[med-svn] [scythe] branch upstream created (now 20d3cff)
Kevin Murray
daube-guest at moszumanska.debian.org
Sun May 10 09:05:37 UTC 2015
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
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