compactor for genomes files should work now


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1388 93d9a472-daf7-0310-8f21-d7befa554562
Rough cut at index creator.  Everything is still subject to change, but
a persistent index is already created.


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1390 93d9a472-daf7-0310-8f21-d7befa554562
added code to do lookup on dense indexes; hardly testeintd


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1398 93d9a472-daf7-0310-8f21-d7befa554562
...


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1400 93d9a472-daf7-0310-8f21-d7befa554562
can actually write indexes bigger than ~2GB now


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1402 93d9a472-daf7-0310-8f21-d7befa554562
oops, forgot some debug code


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1403 93d9a472-daf7-0310-8f21-d7befa554562
cutoff now in index lookup instead of creation


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1404 93d9a472-daf7-0310-8f21-d7befa554562
polished fa2dna somewhat; closes #103


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1408 93d9a472-daf7-0310-8f21-d7befa554562
polished dnaindex somewhat, refactored and cleaned up; closes #104


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1409 93d9a472-daf7-0310-8f21-d7befa554562
selection of seeds should now work in principle (though there's still an
unhandled corner case)


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1420 93d9a472-daf7-0310-8f21-d7befa554562
draft of aligner implementation


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1431 93d9a472-daf7-0310-8f21-d7befa554562
commit to make svn happy...


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1432 93d9a472-daf7-0310-8f21-d7befa554562
small reorg


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1433 93d9a472-daf7-0310-8f21-d7befa554562
primitive aligner seems to work in principle, seeds on RC'd strand seem
wonky


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1437 93d9a472-daf7-0310-8f21-d7befa554562
fixes to alignment core, seeding and lookup on RC strand.  RC's
alignment appears to still get wrong coordinates


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1443 93d9a472-daf7-0310-8f21-d7befa554562
alignments on both strands appear to work now (no backtracing, though)


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1446 93d9a472-daf7-0310-8f21-d7befa554562
added backtracing (and documentation and cleanup), seems to work on
forward strand, but not if reverse-complemented


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1448 93d9a472-daf7-0310-8f21-d7befa554562
removed some silly brainfarts, revcompl still is a mess


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1449 93d9a472-daf7-0310-8f21-d7befa554562
revamped handling of reverse complement strand---much easier to
understand, and now RC'd alignments appear to work, too


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1450 93d9a472-daf7-0310-8f21-d7befa554562
cleaned up minor messes


git-svn-id: http://biofs04/svn/bioinf/anfo/trunk@1451 93d9a472-daf7-0310-8f21-d7befa554562