gordon's Profile

gordon pushed to master at gordon/genometools Fri Dec 18 07:52:47 -0800 2009

HEAD is 11d153f2f2e3ea5fc5763385c43684aa7c5689f7

3 commits »

gordon pushed to master at gordon/genometools Mon Dec 07 15:16:28 -0800 2009

HEAD is 4fd1f032fba7d38f48f3b972f9a9f37eafe64271

Gordon Gremme committed 4fd1f032:

drop unnecessary gth_ prefix

gordon pushed to master at gordon/genometools Mon Dec 07 14:45:59 -0800 2009

HEAD is e6c83c90484bd9287bc94f85c926c3f12f87df5e

Gordon Gremme committed e6c83c90:

add new dev tool

gordon pushed to master at gordon/genometools Mon Dec 07 14:38:50 -0800 2009

HEAD is a194c70416c6ce7c1451b6b6b500dea3a800358e

Gordon Gremme committed a194c704:

add other gt_gth*.[ch] modules

gordon pushed to master at gordon/genometools Mon Dec 07 14:10:40 -0800 2009

HEAD is 7da4c3a7d9ac06a786e47d75bab797606a061fcf

Gordon Gremme committed 7da4c3a7:

add gt_gthconsensus.[ch] module

gordon pushed to master at gordon/genometools Mon Dec 07 14:00:39 -0800 2009

HEAD is 125370dde9679e37d041db7e0efffe837c0c6508

Gordon Gremme committed 125370dd:

add gt_gth.[ch] module

gordon pushed to master at gordon/genometools Mon Dec 07 13:54:06 -0800 2009

HEAD is f7d34b76740f66a5ae11b9f88812515eb251db66

Gordon Gremme committed f7d34b76:

add gth_version_func to GthPlugins

gordon pushed to master at gordon/genometools Mon Dec 07 13:47:00 -0800 2009

HEAD is 2b7c0a544dd79500703f53082a914853dab3c1e8

11 commits »

Gordon Gremme committed 2b7c0a54:

add GthSeqColConstructor to GthPlugins
Gordon Gremme committed 93327c11:

add GthInputFilePreprocessor to GthPlugins
Gordon Gremme committed 2b27f7e3:

constify GthPlugin usage
Gordon Gremme committed 51745424:

introduce GthPlugins
Gordon Gremme committed 4489ff4c:

ChainingInfo -> GthChainingInfo
satta committed 66257dd1:

src_clean
satta committed 91b2fd71:

add unit test for gt_double_* functions
satta committed 5769c45f:

fix gt_str_clone()
satta committed 720aea9a:

'pfamname' -> 'name'
satta committed 5f7c4ddd:

LTRdigest: do not expect HMMs to have 'ACC's
satta committed 39f1b184:

make gt_double_smaller_double() work correctly with negative numbers

gordon pushed to master at gordon/genometools Tue Dec 01 08:20:23 -0800 2009

HEAD is 4494ebdd68a582008ac98449203e1fc9dd33a61f

2 commits »

gordon pushed to master at gordon/genometools Fri Nov 27 02:41:47 -0800 2009

HEAD is 93a10b3a177e398521a80f4cdd08a08daca63b60

4 commits »

gordon pushed to master at gordon/genometools Fri Nov 27 02:08:21 -0800 2009

HEAD is db61d6186ddf3401c161374d708691ef4311226e

Gordon Gremme committed db61d618:

HIGHPRECPROBTYPE -> GthDbl, LOWPRECPROBTYPE -> GthFlt

gordon created tag v1.3.4 at gordon/genometools Thu Nov 19 05:42:46 -0800 2009

New tag is at gordon/genometools/tree/v1.3.4

gordon pushed to master at gordon/genometools Thu Nov 19 05:42:45 -0800 2009

HEAD is a6442df770c4d8b89a1f5620fdb0c4b18bec1a5e

Gordon Gremme committed a6442df7:

update CHANGELOG

gordon pushed to master at gordon/genometools Thu Nov 19 03:54:14 -0800 2009

HEAD is ebb6b0b62fe436edef0cebcdb5c055712b33274b

45 commits »

satta committed d2f95f03:

gtruby: add GT::CustomVisitor
satta committed 5d9b8921:

gtruby: add GT::SequenceNode
satta committed e848f787:

gruby: add GT::CommentNode
satta committed 3eea3dd6:

gtruby: add GT::RegionNode
satta committed 2a4362c0:

gtruby: add seqid accessor and visitor changes
satta committed 65272626:

gtruby: fix exception raising
satta committed 1e481252:

gtruby add GT::Error.set()
satta committed e9f07075:

add -r option to 'gt convertseq'
satta committed 82910006:

change image and wording on front page
satta committed f0d01f1b:

mention new Windows versions on website
satta committed 64cfe70f:

ltrdigest: add support for Pfam trusted and gathering cutoffs
satta committed e8310d9f:

do not fail on non-fatal condition
satta committed 584b8d09:

do not compare integersize with reference
satta committed a5d6c588:

mgth: updates to manual text
satta committed da69dad1:

sort mgth statistics output
satta committed 56929ef6:

include error_api.h in dlist_api.h
satta committed 8df825fc:

Change mgth option giexpfilename from str_array to str
satta committed 2fe62247:

fix bug caused by wrong parameter order in assert
Gordon Gremme committed bce1825f:

src_clean
satta committed db1891dd:

add MetaGenomeThreader publication to webpage

And 25 more commits...

gordon pushed to master at gordon/genometools Wed Oct 14 16:00:07 -0700 2009

HEAD is 1cd7df8c4ba104a345639b8dee4adddca7035b5e

13 commits »

Gordon Gremme committed 1cd7df8c:

src_clean
Stefan Kurtz committed 816ca83b:

Completed repfind manual.
Stefan Kurtz committed 2bde843a:

Added manual for repfind.
Stefan Kurtz committed bf089433:

Now completely integrated the test cases for repfind -r
Stefan Kurtz committed 907acb00:

Added the reverse sequence test files.
Stefan Kurtz committed dbc9e46c:

Added call to repfind -r to work portably.
Stefan Kurtz committed e4f5cdb8:

Verified option -r for all testfiles.
Stefan Kurtz committed fac8ed0e:

Add -allmax to repfind to produce all matches in reverse mode.
Stefan Kurtz committed e89e3d6c:

Allocate space for querymatch once for each matching function.
Stefan Kurtz committed 7d2fb4eb:

Introduce Querymatch which is handled in own file.
Stefan Kurtz committed 02548124:

Output of sequence numbers and relative positions in repfind.
Stefan Kurtz committed eb99a7c3:

Repfind now produces the correct format.
satta committed 55185170:

gtpython/gtruby: allow more idiomatic traversal of feature DAGs

gordon pushed to master at gordon/genometools Tue Oct 13 05:40:22 -0700 2009

HEAD is 299ec72720d2b97bdac50d7bb3a7e9bda7feafdb

Gordon Gremme committed 299ec727:

compile with assert=no

gordon pushed to master at gordon/genometools Tue Oct 13 04:49:47 -0700 2009

HEAD is 2444195099df1d10d93842389aa475b0d474c078

31 commits »

Stefan Kurtz committed 49b70b5d:

Call function for palindromic matching.
Stefan Kurtz committed 9097a474:

Introduce Querysubstring into query matching algorithm.
Stefan Kurtz committed ca940ace:

Move the Queryrep structure from inside runquerysubstringmatch to the outside.
Stefan Kurtz committed fa716954:

Renamed mmsearchiterator into mmsearchiterator_plain
Stefan Kurtz committed b0baa8fd:

Now implemented rununque as an additional testcase.
Stefan Kurtz committed a16ae382:

Implemented calls to runmerge in the testsuite.
Stefan Kurtz committed 78422826:

The comparison of the prj files is now part of the testsuite.
Stefan Kurtz committed ffad590f:

Added reference prjfiles.
Stefan Kurtz committed c7d93408:

entangled loops calling cmpdbfile.sh and rununique.sh
Stefan Kurtz committed 6fef152f:

Replace call to mkvtree/vseqselect by ruby scripts.
Stefan Kurtz committed f17cdab3:

Added script to randomly select sequences from a file
Stefan Kurtz committed 4415059b:

Added program to split files.
Stefan Kurtz committed 49b2da71:

Added break.
Stefan Kurtz committed df198a3a:

renamed fasta2sequencekeyvalues into gt_inputfiles2sequencekeyvalues and add maximum sequence length constraint for 32bit.
Stefan Kurtz committed 6b039664:

Added option -showprogress: progressbar now must be used explicitely.
Stefan Kurtz committed 517b9dce:

Rename Mtime into Sfxprogress.
Stefan Kurtz committed 8f59f0d8:

Removed duplicated words in reference to tallymer paper.
Stefan Kurtz committed d88ecae2:

Add file to describe the symbol for Protein mass matching.
Stefan Kurtz committed 80e5a003:

Use larger maximum size for keys.
Stefan Kurtz committed c0b16dbc:

Generalized script to extract keys from fasta file.

And 11 more commits...

gordon pushed to master at gordon/genometools Thu Oct 08 01:52:38 -0700 2009

HEAD is 32f69eb88a701d3b0383807ab71ea0d4a271c637

Gordon Gremme committed 32f69eb8:

OPrval -> GtOPrval

gordon pushed to master at gordon/genometools Thu Oct 08 01:44:04 -0700 2009

HEAD is 96e999816bb69337df59f70b8d78c81cf146b680

9 commits »

Gordon Gremme committed 96e99981:

GTR -> GtR
Gordon Gremme committed 3fb770b9:

Merge branch 'master' of ssh://gordon@genometools.org/var/www/pub/git/genometools
satta committed 2c5b5219:

add HMMER external source dir to .gitignore
satta committed df097f2c:

gtpython: make GTError a subclass of RuntimeError
satta committed f173b547:

gtpython: make tracks sortable
satta committed 77c1bb89:

gtruby: allow track ordering
satta committed c08ab66c:

make track order sortable
satta committed 880a03d0:

mention LTRdigest publication on website
Gordon Gremme committed ed368d6c:

add gth_input_preprocess()

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