite reads (in parallel).
	[660ff05b7f0e]

	* scripts/maf-convert.py:
	Tweaked maf-convert's BLAST output (thanks: Nick Loman).
	[b93b23a4d23d]

	* src/Alignment.cc, src/Centroid.cc, src/LastalArguments.cc:
	Allow different ins & del costs in probabilistic alignment (thanks:
	T Sato).
	[69107a55e7ab]

2013-07-26  Martin C. Frith  <Martin C. Frith>

	* examples/hoxd70.mat, test/last-test.out:
	Added "N" scores to hoxd70.
	[00b0426f4a4d]

2013-07-25  Martin C. Frith  <Martin C. Frith>

	* examples/multiMito.maf, src/LastalArguments.cc, test/last-test.out:
	! Changed the default for lastal "-x": affects max gap size & run-
	time.
	[a3aae9fc866a]

2013-07-16  Martin C. Frith  <Martin C. Frith>

	* doc/lastdb.txt, test/last-test.out, test/last-test.sh:
	Added doc & tests for recent changes.
	[46bdfb358572]

	* src/CyclicSubsetSeed.cc, src/LastdbArguments.cc:
	Allow comma-separated seed patterns; check for empty seed patterns.
	[bea2065529ce]

	* src/CyclicSubsetSeed.cc, src/CyclicSubsetSeed.hh,
	src/LastdbArguments.cc, src/LastdbArguments.hh, src/lastdb.cc:
	Easy input of transition-constrained seed patterns (undocumented).
	[2ac64facdc4c]

	* src/lastal.cc:
	Made lastal read lastdb files more strictly.
	[38003ee6a77c]

	* src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc:
	Enabled multiple seed patterns in lastal.
	[882fd4b4e364]

	* src/lastdb.cc:
	Enabled multiple seed patterns in lastdb.
	[4649149270c5]

	* src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh, src/lastdb.cc:
	Continued to enable multiple seed patterns...
	[ba7f7354d1eb]

	* src/lastdb.cc:
	Continued to enable multiple seed patterns...
	[c0c62851c1e3]

	* src/lastdb.cc:
	Continued to enable multiple seed patterns.
	[b757a18867f2]

	* src/LastdbArguments.cc, src/LastdbArguments.hh, src/lastdb.cc:
	Started to enable multiple seed patterns.
	[60b4d3648b6f]

	* src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh, src/lastdb.cc:
	Fixed apparent lastdb overflow bug with huge sequence data and w>1.
	[593a8f860a3f]

2013-07-15  Martin C. Frith  <Martin C. Frith>

	* doc/lastdb.txt, src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh,
	src/lastdb.cc:
	! Changed the behaviour of lastdb -s (volume size): simpler &
	cruder.
	[77d6c2b29ecd]

2013-07-14  Martin C. Frith  <Martin C. Frith>

	* src/CyclicSubsetSeed.cc, src/SubsetSuffixArray.cc, src/lastal.cc:
	Added some error-checking when reading files.
	[ae38cba11e0b]

	* src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh, src/lastal.cc,
	src/lastdb.cc:
	! Changed lastdb file format: lastal will refuse to read old lastdb
	files.
	[77648600d92e]

2013-07-13  Martin C. Frith  <Martin C. Frith>

	* src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh, src/lastal.cc:
	Made the suffix-array-reading code more self-contained.
	[89da6a07f3bf]

	* src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh, src/lastdb.cc:
	Made the suffix-array-writing code more self-contained.
	[e85e91f0dbd1]

	* src/CyclicSubsetSeed.cc, src/CyclicSubsetSeed.hh:
	Made it possible to clear & re-read a seed pattern.
	[199611bc4916]

	* src/CyclicSubsetSeed.hh, src/SubsetSuffixArray.hh,
	src/SubsetSuffixArraySort.cc, src/lastdb.cc:
	Refactor: just moved a typedef.
	[4c08ae190646]

2013-07-09  Martin C. Frith  <Martin C. Frith>

	* src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh,
	src/SubsetSuffixArraySort.cc, src/lastal.cc, src/lastdb.cc:
	Refactor: made the subset seed a member of the subset suffix array.
	[054e61cc84f3]

2013-07-03  Martin C. Frith  <Martin C. Frith>

	* doc/lastal.txt, doc/lastdb.txt, test/last-test.out, test/last-
	test.sh:
	Added test & doc for lastdb -i, and running lastal on single
	volumes.
	[4265eaec011c]

2013-06-26  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc, test
	/last-test.out:
	Set the default for lastal "d" separately for each lastdb volume.
	[d567aaece7a3]

2013-06-25  Martin C. Frith  <Martin C. Frith>

	* src/lastdb.cc:
	Made lastdb write 1-volume databases in a simpler set of files.
	[08809771f21b]

	* src/lastal.cc:
	Made lastal able to read one volume (undocumented).
	[a839387881e0]

	* src/lastal.cc:
	Made lastal read the lastdb files a bit more strictly.
	[c1ae4b660da3]

2013-06-24  Martin C. Frith  <Martin C. Frith>

	* src/lastdb.cc:
	Made lastdb write more info in inner prj files (not used yet).
	[5bc0cb31f63f]

2013-06-21  Martin C. Frith  <Martin C. Frith>

	* doc/lastdb.txt, src/LastdbArguments.cc, src/LastdbArguments.hh,
	src/SubsetSuffixArray.hh, src/SubsetSuffixArraySort.cc,
	src/lastal.cc, src/lastdb.cc:
	Added lastdb -i option, to make it faster by incomplete sorting.
	[88a090cfcfda]

	* src/LastalArguments.cc:
	Just changed some help text.
	[58dcba2aa9c9]

2013-06-11  Martin C. Frith  <Martin C. Frith>

	* doc/maf-convert.txt, scripts/maf-convert.py:
	Made maf-convert accept zero or more file names.
	[21ec283344a0]

	* doc/FAQ.txt:
	Added %identity FAQ.
	[5e10487d7fc1]

2013-06-10  Martin C. Frith  <Martin C. Frith>

	* src/gaplessPssmXdrop.cc, src/gaplessTwoQualityXdrop.cc,
	src/gaplessXdrop.cc:
	Made lastal a bit faster (gapless extension phase).
	[d073de15e8ad]

	* src/makefile:
	Get the version more robustly.
	[f39b98c2fb79]

2013-05-23  Martin C. Frith  <Martin C. Frith>

	* .hgignore, makefile, src/makefile:
	Changed version control from subversion to mercurial.
	[d11b0382e04d]

2013-04-22  Martin C. Frith  <Martin C. Frith>

	* doc/maf-convert.txt, scripts/maf-convert.py:
	Added maf-convert dictfile option.
	[064a55a7225f]

	* doc/maf-convert.txt, scripts/maf-convert.py:
	Added maf-convert readgroup option.
	[d4f51fc56453]

2013-04-19  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, doc/maf-convert.txt, scripts/maf-convert.py:
	Made maf-convert's sam output more acceptable to GATK/picard.
	[617c9ab84534]

2013-04-16  Martin C. Frith  <Martin C. Frith>

	* scripts/maf-convert.py:
	Made maf-convert interpret "/1" and "/2" as paired sequences
	(undocumented).
	[d44b9010b0eb]

	* doc/last-pair-probs.txt, scripts/last-pair-probs.py:
	Made last-pair-probs append "/1" and "/2" to query names, if
	missing.
	[f0739cfef39d]

	* doc/bisulfite.txt:
	! Documentation bugfix: the bisulfite paired-end recipe was stupidly
	wrong.
	[a8d169b27919]

2013-04-15  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, doc/Makefile, doc/last-pair-probs.txt, doc/maf-
	convert.txt:
	Some doc updates.
	[96409edb2a36]

	* scripts/last-split-probs.py:
	Just added a comment
	[67c1dc5e4215]

2013-03-05  Martin C. Frith  <Martin C. Frith>

	* src/lastal.cc, test/last-test.out:
	Added a batch marker at start of lastal outputs, so they can be
	concatenated.
	[eb44b445d03d]

	* doc/FAQ.txt, doc/last-tutorial.txt:
	Added GNU parallel recipes to last-tutorial.
	[bcf912c0eb1e]

	* src/lastal.cc:
	Added some checking and error messages for bad input.
	[f90a5b82472d]

2013-03-01  Martin C. Frith  <Martin C. Frith>

	* doc/bisulfite.txt, doc/last-map-probs.txt, doc/last-pair-probs.txt,
	doc/last-split-probs.txt, doc/last-tutorial.txt,
	src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc, test
	/last-test.out:
	! Changed the default setting of lastal option -d.
	[c34146ded8ab]

2013-02-12  Martin C. Frith  <Martin C. Frith>

	* doc/last-map-probs.txt, doc/last-tutorial.txt:
	Doc updates.
	[973270605980]

2013-02-11  Martin C. Frith  <Martin C. Frith>

	* scripts/last-dotplot.py:
	Made last-dotplot faster.
	[461c012731fc]

	* doc/last-scripts.txt, scripts/last-dotplot.py:
	Made last-dotplot able to read MAF format.
	[935227c035b0]

2013-02-06  Martin C. Frith  <Martin C. Frith>

	* src/fileMap.cc:
	Made the mmap error messages more detailed.
	[1ccb6e25d4bf]

2013-02-04  Martin C. Frith  <Martin C. Frith>

	* doc/Makefile, doc/last.txt, doc/maf-cull.txt:
	Minor doc edits.
	[dc1fab3f2f9e]

	* doc/last-tutorial.txt, doc/last.txt:
	Doc updates.
	[cbe2e24fbd9f]

2013-02-03  Martin C. Frith  <Martin C. Frith>

	* doc/lastal.txt, doc/tag-seeds.txt, src/LastalArguments.cc,
	src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh, test/last-
	test.out:
	! Changed the interaction between lastal -m and -l from AND to OR.
	[cd3fb1f3626f]

2013-02-01  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc, src/TwoQualityScoreMatrix.cc,
	src/TwoQualityScoreMatrix.hh, test/last-test.out:
	Made lastal -n default to -m instead of inf. This has no effect
	(yet).
	[9ddd72f3ea16]

2012-12-21  Martin C. Frith  <Martin C. Frith>

	* src/GappedXdropAligner2qual.cc, test/last-test.out, test/last-
	test.sh, test/sd-ccs-100.fq:
	! Bugfix: fastq-v-fastq alignment was using wrong query quality
	data.
	[0efe0e4ea326]

2012-11-14  Martin C. Frith  <Martin C. Frith>

	* test/last-test.out, test/last-test.sh:
	Added a test of gapless alignment.
	[503f5e685bb6]

2012-11-13  Martin C. Frith  <Martin C. Frith>

	* doc/lastal.txt, src/Alignment.cc, src/Alignment.hh,
	src/AlignmentWrite.cc, src/Centroid.cc, src/Centroid.hh, test/last-
	test.out:
	Added fullScore to lastal output.
	[f20af15efa11]

2012-10-29  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/Alignment.hh, src/AlignmentWrite.cc,
	src/LastalArguments.cc, src/lastal.cc:
	Added lastal option to write expected counts (not documented yet).
	[20bee444cd56]

2012-10-23  Martin C. Frith  <Martin C. Frith>

	* doc/Makefile:
	Tried harder to make the HTML documents in a more portable way.
	[b5b0991bf36c]

	* doc/Makefile:
	Tried to make the HTML documents in a more portable way.
	[a0a0b03ed406]

	* doc/last-tutorial.txt:
	Minor doc edits.
	[87b6bb724860]

2012-10-22  Martin C. Frith  <Martin C. Frith>

	* README.txt, doc/Makefile, doc/last.txt:
	Just edited some documentation.
	[cd270cd875d5]

	* doc/last.txt:
	Started moving useful info from the README to the doc directory.
	[9611ae3af223]

2012-10-21  Martin C. Frith  <Martin C. Frith>

	* doc/Makefile, doc/last-doc.css, makefile:
	Added HTML versions of some documents.
	[d012f1d2a8b9]

	* doc/last-pair-probs.txt:
	RST-ified last-pair-probs.txt, and added a GNU parallel recipe.
	[09cd862fa41f]

	* doc/bisulfite.txt, doc/last-map-probs.txt, doc/last-split-probs.txt:
	RST-ified some more documents.
	[d7a26503b802]

	* doc/last-tutorial.txt:
	RST-ified last-tutorial.txt.
	[dca0a1daa165]

	* README.txt, doc/lastal.txt:
	Slight documentation edits.
	[42bc0c18af3c]

	* src/CA_code/nrutil.c:
	Just fixed a compiler warning.
	[c7261447b95a]

2012-10-09  Martin C. Frith  <Martin C. Frith>

	* scripts/last-remove-dominated.py:
	Bugfix: made last-remove-dominated (and hence last-reduce-
	alignments) accept output from lastal version >= r238.
	[a6e9eab3e56d]

2012-08-16  Martin C. Frith  <Martin C. Frith>

	* makefile:
	Minor refactoring of the makefile.
	[70e77489aa2f]

2012-08-05  Martin C. Frith  <Martin C. Frith>

	* src/Alphabet.hh, src/lastal.cc, src/lastex.cc:
	Default to Blosum62 for any alphabet that starts with
	ACDEFGHIKLMNPQRSTVWY.
	[a05f5b5bde91]

2012-07-31  Martin C. Frith  <Martin C. Frith>

	* doc/bisulfite.txt, doc/maf-convert.txt:
	Clarified paired-end bisulfite data, and maf-convert -d, in the
	docs.
	[eb9e8dc97f70]

2012-07-09  Martin C. Frith  <Martin C. Frith>

	* scripts/last-map-probs.py:
	! Made last-map-probs faster, and slightly changed (shortened) its
	output.
	[f8789f48456a]

	* scripts/last-map-probs.py:
	Minor refactoring.
	[f9afa432bcc7]

	* scripts/last-map-probs.py:
	Made last-map-probs a tiny bit faster, maybe.
	[fc467f99add1]

	* scripts/last-map-probs.py:
	Made last-map-probs a bit more efficient, maybe.
	[ce5f011254cf]

	* scripts/last-map-probs.py:
	Made last-map-probs a bit faster.
	[61cb64703481]

	* scripts/last-map-probs.py:
	Made last-map-probs a bit faster.
	[f74edcbcec6b]

2012-07-08  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc, test
	/last-test.out:
	! Changed lastal's default batch size: this can make it faster, but
	it changes the output order.
	[5dbf6b4f872b]

	* doc/bisulfite.txt, doc/last-tutorial.txt, doc/lastdb.txt:
	Improved the docs for bisulfite data, and for running lastdb on huge
	datasets.
	[b03773ef0133]

2012-07-06  Martin C. Frith  <Martin C. Frith>

	* test/last-test.out:
	Updated the test CPU times for the new development computer.
	[f5b7f9ab1725]

	* doc/lastal.txt, src/LastalArguments.cc, src/LastalArguments.hh,
	src/lastal.cc, test/last-test.out:
	Enabled different costs for insertions and deletions.
	[48ad769f870d]

	* src/Alignment.cc, src/Centroid.cc, src/GeneralizedAffineGapCosts.cc,
	src/GeneralizedAffineGapCosts.hh, src/lastal.cc:
	Continued to implement different costs for insertions and deletions.
	[dde4fc49ec9d]

	* src/Alignment.cc, src/GappedXdropAligner.cc,
	src/GappedXdropAligner.hh, src/GappedXdropAligner2qual.cc,
	src/GappedXdropAlignerPssm.cc:
	Started to implement different costs for insertions and deletions.
	[bc1a7edd8235]

2012-06-25  Martin C. Frith  <Martin C. Frith>

	* scripts/last-pair-probs.py:
	Made last-pair-probs a bit faster.
	[f7c78352421f]

2012-06-20  Martin C. Frith  <Martin C. Frith>

	* src/Centroid.cc:
	Minor refactoring.
	[4fcb65616f40]

2012-06-13  Martin C. Frith  <Martin C. Frith>

	* src/GappedXdropAligner.cc, src/GappedXdropAligner3frame.cc, test
	/last-test.out, test/last-test.sh:
	! Bugfix: generalized affine gaps were wrong since version 192.
	[e5bd7a6d664f]

2012-06-12  Martin C. Frith  <Martin C. Frith>

	* src/Centroid.cc, src/Centroid.hh, src/GappedXdropAligner.hh:
	Refactored some of the Centroid code a bit.
	[33297f4d5ffa]

	* src/Centroid.cc, src/Centroid.hh, src/GappedXdropAligner.hh:
	Made probabilistic alignment (lastal j>3) much faster (thanks:
	Toshiyuki Sato).
	[dc09cd9a5340]

2012-06-01  Martin C. Frith  <Martin C. Frith>

	* doc/last-pair-probs.txt:
	Enhanced the last-pair-probs doc.
	[6bd9a1ff7cf2]

2012-05-29  Martin C. Frith  <Martin C. Frith>

	* doc/last-pair-probs.txt, scripts/last-pair-probs.py:
	Allow negative distances in last-pair-probs, and update its doc.
	[174c23386df9]

	* scripts/last-pair-probs.py:
	Made last-pair-probs a bit faster.
	[3a4ef7b226cb]

	* scripts/last-pair-probs.py:
	Added last-pair-probs option to estimate the distribution of
	distances only.
	[143cd098c89d]

	* scripts/last-pair-probs.py:
	! Slightly changed the usage of floating point in last-pair-probs.
	[9069ef23d91e]

	* scripts/last-pair-probs.py:
	Edited some last-pair-probs help messages.
	[59dd7dc8f1ee]

	* scripts/last-pair-probs.py:
	Made last-pair-probs a bit faster.
	[38bcbfd05c0e]

	* scripts/last-pair-probs.py:
	! Made last-pair-probs read by batches instead of sorting.
	[97bcb3f0a424]

2012-05-28  Martin C. Frith  <Martin C. Frith>

	* scripts/last-pair-probs.py:
	Minor refactoring.
	[b9ec919221a4]

	* scripts/last-pair-probs.py:
	Refactored some code in last-pair-probs.
	[7d3009252704]

	* scripts/last-pair-probs.py:
	Made last-pair-probs skip its first pass if both fraglen and sdev
	are set.
	[e1ca1c18be32]

	* scripts/last-pair-probs.py:
	Made last-pair-probs a bit faster (but require header data to be at
	the top).
	[f9bce1362955]

	* scripts/last-pair-probs.py:
	Bugfix: if the final MAF block in a file given to last-pair-probs
	did not end in a blank line, the output MAF blocks were not always
	separated by blank lines.

	Improved a last-pair-probs error message.
	[fb2c9c9e2f81]

	* scripts/last-pair-probs.py:
	Made last-pair-probs faster. ! Its probability estimates are a tiny
	bit different (more reproducible).
	[3e33f2821612]

	* scripts/last-pair-probs.py:
	Made last-pair-probs a bit faster.
	[ed4fbac1d8cf]

	* scripts/last-pair-probs.py:
	Minor refactoring.
	[6f4723d5a83e]

	* scripts/last-pair-probs.py:
	Made last-pair-probs a bit faster.
	[57912534f799]

	* scripts/last-pair-probs.py:
	Minor refactoring.
	[52b150cb1a88]

	* scripts/last-pair-probs.py:
	! Slightly changed how last-pair-probs estimates the standard
	deviation.
	[48a62711ce44]

	* doc/last-pair-probs.txt, scripts/last-pair-probs.py:
	! Changed how last-pair-probs obtains the genome size. This may
	slightly change its probability estimates.
	[f50079ca2227]

2012-05-27  Martin C. Frith  <Martin C. Frith>

	* scripts/last-pair-probs.py:
	Fixed error in last-pair-probs help message.
	[655c1f9449c6]

2012-05-20  Martin C. Frith  <Martin C. Frith>

	* src/AlignmentWrite.cc:
	Fixed a bug that was introduced in version 203 (wrong MAF sequence
	length).
	[0afc11fd9d18]

	* doc/lastal.txt, src/LastalArguments.cc, test/last-test.out:
	! Made lastal options -d and -e synonymous for gapless alignment
	(-j1).
	[977c23d24eb5]

	* doc/FAQ.txt, src/AlignmentWrite.cc, src/Alphabet.cc,
	src/Alphabet.hh:
	Made lastal yet faster at writing MAF output.
	[2b70fa3cd0c3]

2012-05-17  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.hh, src/AlignmentWrite.cc, src/Alphabet.cc,
	src/Alphabet.hh:
	Made lastal even faster at writing MAF output.
	[82625cec7dbc]

	* src/AlignmentWrite.cc:
	Minor refactoring.
	[bcc17bd99c42]

	* src/AlignmentWrite.cc:
	Minor refactoring.
	[ddbc9b8efeba]

2012-05-16  Martin C. Frith  <Martin C. Frith>

	* src/AlignmentWrite.cc:
	Made lastal faster at writing MAF output.
	[78a9da37f5a3]

2012-05-14  Martin C. Frith  <Martin C. Frith>

	* src/SegmentPair.cc:
	Made lastal a teeny bit faster.
	[0a121eb763c5]

	* scripts/last-split-probs.py:
	Minor changes to last-split-probs.
	[90f3031116aa]

2012-05-11  Martin C. Frith  <Martin C. Frith>

	* doc/last-split-probs.txt, scripts/last-split-probs.py:
	Added split-alignment method!
	[294db1a62968]

2012-05-07  Martin C. Frith  <Martin C. Frith>

	* src/makefile:
	Improved the makefile.
	[2248af12c158]

2012-03-30  Martin C. Frith  <Martin C. Frith>

	* README.txt, makefile, src/makefile:
	Turned compile warnings off in the top makefile, on in the src
	makefile.
	[0f45f4585048]

	* src/gumbel_params/njn_approx.hpp:
	Fixed compile error with clang++.
	[4582086da692]

2012-03-13  Martin C. Frith  <Martin C. Frith>

	* README.txt, makefile, src/makefile, test/last-test.sh:
	Added automatic installation by "make install".
	[6f1d925a06c6]

2012-01-06  Martin C. Frith  <Martin C. Frith>

	* doc/lastdb.txt, src/Alignment.cc, src/Alignment.hh,
	src/LastdbArguments.cc, src/lastal.cc, src/makefile:
	Fully enabled fastq-versus-fastq alignment!
	[a8bdd8c9d9d4]

	* doc/bisulfite.txt:
	Clarified something in the bisulfite doc.
	[e3b276863a2d]

2011-12-20  Martin C. Frith  <Martin C. Frith>

	* doc/bisulfite.txt, examples/bisulfite_f.seed,
	examples/bisulfite_r.seed:
	Bisulfite doc: explained biased methylation estimates & how to avoid
	them. Changed the bisulfite seeds to ones that work a bit better in
	some tests.
	[4a4af87299d7]

2011-11-13  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/Alignment.hh, src/Centroid.cc,
	src/Centroid.hh, src/ScoreMatrix.hh, src/ScoreMatrixRow.hh,
	src/Xdrop3FrameAligner.cc, src/Xdrop3FrameAligner.hh,
	src/XdropAligner.cc, src/XdropAligner.hh, src/XdropAlignerPssm.cc,
	src/lastal.cc, src/makefile, test/last-test.out:
	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.
	[0ef8ab8aa902]

	* src/Alignment.cc, src/Alignment.hh, src/Centroid.cc,
	src/Centroid.hh:
	Refactor: preparing to remove the old gapped-alignment code.
	[2b59e5d2cc40]

2011-11-12  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.hh, src/Centroid.cc, src/Centroid.hh,
	src/GeneticCode.cc, src/ScoreMatrix.cc:
	Made the C++ more strictly correct and portable. (Thanks: Fabien
	Campagne)
	[15f74143b748]

2011-10-19  Martin C. Frith  <Martin C. Frith>

	* src/lastal.cc:
	Bugfix: lastal -j0 crashed with fastq input. (Thanks: Fabien
	Campagne)
	[beb8f40d2a0d]

2011-10-15  Martin C. Frith  <Martin C. Frith>

	* src/SubsetSuffixArraySort.cc:
	Made lastdb faster in some cases, e.g. bisulfite alignment.
	[6c7c721e1a3c]

2011-09-20  Martin C. Frith  <Martin C. Frith>

	* src/GappedXdropAligner3frame.cc:
	Just fixed a comment that was wrong.
	[99517a30d10f]

2011-08-17  Martin C. Frith  <Martin C. Frith>

	* src/GappedXdropAligner.cc, src/GappedXdropAligner3frame.cc:
	Added comments explaining the new gapped X-drop algorithms in more
	detail.
	[1c8bcac7122c]

2011-08-15  Martin C. Frith  <Martin C. Frith>

	* src/GappedXdropAligner.cc, src/GappedXdropAligner.hh,
	src/GappedXdropAligner2qual.cc, src/GappedXdropAligner3frame.cc,
	src/GappedXdropAligner3framePssm.cc, src/GappedXdropAlignerInl.hh,
	src/GappedXdropAlignerPssm.cc:
	Added new gapped x-drop alignment code (not used yet).
	[2e40cac8a24f]

2011-08-03  Martin C. Frith  <Martin C. Frith>

	* doc/bisulfite.txt, scripts/last-merge-batches.py:
	Added bisulfite doc, and a script that it refers to.
	[f7dee5ac617b]

2011-07-28  Martin C. Frith  <Martin C. Frith>

	* doc/lastal.txt, doc/lastex.txt, examples/HOXD70, examples/TiTv212,
	examples/bisulfite_f.mat, examples/bisulfite_f.seed,
	examples/bisulfite_r.mat, examples/bisulfite_r.seed,
	examples/hoxd70.mat, examples/titv212.mat, test/last-test.sh:
	Added bisulfite example files, and renamed score-matrix files.
	[45c7af0a029b]

	* test/last-test.out:
	Fixed error in test output, in the previous commit.
	[c6ed0024a2fd]

	* test/last-test.out, test/last-test.sh:
	Added a test of probabilistic alignment with quality scores.
	[b7803b71b74d]

	* doc/last-pair-probs.txt, scripts/last-pair-probs.py:
	Changed how last-pair-probs interprets read names to recognize
	paired reads.
	[13f60cb07842]

2011-07-15  Martin C. Frith  <Martin C. Frith>

	* README.txt:
	Just fixed a citation.
	[671d7d26ccef]

2011-06-07  Martin C. Frith  <Martin C. Frith>

	* src/gumbel_params/njn_localmaxstat.hpp,
	src/gumbel_params/sls_pvalues.cpp:
	Fixed lastex crashing on some systems. (Thanks: Edward Wijaya)
	[6bbd46d308f3]

2011-06-03  Martin C. Frith  <Martin C. Frith>

	* doc/last-tutorial.txt, doc/lastal.txt, doc/maf-convert.txt,
	examples/multiMito.maf, scripts/maf-convert.py, scripts/maf-join.py,
	scripts/maf-swap.py, src/Alignment.cc, src/Alignment.hh,
	src/AlignmentWrite.cc, src/Centroid.cc, src/Centroid.hh,
	src/LastalArguments.cc, test/last-test.out:
	! 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.
	[67a953e00e55]

2011-05-29  Martin C. Frith  <Martin C. Frith>

	* src/SegmentPairPot.cc:
	Fixed lastal slowness when self-comparing many short sequences.
	[d6192a3c88ef]

2011-05-25  Martin C. Frith  <Martin C. Frith>

	* src/Centroid.hh:
	Fixed a compile error with some compilers.
	[6bfb15a7f1d5]

	* src/Alignment.cc, src/Centroid.cc, src/Centroid.hh,
	src/LastalArguments.cc, src/lastal.cc:
	Enabled probabilistic alignment with sequence quality data, and LAMA
	(not documented yet).
	[cb423a218e96]

2011-05-19  Martin C. Frith  <Martin C. Frith>

	* src/SegmentPair.cc, src/SegmentPair.hh, src/SegmentPairPssm.cc,
	src/gaplessPssmXdrop.cc, src/gaplessPssmXdrop.hh,
	src/gaplessTwoQualityXdrop.cc, src/gaplessTwoQualityXdrop.hh,
	src/gaplessXdrop.cc, src/gaplessXdrop.hh, src/lastal.cc,
	src/makefile:
	Made lastal's gapless extensions a bit faster.
	[3734b1b92586]

	* src/MultiSequence.hh, src/lastal.cc, test/last-test.out:
	Write reference size in the lastal output header.
	[0d9ecd24c1f5]

2011-05-10  Martin C. Frith  <Martin C. Frith>

	* README.txt, doc/FAQ.txt, doc/lastex.txt, scripts/maf-convert.py,
	src/LastdbArguments.hh, src/SegmentPairPot.hh, src/XdropAligner.hh,
	src/fileMap.hh, test/last-test.sh:
	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.
	[0e43facd304b]

2011-04-20  Martin C. Frith  <Martin C. Frith>

	* src/MultiSequence.cc, src/MultiSequence.hh, src/lastal.cc,
	src/makefile:
	Enable lastal to read quality data written by lastdb (not useful
	yet).
	[a2c237e87290]

	* src/LastdbArguments.cc, src/LastdbArguments.hh, src/lastdb.cc,
	src/makefile:
	Enabled lastdb to read fastq data (not yet useful).
	[253d2a669c72]

	* src/LastalArguments.cc, src/LastalArguments.hh,
	src/SequenceFormat.hh, src/lastal.cc, src/makefile:
	Refactor: extracted an enum.
	[f07685f9dd74]

2011-04-19  Martin C. Frith  <Martin C. Frith>

	* src/MultiSequence.hh, src/MultiSequenceQual.cc:
	Refactor: made the quality data mmap-able.
	[044a53b12c42]

	* src/Alignment.hh, src/AlignmentWrite.cc, src/VectorOrMmap.hh:
	Enable writing of qualities for both sequences in maf output.
	[2ba224d5ad0c]

	* src/OneQualityScoreMatrix.hh, src/TwoQualityScoreMatrix.cc,
	src/TwoQualityScoreMatrix.hh, src/VectorOrMmap.hh,
	src/qualityScoreUtil.hh:
	Minor code enhancements.
	[93e9a81040c8]

2011-04-15  Martin C. Frith  <Martin C. Frith>

	* doc/lastal.txt, src/MultiSequenceQual.cc,
	src/OneQualityScoreMatrix.cc, src/OneQualityScoreMatrix.hh,
	src/QualityPssmMaker.cc, src/QualityPssmMaker.hh,
	src/QualityScoreCalculator.cc, src/QualityScoreCalculator.hh,
	src/ScoreMatrix.cc, src/TwoQualityScoreMatrix.cc,
	src/TwoQualityScoreMatrix.hh, src/lastal.cc, src/makefile,
	src/qualityScoreUtil.hh:
	! 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.
	[18fc36efc723]

2011-04-14  Martin C. Frith  <Martin C. Frith>

	* test/last-test.out, test/last-test.sh, test/mouse_tss_prb.txt:
	Added a test for sequence quality data in prb format.
	[2027f4e14326]

2011-03-29  Martin C. Frith  <Martin C. Frith>

	* doc/last-pair-probs.txt, scripts/last-map-probs.py, scripts/last-
	pair-probs.py, src/makefile:
	Added --rna option to last-pair-probs.
	[3ac7c4da5743]

2011-03-28  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, src/Xdrop3FrameAligner.cc:
	!! Bugfix: the DNA-vs-protein gapped extension was losing some good
	alignments.
	[37bdfb545cc9]

2011-03-22  Martin C. Frith  <Martin C. Frith>

	* doc/last-map-probs.txt, scripts/last-map-probs.py:
	Made last-map-probs read its input just once, to avoid huge temp
	files. Tried to clarify the last-map-probs document.
	[5068d4835985]

2011-02-14  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, doc/last-map-probs.txt, doc/last-pair-probs.txt, doc
	/last-tutorial.txt, doc/tag-seeds.txt, scripts/last-pair-probs.py,
	scripts/maf-sort.sh, src/Alphabet.cc:
	Added last-pair-probs script and document. Allow "." in sequences
	(appears in some fastq files). Made maf-sort more efficient.
	[6c6ac7c8f6ed]

2011-02-08  Martin C. Frith  <Martin C. Frith>

	* doc/last-scripts.txt, doc/maf-cull.txt, scripts/maf-sort.sh:
	Bugfix: maf-sort mangled alignment data containing "#". Added maf-
	sort option to sort by sequences other than the top one.
	[edcab3015d61]

2011-01-31  Martin C. Frith  <Martin C. Frith>

	* doc/last-map-probs.txt, doc/last-tutorial.txt, doc/lastal.txt,
	scripts/maf-convert.py, src/lastal.cc:
	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.
	[03d481e668b5]

2011-01-19  Martin C. Frith  <Martin C. Frith>

	* scripts/maf-convert.py:
	Bugfix: sam headers should be tab-delimited.
	[3bdbbd585326]

2011-01-08  Martin C. Frith  <Martin C. Frith>

	* doc/maf-convert.txt, scripts/maf-convert.py:
	Added sam header option to maf-convert.
	[effa83a4ab04]

2011-01-07  Martin C. Frith  <Martin C. Frith>

	* doc/last-map-probs.txt, doc/last-tutorial.txt, doc/maf-convert.txt:
	Removed discussion of repeats from docs.
	[3d8ccc865d9c]

2010-12-29  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc, src/lastal.cc:
	Allow all types of lowercase masking when using sequence quality
	data.
	[e61008375f19]

2010-12-28  Martin C. Frith  <Martin C. Frith>

	* README.txt, doc/last-tutorial.txt, doc/lastal.txt:
	Improved the documents (thanks: Hamada-san, Terai-san.
	[fc13354d5296]

2010-12-09  Martin C. Frith  <Martin C. Frith>

	* README.txt, doc/FAQ.txt, doc/last-manual.txt, doc/last-tutorial.txt,
	doc/lastal.txt, doc/lastdb.txt, doc/tag-seeds.txt,
	src/LastalArguments.cc:
	Rewrote much of the documentation: separated tutorial from
	reference.
	[548a2c0737e3]

	* doc/maf-convert.txt, examples/multiMito.sh, scripts/maf-convert.py:
	Bugfix: made maf-convert not crash for blast output format!
	[2d744992211f]

2010-11-26  Martin C. Frith  <Martin C. Frith>

	* doc/last-map-probs.txt, scripts/maf-convert.py:
	Minor enhancements.
	[09d184ab20ae]

2010-11-25  Martin C. Frith  <Martin C. Frith>

	* doc/last-map-probs.txt, doc/last-scripts.txt, doc/maf-convert.txt,
	scripts/last-map-probs.py, scripts/maf-convert.py:
	! 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.
	[f19b6c1181db]

	* scripts/maf-swap.py:
	Made maf-swap keep q lines with s lines.
	[f2a92617f255]

2010-11-18  Martin C. Frith  <Martin C. Frith>

	* src/QualityScoreCalculator.cc:
	Added a partial check for wrong FASTQ format.
	[25b71c13313a]

2010-11-12  Martin C. Frith  <Martin C. Frith>

	* doc/maf-cull.txt, scripts/maf-cull.py:
	Added alignment-culling script.
	[2d7d24ffbaf0]

	* doc/last-scripts.txt, scripts/maf-sort.sh, scripts/maf-swap.py:
	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.
	[bd0c70e36eed]

2010-11-08  Martin C. Frith  <Martin C. Frith>

	* test/illumina100.txt:
	Added a new test file (forgotten in the previous commit).
	[fb7b4acda59d]

	* doc/last-manual.txt, src/LastalArguments.cc, src/LastalArguments.hh,
	src/QualityScoreCalculator.cc, src/lastal.cc, test/last-test.out,
	test/last-test.sh:
	! Changed the interpretation of lastal -Q, to add FASTQ-Illumina
	input format.
	[980c3aa1552f]

	* src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc,
	src/makefile:
	Refactor: use an enum instead of obscure int values.
	[711539bf55bc]

2010-11-02  Martin C. Frith  <Martin C. Frith>

	* doc/last-scripts.txt, scripts/maf-convert.py, scripts/maf2html.py:
	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.
	[977125273601]

2010-10-13  Martin C. Frith  <Martin C. Frith>

	* scripts/last-map-probs.py:
	Fixed last-map-probs.py crashing (math overflow) on large
	alignments.
	[fd7ebdab1b09]

2010-10-12  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, doc/last-manual.txt, doc/tag-seeds.txt,
	src/LastdbArguments.cc:
	Made lastdb's default volume size (-s) unlimited, to simplify
	typical usage.
	[bd155781bf7a]

	* src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc, test
	/last-test.out:
	Changed the default setting of lastal -u: made it depend on lastdb
	-c.
	[9e28051e245c]

	* doc/last-manual.txt, src/LastalArguments.cc, src/LastalArguments.hh,
	src/lastal.cc, test/last-test.out:
	Added lastal -z option: maximum score drop for final gapped
	alignments.
	[6d4d82b3b427]

	* doc/last-manual.txt, src/LastalArguments.cc, src/SegmentPairPot.cc,
	src/SegmentPairPot.hh, src/lastal.cc:
	! Changed lastal -u: new option to mask lowercase during gapped
	extensions but not "final" extensions (i.e. do gapped extensions
	twice).
	[4f0640e38978]

	* scripts/last-dotplot.py, scripts/last-map-probs.py:
	Added colour options to the dotplot script.
	[e908650d665a]

2010-08-20  Martin C. Frith  <Martin C. Frith>

	* src/SegmentPair.hh, src/SegmentPairPot.cc, src/SegmentPairPot.hh,
	src/lastal.cc:
	Reorganized code for gapless & gapped extensions. Results should be
	identical, provided that max gapped dropoff >= max gapless dropoff.
	[10b733b90b9b]

	* src/SegmentPairPot.cc, src/SegmentPairPot.hh, src/lastal.cc:
	Minor refactoring.
	[efe9ee7fecf7]

2010-08-19  Martin C. Frith  <Martin C. Frith>

	* src/gumbel_params/mcf_local_alignment_evaluer.cpp, src/lastex.cc:
	Made lastex check for bad input more carefully.
	[d934e2242ad2]

2010-08-04  Martin C. Frith  <Martin C. Frith>

	* src/CyclicSubsetSeed.cc:
	Bugfix: made lastdb allow non-alphabetic symbols in user-defined
	alphabets.
	[f2d461a671f8]

2010-08-03  Martin C. Frith  <Martin C. Frith>

	* src/CA_code/lambda_calculator.c, src/QualityScoreCalculator.cc,
	src/lastdb.cc:
	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)
	[8649e85be4c2]

2010-06-28  Martin C. Frith  <Martin C. Frith>

	* scripts/last-dotplot.py, src/MultiSequence.cc,
	src/MultiSequenceQual.cc:
	Bugfix: made last-dotplot.pl check for no alignments, instead of
	crashing. Made lastdb and lastal check for '>' in FASTA and '@' in
	FASTQ.
	[3f6d0bf8c8dd]

2010-06-24  Martin C. Frith  <Martin C. Frith>

	* src/gumbel_params/mcf_local_alignment_evaluer.cpp:
	Made lastex results more reproducible, by removing time limits.
	[becf89661310]

2010-06-20  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, src/MultiSequence.hh, src/MultiSequenceQual.cc:
	Read PSSM names; ensure lastal doesn't try to use non-existent
	PSSMs.
	[731614e5b9c5]

2010-06-18  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc:
	Clarified the default values of some lastal options.
	[98e8f237f77a]

	* src/lastal.cc:
	Bugfix: the PSSM reverse-complementation routine was wrong.
	[539c1c670daa]

	* doc/last-manual.txt, src/LastalArguments.cc, src/LastalArguments.hh,
	src/MultiSequence.hh, src/MultiSequenceQual.cc,
	src/ScoreMatrixRow.hh, src/lastal.cc, src/makefile:
	Allow PSSMs as queries for lastal!
	[620742f1b380]

2010-06-17  Martin C. Frith  <Martin C. Frith>

	* src/lastex.cc:
	Made lastex sensibly handle a both-strand translated alignments
	file.
	[449b5ece6113]

	* src/CA_code/lambda_calculator.c, src/QualityScoreCalculator.hh,
	src/ScoreMatrix.cc, src/XdropAlignerPssm.cc,
	src/gumbel_params/sls_alp_data.cpp:
	Bugfix: made lastex work with weird letter frequencies (asymmetric
	with zeros). Improved some error messages & other minor code
	improvements.
	[7cb04489fe4d]

2010-06-02  Martin C. Frith  <Martin C. Frith>

	* scripts/maf-convert.py:
	Made maf-convert.py write expect values in tab output, if present in
	the input.
	[fd95006a5bf7]

2010-05-17  Martin C. Frith  <Martin C. Frith>

	* src/lastdb.cc, src/lastex.cc:
	Fixed compilation error & warning that occurred on some systems.
	[a4096022c048]

2010-05-14  Martin C. Frith  <Martin C. Frith>

	* doc/lastex.txt, src/AlignmentPot.cc, src/Alphabet.cc,
	src/Centroid.cc, src/CyclicSubsetSeed.cc, src/DiagonalTable.hh,
	src/GeneticCode.cc, src/LastalArguments.cc, src/Mmap.hh,
	src/ScoreMatrix.cc, src/SubsetSuffixArraySort.cc, src/io.cc:
	Tried to make the C++ more strictly correct and portable.
	[b69cf6df7e1f]

2010-05-12  Martin C. Frith  <Martin C. Frith>

	* src/makefile:
	Try to put the correct version number in lastex's output.
	[5661473b83f7]

	* makefile, src/lastex.cc:
	Write the version number in lastex's output. Exclude executable
	files from the distribution.
	[f88aec669c0e]

	* doc/evalue-tables.txt, doc/last-manual.txt, doc/last-scripts.txt,
	doc/lastex.txt, examples/HOXD70, examples/TiTv212, makefile,
	src/LastexArguments.cc, src/LastexArguments.hh,
	src/gumbel_params/common/ncbi_export.h,
	src/gumbel_params/corelib/ncbi_limits.h,
	src/gumbel_params/corelib/ncbidbg.hpp,
	src/gumbel_params/corelib/ncbistd.hpp,
	src/gumbel_params/corelib/ncbistl.hpp,
	src/gumbel_params/corelib/ncbistre.hpp,
	src/gumbel_params/corelib/ncbitype.h,
	src/gumbel_params/mcf_local_alignment_evaluer.cpp,
	src/gumbel_params/mcf_local_alignment_evaluer.hpp,
	src/gumbel_params/ncbi_pch.hpp, src/gumbel_params/njn_approx.hpp,
	src/gumbel_params/njn_doubletype.hpp,
	src/gumbel_params/njn_dynprogprob.cpp,
	src/gumbel_params/njn_dynprogprob.hpp,
	src/gumbel_params/njn_dynprogproblim.cpp,
	src/gumbel_params/njn_dynprogproblim.hpp,
	src/gumbel_params/njn_dynprogprobproto.cpp,
	src/gumbel_params/njn_dynprogprobproto.hpp,
	src/gumbel_params/njn_function.hpp,
	src/gumbel_params/njn_integer.hpp, src/gumbel_params/njn_ioutil.cpp,
	src/gumbel_params/njn_ioutil.hpp,
	src/gumbel_params/njn_localmaxstat.cpp,
	src/gumbel_params/njn_localmaxstat.hpp,
	src/gumbel_params/njn_localmaxstatmatrix.cpp,
	src/gumbel_params/njn_localmaxstatmatrix.hpp,
	src/gumbel_params/njn_localmaxstatutil.cpp,
	src/gumbel_params/njn_localmaxstatutil.hpp,
	src/gumbel_params/njn_matrix.cpp, src/gumbel_params/njn_matrix.hpp,
	src/gumbel_params/njn_memutil.hpp, src/gumbel_params/njn_root.hpp,
	src/gumbel_params/njn_vector.hpp, src/gumbel_params/random_gen.cpp,
	src/gumbel_params/sls_alp.cpp, src/gumbel_params/sls_alp.hpp,
	src/gumbel_params/sls_alp_data.cpp,
	src/gumbel_params/sls_alp_data.hpp,
	src/gumbel_params/sls_alp_regression.cpp,
	src/gumbel_params/sls_alp_regression.hpp,
	src/gumbel_params/sls_alp_sim.cpp,
	src/gumbel_params/sls_alp_sim.hpp,
	src/gumbel_params/sls_normal_distr_array.hpp,
	src/gumbel_params/sls_pvalues.cpp,
	src/gumbel_params/sls_pvalues.hpp,
	src/gumbel_params/util/random_gen.hpp, src/lastex.cc, src/makefile:
	Added lastex: expected numbers of alignments for random sequences!
	[0356ab56fc53]

	* src/LastalArguments.cc, src/LastalArguments.hh, test/asymmetric.mat:
	Changed the prefix for options in the matrix file, from "#lastal" to
	just "#last". ("#lastal" still works.)
	[3a8017f99bce]

	* src/lastdb.cc:
	Added lastdb warning if the input doesn't look like DNA.
	[489e81296b19]

2010-05-10  Martin C. Frith  <Martin C. Frith>

	* src/LastdbArguments.cc, src/LastdbArguments.hh, src/lastdb.cc:
	Gave lastdb an option to just count sequences & letters.
	[86faa9559bca]

	* src/Alphabet.cc, src/Alphabet.hh, src/lastdb.cc:
	Made lastdb count sequences & letters (not used yet).
	[5d322b56849a]

	* src/MultiSequence.cc:
	Made FASTA-reading faster.
	[2d05b4ae9488]

2010-05-08  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, src/LambdaCalculator.hh,
	src/LastdbArguments.cc, src/lastdb.cc:
	Made yass.seed the default for DNA only.
	[223bac5a97a9]

2010-04-08  Martin C. Frith  <Martin C. Frith>

	* src/CA_code/lambda_calculator.c, src/CA_code/lambda_calculator.h,
	src/LambdaCalculator.cc, src/LambdaCalculator.hh, src/lastal.cc,
	test/last-test.out:
	Rewrote some code for getting probabilities from a scoring matrix.
	[d984c04b8599]

	* test/asymmetric.mat, test/last-test.out, test/last-test.sh:
	Added a test with an asymmetric scoring matrix.
	[a79e00ba5f46]

	* doc/last-manual.txt, src/Alignment.cc, src/Alignment.hh,
	src/AlignmentWrite.cc, test/last-test.out:
	Made centroid alignment report the score of the ordinary gapped
	alignment.
	[cee3aa1623dc]

	* src/AlignmentWrite.cc, src/lastal.cc, src/lastdb.cc:
	Minor refactoring.
	[ea70b9170817]

	* src/GeneralizedAffineGapCosts.hh, src/Xdrop3FrameAligner.cc,
	src/XdropAligner.cc, src/io.hh:
	Made file I/O error messages a bit more specific; minor refactoring.
	[cde91a34dd89]

2010-04-02  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, doc/evalue-tables.txt, doc/last-manual.txt, doc/tag-
	seeds.txt, examples/multiMito.sh, src/Alignment.hh,
	src/CyclicSubsetSeed.cc, src/CyclicSubsetSeed.hh,
	src/LastdbArguments.cc, src/SegmentPairPot.hh,
	src/SubsetSuffixArraySort.cc, src/lastal.cc, src/lastdb.cc, test
	/last-test.sh:
	Made yass.seed the default seed pattern. Greatly improved the
	documents & LAST recipes: please re-read them!
	[24f943b3495a]

2010-03-23  Martin C. Frith  <Martin C. Frith>

	* scripts/maf-convert.py, src/LastalArguments.cc,
	src/LastdbArguments.cc, src/SubsetSuffixArray.cc,
	src/SubsetSuffixArray.hh, src/lastal.cc, src/lastdb.cc:
	Made maf-convert.py work with older versions of python. Avoided some
	warnings with some compilers.
	[21e8d6b7a674]

	* doc/last-scripts.txt, scripts/maf-convert.py, scripts/maf2tab.py:
	Bugfix: maf2tab didn't work on translated alignments. Replaced it
	with maf-convert.py (can also write AXT format).
	[56fd23dee4be]

2010-03-18  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, src/Alignment.hh, src/AlignmentWrite.cc,
	src/MultiSequence.cc, src/MultiSequence.hh,
	src/MultiSequenceQual.cc, src/lastal.cc, src/lastdb.cc:
	Bugfix: fixed errors related to volumes and batches >~4 gigabytes.
	[d91b6a9d0bfb]

2010-03-06  Martin C. Frith  <Martin C. Frith>

	* scripts/maf2tab.py, src/lastal.cc, test/last-test.out:
	Made lastal write a comment line between query batches: might help
	parsers. Made maf2tab.py preserve comment lines (but it might move
	them).
	[232af295bff6]

2010-02-27  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, doc/tag-seeds.txt, src/LastalArguments.cc,
	src/LastalArguments.hh, src/LastdbArguments.cc, src/lastal.cc, test
	/last-test.out:
	Added lastal -n option to limit gapless alignments.
	[69172cf2778d]

2010-02-16  Martin C. Frith  <Martin C. Frith>

	* examples/TiTv212, src/LastalArguments.cc, src/LastdbArguments.cc:
	Made lastdb and lastal require at least one sequence file.
	[24ef4fb0d864]

2010-02-02  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, src/Mmap.hh, src/MultiSequence.cc,
	src/MultiSequence.hh, src/MultiSequenceQual.cc,
	src/SubsetSuffixArray.cc, src/SubsetSuffixArray.hh,
	src/SubsetSuffixArraySort.cc, src/VectorOrMmap.hh, src/fileMap.cc,
	src/fileMap.hh, src/makefile:
	Enabled memory sharing by parallel lastal runs.
	[e2171f4d2fde]

2010-02-01  Martin C. Frith  <Martin C. Frith>

	* doc/last-scripts.txt, scripts/last-dotplot.py:
	Enable dotplots to have zero margins.
	[f6c21d78378a]

2010-01-31  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, scripts/last-map-probs.py, scripts/last-remove-
	dominated.py, scripts/maf-join.py, scripts/maf-sort.sh, scripts/maf-
	swap.py, scripts/maf2html.py, scripts/maf2tab.py:
	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.
	[9b9b3d422dcd]

2010-01-18  Martin C. Frith  <Martin C. Frith>

	* src/Alphabet.cc, src/Alphabet.hh, src/LastalArguments.cc:
	Fixed build error & warning that occurred on some platforms.
	[48eda6d3dc73]

	* doc/FAQ.txt, doc/last-manual.txt:
	Added citations & FAQs to the docs.
	[db3f15bf5c2e]

	* src/Alignment.hh, src/AlignmentWrite.cc, src/Alphabet.cc,
	src/Alphabet.hh, src/GeneticCode.cc, src/GeneticCode.hh,
	src/MultiSequence.cc, src/MultiSequence.hh, src/io.hh,
	src/lastal.cc, src/lastdb.cc:
	Refactor: finished encapsulating the sequence data.
	[988c97f73036]

2010-01-15  Martin C. Frith  <Martin C. Frith>

	* src/AlignmentWrite.cc, src/MultiSequence.hh, src/lastal.cc,
	src/lastdb.cc:
	Refactor: further reduced direct access to the seqeunce data...
	[e9fb994c7f43]

2010-01-14  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.hh, src/AlignmentWrite.cc, src/Alphabet.cc,
	src/Alphabet.hh, src/MultiSequence.hh, src/lastal.cc:
	Refactor: reduce direct access to the seqeunce data (aim to
	encapsulate it).
	[97bf019f979f]

	* src/Alphabet.cc, src/Alphabet.hh:
	Refactor: simplified some code.
	[2a4e310a75d8]

2009-10-30  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, doc/evalue-tables.txt, doc/last-manual.txt,
	src/Alignment.cc, src/AlignmentWrite.cc, src/Xdrop3FrameAligner.hh,
	src/lastal.cc:
	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.
	[a6a6350e9130]

2009-10-29  Martin C. Frith  <Martin C. Frith>

	* src/XdropAligner.hh:
	Made lastal gapped extension a fair bit faster. (I don't understand
	why.)
	[29e993bcdf94]

	* src/Xdrop3FrameAligner.cc, src/XdropAligner.cc, src/XdropAligner.hh,
	src/XdropAlignerPssm.cc, src/lastal.cc:
	Made lastal gapped extension a bit faster. Made lastal -v write the
	count of initial matches.
	[f17b15f16c84]

2009-10-26  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt:
	Explain lowercase & repeats a bit in the manual.
	[197c09afb831]

	* src/SubsetSuffixArray.cc:
	Made lastal match-finding slightly faster.
	[1939a7f661cb]

2009-10-23  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, examples/multiMito.sh, examples/myalns.maf,
	src/Alphabet.cc, src/Alphabet.hh, src/LastalArguments.cc,
	src/LastdbArguments.cc, src/lastal.cc, src/lastdb.cc, test/last-
	test.out, test/last-test.sh:
	! 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.
	[993c8ffa844f]

2009-10-22  Martin C. Frith  <Martin C. Frith>

	* examples/yass.seed, src/lastal.cc, src/lastdb.cc, test/last-
	test.out, test/last-test.sh:
	Added a test of subset seeds; a few cosmetic changes.
	[a9dee751cc84]

	* doc/last-manual.txt, doc/tag-seeds.txt, src/Alphabet.cc,
	src/Alphabet.hh, src/CyclicSubsetSeed.cc, src/CyclicSubsetSeed.hh,
	src/LastalArguments.cc, src/LastdbArguments.cc,
	src/LastdbArguments.hh, src/PeriodicSpacedSeed.cc,
	src/PeriodicSpacedSeed.hh, src/SubsetSuffixArray.cc,
	src/SubsetSuffixArray.hh, src/SubsetSuffixArraySort.cc,
	src/SuffixArray.cc, src/SuffixArray.hh, src/SuffixArraySort.cc,
	src/lastal.cc, src/lastdb.cc, src/makefile:
	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.
	[d8f213e7fcfa]

2009-10-21  Martin C. Frith  <Martin C. Frith>

	* src/SuffixArray.cc, src/SuffixArray.hh, src/lastal.cc:
	Just re-organized some calculations. Lastal will now refuse to read
	older lastdb databases if the bucket depth = 0.
	[b75124274b95]

2009-10-16  Martin C. Frith  <Martin C. Frith>

	* src/SuffixArray.hh, src/SuffixArraySort.cc:
	Trivially re-organised the suffix sorting code.
	[5df0e44baf76]

	* src/SuffixArray.cc, src/SuffixArray.hh, src/SuffixArraySort.cc,
	src/lastal.cc, src/lastdb.cc:
	Refactored the suffix array code yet more (removed the
	constructor)...
	[f66e82b62f6f]

	* src/PeriodicSpacedSeed.cc, src/PeriodicSpacedSeed.hh,
	src/SuffixArray.cc, src/SuffixArray.hh, src/SuffixArraySort.cc,
	src/lastal.cc, src/lastdb.cc:
	Refactored the suffix array code some more (removed reference
	members)...
	[b26861ffe380]

	* src/SuffixArray.hh, src/SuffixArraySort.cc:
	Refactored suffix sorting a bit.
	[2480447181f8]

2009-10-13  Martin C. Frith  <Martin C. Frith>

	* test/SRR001981-1k.fastq:
	Added missing FASTQ test data!
	[0bfadb999cb3]

	* src/Alignment.cc, src/Alphabet.cc, src/Alphabet.hh,
	src/SuffixArray.cc:
	Minor refactoring.
	[ecbe255af190]

	* src/SuffixArray.cc, src/SuffixArray.hh, src/SuffixArraySort.cc,
	src/lastdb.cc, src/makefile:
	Code reorganization.
	[91b883ed7dd7]

	* src/LastdbArguments.cc, src/LastdbArguments.hh, src/SuffixArray.cc,
	src/SuffixArray.hh, src/lastal.cc, src/lastdb.cc:
	Minor code cleaning.
	[db41c7b6f398]

2009-10-05  Martin C. Frith  <Martin C. Frith>

	* test/last-test.out, test/last-test.sh:
	Added a test with FASTQ sequence quality data.
	[45b643a37d64]

2009-10-04  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc, test
	/last-test.out, test/last-test.sh:
	Changed the default "maximum score dropoff for gapless extensions"
	(lastal -y): made it adapt better to the scoring matrix.
	[b3092a865c66]

	* doc/last-manual.txt, src/Alignment.cc, src/Alignment.hh,
	src/GeneticCode.hh, src/LastalArguments.cc, src/ScoreMatrix.hh,
	src/Xdrop3FrameAligner.cc, src/Xdrop3FrameAligner.hh,
	src/XdropAligner.cc, src/XdropAligner.hh, src/lastal.cc,
	src/makefile, test/last-test.out:
	Added frameshifting alignment!
	[0c5add9fff75]

2009-10-02  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, scripts/last-dotplot.py, scripts/last-map-
	probs.py, scripts/last-reduce-alignments.sh, scripts/last-remove-
	dominated.py, scripts/maf-join.py, scripts/maf-sort.sh, scripts/maf-
	swap.py, scripts/maf2html.py, scripts/maf2tab.py,
	src/LastalArguments.cc, src/LastdbArguments.cc,
	src/LastdbArguments.hh, src/lastal.cc, src/lastdb.cc, test/last-
	test.out, test/last-test.sh:
	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.
	[d68ccbc06d73]

2009-09-30  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, src/Alignment.cc, src/Alignment.hh,
	src/AlignmentWrite.cc, src/GeneralizedAffineGapCosts.cc,
	src/GeneticCode.cc, src/GeneticCode.hh, src/LastalArguments.hh,
	src/lastal.cc:
	Generalized some of the code in preparation for frameshifts.
	[926d2c979e2d]

2009-09-28  Martin C. Frith  <Martin C. Frith>

	* examples/vertebrateMito.gc, src/Alignment.hh, src/AlignmentWrite.cc,
	src/GeneticCode.cc, src/GeneticCode.hh, src/LastalArguments.cc,
	src/LastalArguments.hh, src/lastal.cc, src/makefile, test/Q2LCP8.fa,
	test/last-test.out, test/last-test.sh:
	Added translated alignment (but without frameshifts for now)!
	[82232c885289]

	* doc/last-manual.txt, doc/tag-seeds.txt, src/Alignment.hh,
	src/AlignmentWrite.cc, src/CA_code/lambda_calculator.c,
	src/LastalArguments.cc, src/SuffixArray.cc, src/lastal.cc, test
	/last-test.sh:
	!! 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.
	[4ab7d1100a4b]

2009-09-24  Martin C. Frith  <Martin C. Frith>

	* src/SuffixArray.cc, src/SuffixArray.hh, src/lastal.cc,
	src/lastdb.cc:
	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.
	[b6eac8b7ef80]

2009-09-15  Martin C. Frith  <Martin C. Frith>

	* doc/tag-seeds.txt, src/lastal.cc, test/last-test.out, test/last-
	test.sh:
	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.
	[2cffd9814c4f]

2009-08-31  Martin C. Frith  <Martin C. Frith>

	* doc/last-scripts.txt, scripts/last-map-probs.py, src/lastal.cc, test
	/last-test.out:
	Added a script to calculate mapping probabilities (& minimal
	documentation). Made lastal always try to calculate lambda (hence
	default temperature).
	[e3aa13898c8a]

2009-08-22  Martin C. Frith  <Martin C. Frith>

	* src/SuffixArray.cc, src/SuffixArray.hh:
	Made lastdb faster for DNA, with a specialized 4-letter radix sort.
	[00533dfd758e]

	* doc/last-manual.txt, doc/tag-seeds.txt,
	src/QualityScoreCalculator.cc, src/QualityScoreCalculator.hh,
	src/SegmentPair.cc, src/lastal.cc, src/lastdb.cc:
	Fixed underflow error with phred score=0 and huge mismatch cost.
	Friendlier out-of-memory message. Improved the documentation a bit.
	[c4f692277a02]

2009-06-14  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, doc/tag-seeds.txt, src/Alignment.cc,
	src/Alignment.hh, src/AlignmentWrite.cc, src/LastalArguments.cc,
	src/LastalArguments.hh, src/MultiSequence.hh,
	src/MultiSequenceQual.cc, src/QualityScoreCalculator.cc,
	src/QualityScoreCalculator.hh, src/SegmentPair.cc,
	src/SegmentPair.hh, src/SegmentPairPssm.cc, src/XdropAligner.cc,
	src/XdropAligner.hh, src/XdropAlignerPssm.cc, src/lastal.cc,
	src/makefile:
	Made lastal able to use sequence quality scores!
	[11287126adb6]

	* doc/tag-seeds.txt, scripts/maf-swap.py, src/Alphabet.cc,
	src/SegmentPairPot.hh, src/lastal.cc, src/makefile:
	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.
	[2cf11c3ac7d0]

2009-06-08  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc:
	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.
	[561788605741]

2009-06-07  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/AlignmentWrite.cc, src/SegmentPair.cc,
	src/SegmentPair.hh, src/XdropAligner.cc, src/XdropAligner.hh,
	src/lastal.cc, src/makefile:
	Minor code re-organization.
	[635e94b537b2]

2009-05-30  Martin C. Frith  <Martin C. Frith>

	* src/MultiSequence.cc, src/MultiSequence.hh, src/SuffixArray.cc,
	src/lastal.cc, src/lastdb.cc, test/last-test.maf, test/last-
	test.out, test/last-test.sh:
	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.
	[3e822d0420a6]

2009-05-27  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt, src/GeneralizedAffineGapCosts.hh, src/lastal.cc:
	Added a FAQ item. Refactor: reduced parameter-passing in lastal.cc.
	[49fb8c5ea7dd]

2009-05-08  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, doc/last-scripts.txt, scripts/maf2html.py:
	Added maf2html.py: converts MAF-format alignments to coloured HTML
	format. Disguised the email address in last-manual.txt.
	[bf790a859c2a]

2009-05-02  Martin C. Frith  <Martin C. Frith>

	* scripts/last-dotplot.py, src/XdropAligner.cc, src/makefile:
	Made lastal gapped extension faster, by removing an assert
	(surprising). Bugfix: made last-dotplot.py not crash on small
	sequences.
	[726cb608cd2b]

2009-04-08  Martin C. Frith  <Martin C. Frith>

	* examples/myalns.maf, src/SegmentPair.cc:
	Minor code cleaning: variable name, comments.
	[b5d20c0600b5]

2009-04-02  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, examples/myalns.maf:
	Updated examples/myalns.maf to reflect the new default score
	parameters. Minor changes to last-manual.txt.
	[9b28ee63a537]

2009-04-01  Martin C. Frith  <Martin C. Frith>

	* scripts/maf-sort.sh:
	Removed unnecessary robustness from maf-sort.sh, to avoid bugs in
	unix sort(!)
	[c935c2c76860]

	* doc/evalue-tables.txt, doc/last-manual.txt, doc/last-scripts.txt,
	doc/tag-seeds.txt, examples/HOXD70, examples/TiTv212,
	examples/chickenMito.fa, examples/mouseMito.fa,
	examples/multiMito.maf, examples/multiMito.sh, scripts/maf-join.py,
	scripts/maf-sort.sh, scripts/maf-swap.py, src/LastalArguments.cc:
	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.
	[f5eadd663148]

2009-03-31  Martin C. Frith  <Martin C. Frith>

	* scripts/last-remove-dominated.py:
	Made last-remove-dominated.py faster.
	[b0006c034de9]

2009-03-30  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, doc/tag-seeds.txt, scripts/maf-sort.sh,
	src/Alignment.cc, test/last-test.maf, test/last-test.sh:
	Added gaps to MAF probability lines: easier to parse. Made maf-
	sort.sh more robust. Improved the documents a bit.
	[e6f6ff270445]

2009-03-18  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, src/LastalArguments.cc, src/LastdbArguments.cc,
	src/stringify.hh:
	Allow suffixes K(ibibyte), M(ebibyte), and G(ibibyte) for sizes.
	[1b144155c74c]

2009-03-06  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/Centroid.cc, src/Centroid.hh:
	Simplified the probability & centroid code. (Thanks: Hamada-san)
	[1121b0c98227]

2009-03-03  Martin C. Frith  <Martin C. Frith>

	* src/GeneralizedAffineGapCosts.cc, src/LastalArguments.cc, test/last-
	test.maf:
	Bugfix: overflow error made lastal discard some gapped alignments.
	[39b97ca18568]

2009-02-28  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, examples/HOXD70, src/LastalArguments.cc,
	src/LastalArguments.hh, src/ScoreMatrix.cc, src/ScoreMatrix.hh,
	src/io.cc, src/io.hh, src/lastal.cc, test/last-test.sh:
	Allow lastal options to be set in the score-matrix file.
	[9d3956d3d902]

	* src/LastalArguments.cc, src/LastalArguments.hh,
	src/LastdbArguments.cc, src/LastdbArguments.hh, src/lastal.cc,
	src/lastdb.cc:
	Minor refactoring.
	[d0a950027ac7]

2009-01-30  Martin C. Frith  <Martin C. Frith>

	* src/Alphabet.cc:
	Bugfix: for protein alignments, tyrosine was forbidden in initial
	matches. !! Old lastdb protein databases won't work properly: you
	need to re-run lastdb.
	[de27a8780950]

2008-12-30  Martin C. Frith  <Martin C. Frith>

	* src/lastal.cc, src/lastdb.cc:
	Refactor: removed some namespace tedium from the code.
	[4f503fee369c]

2008-12-24  Martin C. Frith  <Martin C. Frith>

	* doc/evalue-tables.txt, doc/last-manual.txt, doc/tag-seeds.txt:
	Updated the documentation, including a table of optimal spaced
	seeds.
	[daaf5739510a]

2008-12-22  Martin C. Frith  <Martin C. Frith>

	* src/SuffixArray.cc:
	Made lastdb bucket-making code slightly simpler & faster.
	[57c165efb568]

	* src/LastalArguments.cc, src/SuffixArray.cc, src/io.hh:
	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.
	[3ca5ea230751]

2008-12-09  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/Alignment.hh, src/ScoreMatrix.hh,
	src/XdropAligner.cc, src/XdropAligner.hh, src/lastal.cc:
	Made gapped extension faster for short sequences (e.g. tag mapping).
	[60d29e3957c5]

2008-12-08  Martin C. Frith  <Martin C. Frith>

	* src/lastal.cc:
	Bugfix: the sequence names weren't printed correctly for match-
	counting output (-j 0).
	[12d9030cf05e]

2008-12-05  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/ScoreMatrix.cc, src/makefile:
	Fixed compiler warnings with gcc 4.3
	[18843b10d9e8]

2008-11-06  Martin C. Frith  <Martin C. Frith>

	* makefile:
	Added "." after "svnversion" to support older versions of svn.
	(Thanks: Nicolas Sierro)
	[00b3dbb8f618]

2008-11-04  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc, src/LastdbArguments.cc:
	Added unistd.h includes, for getopt, so it compiles more portably(?)
	[fd6101b67cb2]

	* src/Centroid.cc, src/Centroid.hh, src/XdropAligner.cc,
	src/XdropAligner.hh, src/lastal.cc:
	Refactor: replaced a magic number with a named constant (score
	matrix size).
	[ffa2614e18f7]

2008-11-01  Martin C. Frith  <Martin C. Frith>

	* doc/last-scripts.txt, scripts/last-dotplot.py:
	Made last-dotplot.py work with older versions of Python (not
	tested).
	[0f2074e6853e]

2008-10-31  Martin C. Frith  <Martin C. Frith>

	* test/last-test.sh:
	Fixed the test script, which broke after moving HOXD70.
	[6e1ba8d97637]

	* doc/HOXD70, doc/last-manual.txt, examples/HOXD70,
	examples/fuguMito.fa, examples/humanMito.fa, examples/myalns.maf,
	makefile:
	Added the examples directory.
	[320185d87b4d]

2008-10-29  Martin C. Frith  <Martin C. Frith>

	* src/DiagonalTable.hh:
	Removed an obsolete comment.
	[42c5e4ccebcf]

	* src/DiagonalTable.hh:
	Made lastal a bit faster, by using fewer bins in DiagonalTable.
	[0d3bddb645db]

2008-10-25  Martin C. Frith  <Martin C. Frith>

	* src/Centroid.cc:
	Made the probability calculations slightly faster, by micro-
	optimization.
	[7c0912ff5085]

	* doc/last-manual.txt, src/Alignment.cc, src/Alignment.hh,
	src/Centroid.cc, src/Centroid.hh, src/lastal.cc:
	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.
	[c86b6d48881c]

2008-10-21  Martin C. Frith  <Martin C. Frith>

	* src/lastal.cc:
	Changed how seeds for gapped alignments are derived from gapless
	alignments, to prevent occasionally getting the same gapped
	alignment more than once.
	[59d3f3bb88b5]

2008-10-10  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, src/CA_code/nrutil.c:
	Removed malloc.h from nrutil.c, so it compiles on Mac OS X. Small
	additions to the manual.
	[610626404a5f]

2008-10-02  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt, doc/last-scripts.txt, makefile,
	src/Alignment.cc, src/Alignment.hh, src/CA_code/lambda_calculator.c,
	src/CA_code/lambda_calculator.h, src/CA_code/lubksb.c,
	src/CA_code/ludcmp.c, src/CA_code/nrutil.c, src/CA_code/nrutil.h,
	src/Centroid.cc, src/Centroid.hh, src/LambdaCalculator.cc,
	src/LambdaCalculator.hh, src/LastalArguments.cc,
	src/LastalArguments.hh, src/XdropAligner.hh, src/lastal.cc,
	src/makefile, test/last-test.maf, test/last-test.sh:
	Added probabilistic & centroid alignment!
	[de5ce9b3bb54]

2008-10-01  Martin C. Frith  <Martin C. Frith>

	* scripts/last-remove-dominated.py, scripts/maf-swap.py:
	Made the MAF-reading scripts cope with an extra 'p' line
	(probabilities).
	[65a3cc262718]

2008-09-30  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/Alignment.hh:
	Minor comment changes.
	[cd714102b3a2]

	* doc/last-manual.txt, doc/tag-seeds.txt, src/LastalArguments.cc,
	src/LastdbArguments.cc, src/LastdbArguments.hh, test/last-test.maf:
	!! 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.
	[1f6f2a03eb98]

	* doc/last-scripts.txt, scripts/maf-swap.py:
	Made maf-swap.py work with Python 2.3.3.
	[909d2ee4175a]

2008-09-18  Martin C. Frith  <Martin C. Frith>

	* src/AlignmentPot.hh, src/SegmentPairPot.hh, src/lastal.cc:
	Minor refactoring.
	[3dd1168849df]

	* src/XdropAligner.cc, src/XdropAligner.hh:
	Refactor: templatized some XdropAligner functions. This will be
	useful when probabilistic alignment gets added.
	[d801172578e3]

2008-09-17  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/XdropAligner.cc:
	Refactored the conversion of gapped Xdrop extensions to alignments.
	[1fedc2555ed5]

2008-09-16  Martin C. Frith  <Martin C. Frith>

	* doc/FAQ.txt:
	Added FAQ (just one entry so far).
	[58e83e93f3e0]

	* src/Alignment.cc, src/Alignment.hh, src/lastal.cc:
	Refactor: Made gapped alignments remember their seeds.
	[91e05856d155]

	* test/galGal3-M-32.fa, test/last-test.maf, test/last-test.sh:
	Added a minimal regression test.
	[aac5b622dcaa]

2008-09-11  Martin C. Frith  <Martin C. Frith>

	* src/Alignment.cc, src/AlignmentPot.hh, src/Alphabet.cc,
	src/MultiSequence.cc, src/PeriodicSpacedSeed.cc, src/ScoreMatrix.cc,
	src/ScoreMatrix.hh, src/SuffixArray.hh, src/XdropAligner.hh,
	src/lastal.cc, src/lastdb.cc:
	Added some "#include"s so that it compiles on picky systems.
	(Thanks: Charles Plessy)
	[cb9508f0bfa3]

2008-09-10  Martin C. Frith  <Martin C. Frith>

	* src/LastalArguments.cc:
	Added lastdbName to the header of the lastal output.
	[03416761788f]

	* src/lastdb.cc, src/makefile:
	Added version to lastdb ".prj" file.
	[36c3da67e3ac]

	* src/lastal.cc:
	Tiny change to the header in lastal output.
	[a598325bc0c3]

2008-09-09  Martin C. Frith  <Martin C. Frith>

	* doc/last-manual.txt:
	Added Harada-san to credits.
	[0a39bc158029]

2008-09-08  Martin C. Frith  <Martin C. Frith>

	* makefile:
	Separated "make dist" from "make all".
	[724a4bdb7734]

	* doc/last-manual.txt:
	Added Credits & Citation to last-manual.txt.
	[5125dcc2a9d8]

	* COPYING.txt, README.txt, doc/HOXD70, doc/evalue-tables.txt, doc
	/last-manual.txt, doc/last-scripts.txt, doc/tag-seeds.txt, makefile,
	scripts/last-dotplot.py, scripts/last-reduce-alignments.sh, scripts
	/last-remove-dominated.py, scripts/maf-sort.sh, scripts/maf-swap.py,
	scripts/maf2tab.py, src/Alignment.cc, src/Alignment.hh,
	src/AlignmentPot.cc, src/AlignmentPot.hh, src/Alphabet.cc,
	src/Alphabet.hh, src/DiagonalTable.cc, src/DiagonalTable.hh,
	src/GeneralizedAffineGapCosts.cc, src/GeneralizedAffineGapCosts.hh,
	src/LastalArguments.cc, src/LastalArguments.hh,
	src/LastdbArguments.cc, src/LastdbArguments.hh,
	src/MultiSequence.cc, src/MultiSequence.hh,
	src/PeriodicSpacedSeed.cc, src/PeriodicSpacedSeed.hh,
	src/ScoreMatrix.cc, src/ScoreMatrix.hh, src/SegmentPair.cc,
	src/SegmentPair.hh, src/SegmentPairPot.cc, src/SegmentPairPot.hh,
	src/SuffixArray.cc, src/SuffixArray.hh, src/XdropAligner.cc,
	src/XdropAligner.hh, src/io.cc, src/io.hh, src/lastal.cc,
	src/lastdb.cc, src/makefile, src/stringify.hh:
	First commit!
	[2b2012e60ac3]

2013-05-21  Martin C. Frith  <Martin C. Frith>

	* 0:
	Make Mercurial start counting from 1.
	[3f223f5d8e13]

