This is an automated email from the git hooks/post-receive script. daube-guest pushed a change to branch upstream in repository scythe.
at 20d3cff fixed error in readme, thanks to @kbradnam This branch includes the following new commits: new f22a891 intial import new 4cb37f1 error fixed in readme: scythe does not pick out 5'-end contaminants new e61f86f added solexa 3'-end adapter sequences new 30987f9 version bump in README.md, added caveat about usage new 26f59b3 fixed typo in readme (thanks peterjc for finding this) new 19b5c2d moved license, added more in readme, and enabled min match argument new e94c798 fixed improper format in readme new a8d0624 more minor formatting changes to readme new 328d98b added sequence header tags an option, added O3 opt, refactored makefile, got rid of c++ style comments new 5784292 resolved merge conflict from changes with min-match new 37a8db0 removed 5' code, which scythe will maybe handle later new acc1c0f nicer handling of not found FASTQ files new df5cf08 removed unnecessary enum new 4ffefaa fixed bug that occurred when FASTA headers didn't have a space, added PHRED qualities, added quality info to usage new c3bd010 reformatted usage string to support ISO C90 fputs max length requirements new 3751569 fixed bug in quality to probability conversion, added solexa conversion too new f865cd4 added note about min-match default change new 8472bb2 updated qrqc url new fb82722 version bump new c7d6350 added read sim new 2712654 touched read sim new 9aea85f read simulation for testing added new 5c4f532 fixed second FASTQ header issue new 3fb06d1 finished read-sim.R, added results-parsing new 2b8d7c9 added prob base correct reporting to matches.txt new ee54436 Merge branches 'test' and 'master' new fa64982 added quality reporting to matches.txt and parsing in results_parse.py new 02664e2 added R script to run tests and create ROC curve new 43bfc67 minor roc curve changes new 3bc8d12 fixed bug with FN, added lattice based graphics for ROC curves new 7516fbc added code to save roc plot new 493d005 minor bug fix; FAQ added new 174796c minor readme correction new 8d84896 removed output from stdout; moved to stderr so > works. new abb4d52 documentation correction in FAQ new 9694873 corrected minor bug/typo new f4fbae5 minor bug fix new 4c50855 added contam diff measures new d378629 Merge branch 'master' of github.com:vsbuffalo/scythe new c9670c6 testing code checkin - still buggy new e76174a check in paper progress new 8d6d897 Merge branch 'testing' new 72800ff Merge branch 'master' of github.com:vsbuffalo/scythe new 01bb23a cleaned up some writing new fcdbb1f more updates to paper new 5d6fbcc added new generic comparison file new 716e83c more testing code added new 760a6b6 added new bounds checking for qualities new 612b725 made error messages more consistent new e778eea added func prototype to avoid GNU/Linux build warning new d66ec19 new version of compare.py with hashing on heades new e09168a added output info on left out reads with trimmer new 0b6ae5b uncommented code out, for entire new run new 3995b85 added testing files new 54af8fe added read simulation new e89d180 updated scythe's output of headers so that it writes full header string new 53ba45f version bump new 556ff2b udpated readme new 133fc91 increased max adapters to 1000 new fcc06c1 paper edits, removing lost of materials to shift to sup materials new d4adae9 revamped adapter sequences new 535b638 added adapter+barcode instructions to README.md new b20c02b edited README and adapter files for legal reasons new 51608bd added btrim adapters for testing new f5b5021 fixed bugs to testing new 5c487da added new R analysis file new ce1d1ec more extensive testing in R new 1ea9ff7 file processing mostly working new db86ebb split d new ae54cba changed testing so that stats calculated earlier new 2e41092 ggplot roc curve of results new fc36572 ggplot image save and fixed btrim options new e7b2195 massive refactor to get new-testing changed to testing new 6593b97 multiple contam rate testing new f6bafd1 changed program to var new 14f3087 fixed Makefile targets new 1a6823e added incorrect length stats new fbd2c00 added refs new 8361197 Merge branch 'master' of github.com:vsbuffalo/scythe new 2bb72f9 added Bioinformatics Journal style new ecce9f9 additions to paper new 3f1ec01 more paper additions, graphics, and supplementary materials new 561e6c8 more additions to paper new 33784fb few edits to paper new 0e29b02 editing paper down in size new 667e56a r package citations added new 5cef1e9 fixed some minor errors in paper new 26addb6 replaced adapter files and added explanatory text to README new 4e1d7a3 Merge remote branch 'upstream/master' new 872a54c Merge pull request #1 from jfass/master new c5c33e6 Was getting this upon a fresh clone of the repo: new 24b6710 Merge pull request #8 from mylons/master new b24583c initial new matching prototype new 9b623e2 fixed formatting issues new 285a786 simplified comment output new e540bfc added news, todo, new truseq seqs for test new 6e21e87 removed heuristic which causes non-exhaustive search across adapters new 141fcbf swapped for loops for safer matching with heuristic stopping point new 45b91d3 commented out adapter occurence array; fixed mem leak new 6ccdeb1 more mem leak fixing new 5657dfc fixed another memory leak new 18fa6c1 fixed double free issue new 7f49366 merge of experimental branch that does full seq matching new 29ac0e5 fixed typo in readme (thanks JRI), updated with new matching algo from merge in previous commit; version bump new 9f3b86a increased default prior; tests show this is a better choice new ffd6902 replace empty lines with Ns new 6e1ba55 fixed issue with shift new ffc7767 fixed opt flag new c94f130 fixed min_keep parameter new cb0695a added note about min_keep in readme, fixed makefile new dd95ac4 added makefile targets for libscythe.so; cleaned up other parts of Makefile new 0410cc0 modified makefile so that it can find zlib new fb31147 added option for stdin processing new 2b84e28 fixed compiler warnings from Linux gcc 4.7.3 new b459381 added two other adapters new c5548d1 new minimal (non-redundant set of adapter) new 6a51b6d new adapter proposal new dd8f8d8 jnfass's additions, without truncated cases new eedd2e3 Fix the adapter in the matches report. new 9b965ee Merge pull request #13 from jarondl/fix_matches_report new 9b28040 fixed readme, changing makefile readme to all new d773d96 Typo fix in libscythe.so target, LDFLAGS order fix in all targets. new 9b40df7 Merge pull request #16 from rjacobsen/master new 6c6e6a6 small optimisations to match functions & sum new d3712b9 version bump new 8bfe3c6 update copyright new 6d92a57 further optimisations which reduce num of allocs new 369cd64 [scythe.c] fix to fclose output_fp w/ -o option new 7c49783 update tests w/ optimised score_sequence API new 8ffdb67 Merge pull request #18 from kdmurray91/optimised new 2aad12e Merge pull request #19 from kdmurray91/fix-fclose new c128b19 version bump; removed paper, this will go into separate repository new 20d3cff fixed error in readme, thanks to @kbradnam The 133 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/scythe.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit