fa6b295a9f96ce44a5773e7e90e593dd7071c8fa to 409da38feb6eebfaa307f0bc4448f783db030997 · Debian Med / scythe · GitLab

Commits on Source 142

f22a8910 intial import
Feb 02, 2011
4cb37f19 error fixed in readme: scythe does not pick out 5'-end contaminants
Feb 02, 2011
e61f86f4 added solexa 3'-end adapter sequences
Feb 02, 2011
30987f91 version bump in README.md, added caveat about usage
Feb 02, 2011
26f59b35 fixed typo in readme (thanks peterjc for finding this)
Feb 03, 2011
19b5c2d7 moved license, added more in readme, and enabled min match argument
Feb 03, 2011
e94c7981 fixed improper format in readme
Feb 03, 2011
a8d06244 more minor formatting changes to readme
Feb 03, 2011
328d98bc added sequence header tags an option, added O3 opt, refactored makefile, got...
Feb 15, 2011
5784292b resolved merge conflict from changes with min-match
Feb 15, 2011
37a8db0e removed 5' code, which scythe will maybe handle later
Apr 12, 2011
acc1c0f9 nicer handling of not found FASTQ files
Apr 12, 2011
df5cf08b removed unnecessary enum
Apr 12, 2011
4ffefaad fixed bug that occurred when FASTA headers didn't have a space, added PHRED...
May 28, 2011
c3bd0105 reformatted usage string to support ISO C90 fputs max length requirements
May 28, 2011
37515693 fixed bug in quality to probability conversion, added solexa conversion too
May 29, 2011
f865cd47 added note about min-match default change
May 29, 2011
8472bb2a updated qrqc url
May 29, 2011
fb82722b version bump
Jun 01, 2011
c7d6350e added read sim
Jul 25, 2011
27126543 touched read sim
Jul 25, 2011
9aea85f0 read simulation for testing added
Jul 25, 2011
5c4f5324 fixed second FASTQ header issue
Jul 25, 2011
3fb06d16 finished read-sim.R, added results-parsing
Jul 27, 2011
2b8d7c9b added prob base correct reporting to matches.txt
Jul 27, 2011
ee544363 Merge branches 'test' and 'master'
Jul 27, 2011
fa649829 added quality reporting to matches.txt and parsing in results_parse.py
Jul 27, 2011
02664e2b added R script to run tests and create ROC curve
Jul 27, 2011
43bfc67a minor roc curve changes
Jul 27, 2011
3bc8d125 fixed bug with FN, added lattice based graphics for ROC curves
Aug 10, 2011
7516fbc6 added code to save roc plot
Aug 16, 2011
493d0059 minor bug fix; FAQ added
Aug 16, 2011
174796ca minor readme correction
Aug 16, 2011
8d848960 removed output from stdout; moved to stderr so > works.
Aug 16, 2011
abb4d523 documentation correction in FAQ
Aug 16, 2011
96948736 corrected minor bug/typo
Aug 17, 2011
f4fbae5d minor bug fix
Aug 24, 2011
4c508553 added contam diff measures
Aug 24, 2011
d378629f Merge branch 'master' of github.com:vsbuffalo/scythe
Aug 24, 2011
c9670c60 testing code checkin - still buggy
Aug 24, 2011
e76174ad check in paper progress
Sep 29, 2011
8d6d8977 Merge branch 'testing'
Sep 29, 2011
72800ff0 Merge branch 'master' of github.com:vsbuffalo/scythe
Sep 29, 2011
01bb23a0 cleaned up some writing
Sep 29, 2011
fcdbb1fb more updates to paper
Sep 30, 2011
5d6fbcc5 added new generic comparison file
Oct 03, 2011
716e83cb more testing code added
Oct 04, 2011
760a6b65 added new bounds checking for qualities
Oct 28, 2011
612b725a made error messages more consistent
Oct 28, 2011
e778eea4 added func prototype to avoid GNU/Linux build warning
Oct 28, 2011
d66ec198 new version of compare.py with hashing on heades
Dec 19, 2011
e09168a2 added output info on left out reads with trimmer
Dec 19, 2011
0b6ae5b2 uncommented code out, for entire new run
Jan 05, 2012
3995b85b added testing files
Jan 05, 2012
54af8fe1 added read simulation
Jan 05, 2012
e89d1802 updated scythe's output of headers so that it writes full header string
Feb 18, 2012
53ba45f0 version bump
Feb 18, 2012
556ff2b1 udpated readme
Feb 18, 2012
133fc91c increased max adapters to 1000
Mar 02, 2012
fcc06c14 paper edits, removing lost of materials to shift to sup materials
Mar 08, 2012
d4adae96 revamped adapter sequences
Mar 13, 2012
535b6387 added adapter+barcode instructions to README.md
Mar 13, 2012
b20c02bd edited README and adapter files for legal reasons
Mar 14, 2012
51608bd7 added btrim adapters for testing
Apr 20, 2012
f5b50218 fixed bugs to testing
Apr 20, 2012
5c487dab added new R analysis file
Apr 23, 2012
ce1d1ecd more extensive testing in R
Apr 23, 2012
1ea9ff77 file processing mostly working
Apr 24, 2012
db86ebb8 split d
Apr 25, 2012
ae54cbaa changed testing so that stats calculated earlier
Apr 30, 2012
2e410921 ggplot roc curve of results
Apr 30, 2012
fc365724 ggplot image save and fixed btrim options
Apr 30, 2012
e7b2195d massive refactor to get new-testing changed to testing
Apr 30, 2012
6593b973 multiple contam rate testing
Apr 30, 2012
f6bafd1d changed program to var
Apr 30, 2012
14f30873 fixed Makefile targets
Apr 30, 2012
1a6823ef added incorrect length stats
May 01, 2012
fbd2c008 added refs
May 01, 2012
8361197b Merge branch 'master' of github.com:vsbuffalo/scythe
May 01, 2012
2bb72f9d added Bioinformatics Journal style
May 01, 2012
ecce9f98 additions to paper
May 01, 2012
3f1ec014 more paper additions, graphics, and supplementary materials
May 02, 2012
561e6c8e more additions to paper
May 02, 2012
33784fb6 few edits to paper
May 03, 2012
0e29b024 editing paper down in size
May 03, 2012
667e56a5 r package citations added
May 03, 2012
5cef1e9a fixed some minor errors in paper
May 04, 2012
26addb64 replaced adapter files and added explanatory text to README
May 29, 2012
4e1d7a31 Merge remote branch 'upstream/master'
May 29, 2012
872a54c9 Merge pull request #1 from jfass/master
May 31, 2012
c5c33e6c Was getting this upon a fresh clone of the repo:
Nov 07, 2012
24b6710f Merge pull request #8 from mylons/master
Dec 18, 2012
b24583cf initial new matching prototype
Dec 18, 2012
9b623e29 fixed formatting issues
Dec 19, 2012
285a7863 simplified comment output
Dec 19, 2012
e540bfc8 added news, todo, new truseq seqs for test
Dec 19, 2012
6e21e873 removed heuristic which causes non-exhaustive search across adapters
Dec 19, 2012
141fcbfa swapped for loops for safer matching with heuristic stopping point
Dec 19, 2012
45b91d30 commented out adapter occurence array; fixed mem leak
Dec 19, 2012
6ccdeb1e more mem leak fixing
Dec 19, 2012

42 additional commits have been omitted to prevent performance issues.