Activity for Tagger
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Christian Iseli committed [c50b77]
cleanup after CVS to git conversion
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c4chris <> committed [a2b022]
Use new word length. Generate first and last markers.
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gio31415 <> committed [b7830e]
change tag printout for reverse strand
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c4chris <> committed [d59eb5]
No longer use repeats file.
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c4chris <> committed [90e5e9]
Move to 16 nt index, and no AC in index itself.
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c4chris <> committed [1fa6b6]
Add couple TODO items.
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FIXME <> committed [ad23f5]
This commit was manufactured by cvs2svn to create tag 'GWI_25_nt'.
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gio31415 <> committed [5b91a4]
remove generation of repeats
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c4chris <> committed [bbf8ca]
Generate partial words.
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c4chris <> committed [2d1c3f]
Implement avoiding same word search multiple times.
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c4chris <> committed [f3feff]
Remove MAX_WORD and handle all queries in one go. Introduce failed word markers.
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c4chris <> committed [30e711]
Speed things up with small buffers. For a 1GB file merge, down from over 5 minutes to 25 seconds.
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c4chris <> committed [26541c]
Skip groups of Ns in one go.
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FIXME <> committed [89f8d5]
This commit was manufactured by cvs2svn to create tag 'GWI_16_nt_noac'.
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c4chris <> committed [7f10b6]
Start update to use 21 nt tags.
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c4chris <> committed [62e8ca]
Use 25 nt word length.
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c4chris <> committed [6ccec1]
Add runme as sample.
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root <> committed [88f7a8]
initial checkin
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c4chris <> committed [640fa6]
Import into SF CVS.
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c4chris <> committed [699f83]
Fix usage message. Avoid GCC wrong warning.
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FIXME <> committed [21a635]
This commit was manufactured by cvs2svn to create tag 'GWI_single_idx_end'.
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c4chris <> committed [efbe77]
Continue update to use 21 nt tags.
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c4chris <> committed [fdbcfe]
Add some debug output.
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c4chris <> committed [93b273]
Added sortGWI.c decodeGWI.c dumpGWI.c genwin.c fetchGWI.c.
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FIXME <> committed [98c45f]
This commit was manufactured by cvs2svn to create tag 'GWI_21_nt'.
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c4chris <> committed [0eb6c6]
Use new word length.
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c4chris <> committed [0ac286]
Add TODO item.
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c4chris <> committed [ddee3f]
Use new word length.
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c4chris <> committed [aaad5b]
Allow for words > 32. Sort queries for speed.
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c4chris <> committed [fb5592]
Go back to 25 nt, increase to 16-bits acidx, drop first and last.
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c4chris <> committed [8b7508]
Add missing idx masking. Add debug code.
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c4chris <> committed [444492]
Fix leftover short. Silence gcc warning.
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c4chris <> committed [56e9d1]
Fix thinko on function exit.
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c4chris <> committed [e9b3c5]
Use 128 bits for the tag.
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c4chris <> committed [804306]
Update changelog.
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c4chris <> committed [90e5e9]
Move to 16 nt index, and no AC in index itself.
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c4chris <> committed [ded303]
Add fixGWIac.
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FIXME <> committed [9cdb9e]
This commit was manufactured by cvs2svn to create tag 'GWI_dual_offset'.
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c4chris <> committed [1e08b0]
Quieten -Wconversion warnings.
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c4chris <> committed [c4a3ca]
Add new switch info in the man page.
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c4chris <> committed [14cd8a]
Add sortGWI.1.
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c4chris <> committed [d9f96a]
Deal with incomplete reads.
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c4chris <> committed [38a89f]
Knock off 1 conversion warning.
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c4chris <> committed [7dfe80]
Tweak for i386 (32 bits).
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c4chris <> committed [e43930]
Add same output format as fetchGWI (options -n and -T).
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c4chris <> committed [968008]
Add -g option to read FASTA files. Remove mismatch option.
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c4chris <> committed [e6f44c]
Use bigger read buffer in grab_cidx() when nearing search end, but use smaller chunks at start.
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c4chris <> committed [0850dc]
Add genwin.1.
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c4chris <> committed [d6b98e]
Add tagger.spec.
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c4chris <> committed [fb5592]
Go back to 25 nt, increase to 16-bits acidx, drop first and last.
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c4chris <> committed [9a1dd7]
Add -v command line switch.
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FIXME <> committed [a01489]
This commit was manufactured by cvs2svn to create tag 'tagger_1_1'.
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c4chris <> committed [cde81e]
Add runme.
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c4chris <> committed [770269]
Silence compiler warnings.
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c4chris <> committed [2fc924]
Bump to version 1.6.
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c4chris <> committed [6bbd60]
Fix indent.
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c4chris <> committed [044ce6]
Add -d command line switch.
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c4chris <> committed [9c3f14]
Generate secondary index.
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c4chris <> committed [e47d75]
Implement long and short offsets (only comment change needed here).
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c4chris <> committed [5dbad9]
Implement long and short offsets. Add -i switch.
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c4chris <> committed [b658c2]
Fix typo and pasto.
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c4chris <> committed [3426b8]
Fix typo.
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c4chris <> committed [50e4ee]
Handle (not completely correctly) streams of Ns. Fix off by one thinko.
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c4chris <> committed [69bdca]
Start implement read files with secondary index.
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c4chris <> committed [de11da]
Cleanup warnings.
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FIXME <> committed [ac2e65]
This commit was manufactured by cvs2svn to create tag 'GWI_25_nt_wabi'.
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c4chris <> committed [27cfd8]
Implement -m switch to allow one mismatch.
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c4chris <> committed [e9f891]
Actualy finish implement read files with secondary index.
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c4chris <> committed [1af770]
Adjust temp file name.
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c4chris <> committed [bba21f]
Complete implementing IUPAC in the sequences.
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c4chris <> committed [b6d855]
Use 128 bits for the tag.
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c4chris <> committed [ab29e8]
Add GWI stuff.
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c4chris <> committed [863b0b]
Allow any number of mismatches.
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c4chris <> committed [2f7051]
Use compressed index files.
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c4chris <> committed [c471c4]
Deal with incomplete reads and writes.
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c4chris <> committed [13ba0b]
Fix size issue in lseek.
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c4chris <> committed [c16208]
Fix compressed format.
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c4chris <> committed [3c75f7]
Cleanup warnings and fix thinko for tag words order in sortWI.
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FIXME <> committed [4e72d2]
This commit was manufactured by cvs2svn to create tag 'start'.
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c4chris <> committed [72779f]
Quieten -Wconversion warnings.
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c4chris <> committed [30e711]
Speed things up with small buffers. For a 1GB file merge, down from over 5 minutes to 25 seconds.
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c4chris <> committed [0d6ecf]
Use 128 bits for the tag.
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c4chris <> committed [97f368]
Implement unspecified nucleotides for queries. Keep full line context in results. Implement -t switch for column separator.
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FIXME <> committed [1c6101]
This commit was manufactured by cvs2svn to create tag 'tagger_1_3'.
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c4chris <> committed [8a0b18]
Forgot to properly mask tag.
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c4chris <> committed [d7875e]
Cast properly to quieten compiler warnings.
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c4chris <> committed [842e9e]
Update copyright notice.
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c4chris <> committed [ed839d]
Implement word length up to 128 nucleotides.
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c4chris <> committed [157a2e]
Deal with incomplete writes.
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c4chris <> committed [b07184]
Implement -r option.
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c4chris <> committed [c7ef38]
Add wishlist.
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c4chris <> committed [167f72]
Fix stupid size mismatch.
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c4chris <> committed [f1167a]
Secondary index is endian specific. Deal with it.
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c4chris <> committed [a6435d]
Implement short read buffer in grab_cidx().
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c4chris <> committed [112f4a]
Update changelog.
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c4chris <> committed [f2fad4]
Use new index preparation method.
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c4chris <> committed [3e0b40]
Add mouse chromosome equivalences.
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c4chris <> committed [614b26]
Use -r instead of -c for rules definition file, to avoid confusion with -c for compressed index files.
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c4chris <> committed [1d5631]
Use a binary tree to track AC names and index.
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c4chris <> committed [b2fa3b]
Add decodeWI.c.
