[med-svn] [Git][med-team/scythe][master] 142 commits: intial import

Andreas Tille gitlab at salsa.debian.org
Fri Aug 24 16:57:39 BST 2018 

Andreas Tille pushed to branch master at Debian Med / scythe


Commits:
f22a8910 by Vince Buffalo at 2011-02-03T03:22:52Z
intial import

- - - - -
4cb37f19 by Vince Buffalo at 2011-02-03T03:23:53Z
error fixed in readme: scythe does not pick out 5'-end contaminants

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e61f86f4 by Vince Buffalo at 2011-02-03T03:25:42Z
added solexa 3'-end adapter sequences

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30987f91 by Vince Buffalo at 2011-02-03T03:28:18Z
version bump in README.md, added caveat about usage

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26f59b35 by Vince Buffalo at 2011-02-03T16:48:32Z
fixed typo in readme (thanks peterjc for finding this)

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19b5c2d7 by Vince Buffalo at 2011-02-03T18:33:31Z
moved license, added more in readme, and enabled min match argument

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e94c7981 by Vince Buffalo at 2011-02-03T18:34:12Z
fixed improper format in readme

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a8d06244 by Vince Buffalo at 2011-02-03T18:36:44Z
more minor formatting changes to readme

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328d98bc by Vince Buffalo at 2011-02-16T00:29:28Z
added sequence header tags an option, added O3 opt, refactored makefile, got rid of c++ style comments

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5784292b by Vince Buffalo at 2011-02-16T00:31:34Z
resolved merge conflict from changes with min-match

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37a8db0e by Vince Buffalo at 2011-04-12T23:06:39Z
removed 5' code, which scythe will maybe handle later

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acc1c0f9 by Vince Buffalo at 2011-04-12T23:12:41Z
nicer handling of not found FASTQ files

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df5cf08b by Vince Buffalo at 2011-04-13T01:13:47Z
removed unnecessary enum

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4ffefaad by Vince Buffalo at 2011-05-28T23:38:56Z
fixed bug that occurred when FASTA headers didn't have a space, added PHRED qualities, added quality info to usage

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c3bd0105 by Vince Buffalo at 2011-05-28T23:42:58Z
reformatted usage string to support ISO C90 fputs max length requirements

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37515693 by Vince Buffalo at 2011-05-30T03:15:35Z
fixed bug in quality to probability conversion, added solexa conversion too

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f865cd47 by Vince Buffalo at 2011-05-30T03:25:36Z
added note about min-match default change

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8472bb2a by Vince Buffalo at 2011-05-30T03:31:30Z
updated qrqc url

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fb82722b by Vince Buffalo at 2011-06-01T20:19:03Z
version bump

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c7d6350e by Vince Buffalo at 2011-07-25T17:51:54Z
added read sim

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27126543 by Vince Buffalo at 2011-07-25T17:52:25Z
touched read sim

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9aea85f0 by Vince Buffalo at 2011-07-26T00:28:53Z
read simulation for testing added

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5c4f5324 by Vince Buffalo at 2011-07-26T00:37:01Z
fixed second FASTQ header issue

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3fb06d16 by Vince Buffalo at 2011-07-27T16:39:55Z
finished read-sim.R, added results-parsing

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2b8d7c9b by Vince Buffalo at 2011-07-27T19:09:05Z
added prob base correct reporting to matches.txt

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ee544363 by Vince Buffalo at 2011-07-27T19:09:40Z
Merge branches 'test' and 'master'

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fa649829 by Vince Buffalo at 2011-07-27T20:50:54Z
added quality reporting to matches.txt and parsing in results_parse.py

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02664e2b by Vince Buffalo at 2011-07-27T23:13:47Z
added R script to run tests and create ROC curve

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43bfc67a by Vince Buffalo at 2011-07-27T23:40:57Z
minor roc curve changes

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3bc8d125 by Vince Buffalo at 2011-08-10T21:25:40Z
fixed bug with FN, added lattice based graphics for ROC curves

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7516fbc6 by Vince Buffalo at 2011-08-16T17:57:20Z
added code to save roc plot

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493d0059 by Vince Buffalo at 2011-08-16T21:17:37Z
minor bug fix; FAQ added

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174796ca by Vince Buffalo at 2011-08-16T21:28:03Z
minor readme correction

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8d848960 by Vince Buffalo at 2011-08-16T21:53:49Z
removed output from stdout; moved to stderr so > works.

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abb4d523 by Vince Buffalo at 2011-08-16T21:54:12Z
documentation correction in FAQ

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96948736 by Vince Buffalo at 2011-08-17T20:50:45Z
corrected minor bug/typo

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f4fbae5d by Vince Buffalo at 2011-08-25T01:40:16Z
minor bug fix

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4c508553 by Vince Buffalo at 2011-08-25T01:41:45Z
added contam diff measures

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d378629f by Vince Buffalo at 2011-08-25T01:41:52Z
Merge branch 'master' of github.com:vsbuffalo/scythe

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c9670c60 by Vince Buffalo at 2011-08-25T02:50:31Z
testing code checkin - still buggy

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e76174ad by Vince Buffalo at 2011-09-29T18:02:13Z
check in paper progress

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8d6d8977 by Vince Buffalo at 2011-09-29T18:07:33Z
Merge branch 'testing'

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72800ff0 by Vince Buffalo at 2011-09-29T18:08:19Z
Merge branch 'master' of github.com:vsbuffalo/scythe

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01bb23a0 by Vince Buffalo at 2011-09-29T23:46:58Z
cleaned up some writing

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fcdbb1fb by Vince Buffalo at 2011-10-01T01:27:24Z
more updates to paper

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5d6fbcc5 by Vince Buffalo at 2011-10-03T19:56:49Z
added new generic comparison file

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716e83cb by Vince Buffalo at 2011-10-04T21:52:17Z
more testing code added

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760a6b65 by Vince Buffalo at 2011-10-28T21:29:26Z
added new bounds checking for qualities

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612b725a by Vince Buffalo at 2011-10-28T21:36:18Z
made error messages more consistent

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e778eea4 by Vince Buffalo at 2011-10-28T21:39:34Z
added func prototype to avoid GNU/Linux build warning

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d66ec198 by Vince Buffalo at 2011-12-19T22:17:03Z
new version of compare.py with hashing on heades

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e09168a2 by Vince Buffalo at 2011-12-19T23:48:13Z
added output info on left out reads with trimmer

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0b6ae5b2 by Vince Buffalo at 2012-01-05T19:20:35Z
uncommented code out, for entire new run

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3995b85b by Vince Buffalo at 2012-01-05T19:22:00Z
added testing files

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54af8fe1 by Vince Buffalo at 2012-01-05T21:33:37Z
added read simulation

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e89d1802 by Vince Buffalo at 2012-02-19T00:20:43Z
updated scythe's output of headers so that it writes full header string

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53ba45f0 by Vince Buffalo at 2012-02-19T00:26:14Z
version bump

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556ff2b1 by Vince Buffalo at 2012-02-19T00:43:19Z
udpated readme

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133fc91c by Vince Buffalo at 2012-03-02T21:53:23Z
increased max adapters to 1000

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fcc06c14 by Vince Buffalo at 2012-03-08T22:05:20Z
paper edits, removing lost of materials to shift to sup materials

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d4adae96 by Joseph Fass at 2012-03-14T00:41:19Z
revamped adapter sequences

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535b6387 by Joseph Fass at 2012-03-14T00:49:47Z
added adapter+barcode instructions to README.md

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b20c02bd by Joe Fass at 2012-03-14T20:49:51Z
edited README and adapter files for legal reasons

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51608bd7 by Vince Buffalo at 2012-04-21T00:16:02Z
added btrim adapters for testing

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f5b50218 by Vince Buffalo at 2012-04-21T00:36:53Z
fixed bugs to testing

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5c487dab by Vince Buffalo at 2012-04-23T19:17:22Z
added new R analysis file

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ce1d1ecd by Vince Buffalo at 2012-04-24T01:40:42Z
more extensive testing in R

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1ea9ff77 by Vince Buffalo at 2012-04-25T00:19:45Z
file processing mostly working

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db86ebb8 by Vince Buffalo at 2012-04-25T19:28:04Z
split d

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ae54cbaa by Vince Buffalo at 2012-04-30T20:31:59Z
changed testing so that stats calculated earlier

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2e410921 by Vince Buffalo at 2012-04-30T23:27:22Z
ggplot roc curve of results

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fc365724 by Vince Buffalo at 2012-05-01T00:10:27Z
ggplot image save and fixed btrim options

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e7b2195d by Vince Buffalo at 2012-05-01T00:34:27Z
massive refactor to get new-testing changed to testing

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6593b973 by Vince Buffalo at 2012-05-01T01:15:42Z
multiple contam rate testing

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f6bafd1d by Vince Buffalo at 2012-05-01T03:12:31Z
changed program to var

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14f30873 by Vince Buffalo at 2012-05-01T03:21:48Z
fixed Makefile targets

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1a6823ef by Vince Buffalo at 2012-05-01T18:35:15Z
added incorrect length stats

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fbd2c008 by Vince Buffalo at 2012-05-01T23:13:42Z
added refs

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8361197b by Vince Buffalo at 2012-05-01T23:14:06Z
Merge branch 'master' of github.com:vsbuffalo/scythe

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2bb72f9d by Vince Buffalo at 2012-05-01T23:36:32Z
added Bioinformatics Journal style

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ecce9f98 by Vince Buffalo at 2012-05-02T01:27:21Z
additions to paper

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3f1ec014 by Vince Buffalo at 2012-05-02T21:53:56Z
more paper additions, graphics, and supplementary materials

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561e6c8e by Vince Buffalo at 2012-05-03T00:48:10Z
more additions to paper

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33784fb6 by Vince Buffalo at 2012-05-03T19:53:36Z
few edits to paper

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0e29b024 by Vince Buffalo at 2012-05-03T20:12:27Z
editing paper down in size

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667e56a5 by Vince Buffalo at 2012-05-03T20:17:34Z
r package citations added

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5cef1e9a by Vince Buffalo at 2012-05-04T18:36:36Z
fixed some minor errors in paper

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26addb64 by Joseph Fass at 2012-05-29T23:33:10Z
replaced adapter files and added explanatory text to README

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4e1d7a31 by Joseph Fass at 2012-05-29T23:47:32Z
Merge remote branch 'upstream/master'

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872a54c9 by Vince Buffalo at 2012-06-01T00:17:13Z
Merge pull request #1 from jfass/master

revamped adapter files (one for older solexa adapters, one for Illumina's current TruSeq adapter), and added description of adapters and how to modify with barcodes
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c5c33e6c by mylons at 2012-11-07T12:57:48Z
Was getting this upon a fresh clone of the repo:

gcc -Wall -pedantic -DVERSION=0.981 -std=gnu99 -lz -lm match.o scythe.o util.o prob.o -o scythe
scythe.o: In function `ks_getc':
scythe.c:(.text+0x18a): undefined reference to `gzread'
scythe.o: In function `ks_getuntil':
scythe.c:(.text+0x289): undefined reference to `gzread'
scythe.o: In function `main':
scythe.c:(.text+0xc4b): undefined reference to `gzopen'
scythe.c:(.text+0x1024): undefined reference to `gzclose'
scythe.c:(.text+0x1044): undefined reference to `gzopen'
scythe.c:(.text+0x151a): undefined reference to `gzclose'
util.o: In function `ks_getc':
util.c:(.text+0x18a): undefined reference to `gzread'
util.o: In function `ks_getuntil':
util.c:(.text+0x289): undefined reference to `gzread'
prob.o: In function `qual_to_probs':
prob.c:(.text+0x129): undefined reference to `powf'
prob.c:(.text+0x1a8): undefined reference to `powf'
collect2: ld returned 1 exit status
make: *** [build] Error 1

Comments in this thread led me to this solution: moving the $(LDFLAGS) after the
sources ensures some linux compatibility

http://stackoverflow.com/questions/9145177/undefined-reference-to-gzopen-error

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24b6710f by Vince Buffalo at 2012-12-18T10:12:23Z
Merge pull request #8 from mylons/master

Possible Makefile linux compatibility issue
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b24583cf by Vince Buffalo at 2012-12-19T07:53:08Z
initial new matching prototype

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9b623e29 by Vince Buffalo at 2012-12-19T09:51:20Z
fixed formatting issues

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285a7863 by Vince Buffalo at 2012-12-19T10:17:16Z
simplified comment output

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e540bfc8 by Vince Buffalo at 2012-12-19T10:28:23Z
added news, todo, new truseq seqs for test

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6e21e873 by Vince Buffalo at 2012-12-19T11:37:12Z
removed heuristic which causes non-exhaustive search across adapters

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141fcbfa by Vince Buffalo at 2012-12-20T00:41:06Z
swapped for loops for safer matching with heuristic stopping point

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45b91d30 by Vince Buffalo at 2012-12-20T01:07:26Z
commented out adapter occurence array; fixed mem leak

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6ccdeb1e by Vince Buffalo at 2012-12-20T01:12:14Z
more mem leak fixing

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5657dfcb by Vince Buffalo at 2012-12-20T02:14:44Z
fixed another memory leak

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18fa6c10 by Vince Buffalo at 2012-12-21T00:06:56Z
fixed double free issue

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7f49366e by Vince Buffalo at 2013-03-27T22:07:17Z
merge of experimental branch that does full seq matching

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29ac0e56 by Vince Buffalo at 2013-03-27T22:17:49Z
fixed typo in readme (thanks JRI), updated with new matching algo from merge in previous commit; version bump

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9f3b86aa by Vince Buffalo at 2013-03-28T19:34:46Z
increased default prior; tests show this is a better choice

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ffd69027 by Vince Buffalo at 2013-04-14T01:00:51Z
replace empty lines with Ns

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6e1ba55e by Vince Buffalo at 2013-04-14T01:55:32Z
fixed issue with shift

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ffc7767c by Vince Buffalo at 2013-04-14T01:57:50Z
fixed opt flag

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c94f130b by Vince Buffalo at 2013-04-14T02:17:21Z
fixed min_keep parameter

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cb0695a7 by Vince Buffalo at 2013-04-14T02:21:43Z
added note about min_keep in readme, fixed makefile

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dd95ac42 by Vince Buffalo at 2013-05-11T20:05:54Z
added makefile targets for libscythe.so; cleaned up other parts of Makefile

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0410cc0c by Vince Buffalo at 2013-06-13T20:03:38Z
modified makefile so that it can find zlib

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fb311474 by Vince Buffalo at 2013-07-22T23:57:37Z
added option for stdin processing

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2b84e28e by Vince Buffalo at 2013-09-30T18:32:43Z
fixed compiler warnings from Linux gcc 4.7.3

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b459381f by Vince Buffalo at 2013-09-30T18:36:54Z
added two other adapters

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c5548d11 by Vince Buffalo at 2013-09-30T19:09:59Z
new minimal (non-redundant set of adapter)

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6a51b6da by Vince Buffalo at 2013-09-30T19:21:24Z
new adapter proposal

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dd8f8d8d by Vince Buffalo at 2013-09-30T20:02:00Z
jnfass's additions, without truncated cases

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eedd2e30 by Yaron de Leeuw at 2013-11-27T09:57:04Z
Fix the adapter in the matches report.

Saved the current adapter index in best_adapter

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9b965ee3 by Vince Buffalo at 2013-12-16T18:56:03Z
Merge pull request #13 from jarondl/fix_matches_report

Fix the adapter in the matches report.
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9b280401 by Vince Buffalo at 2014-02-08T05:12:21Z
fixed readme, changing makefile readme to all

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d773d96f by Richard Feltstykket at 2014-04-04T21:58:47Z
Typo fix in libscythe.so target, LDFLAGS order fix in all targets.

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9b40df7f by Vince Buffalo at 2014-04-05T18:56:35Z
Merge pull request #16 from rjacobsen/master

Typo fix in libscythe.so target, LDFLAGS order fix in all targets.
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6c6e6a6d by Kevin Murray at 2014-04-14T04:50:35Z
small optimisations to match functions & sum

Mangaged to decrease runtime to ~75% of what it was with some simple
optimisations. md5sums of output appear the same

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d3712b97 by Vince Buffalo at 2014-04-14T06:19:33Z
version bump

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8bfe3c6e by Vince Buffalo at 2014-04-14T06:20:43Z
update copyright

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6d92a57e by Kevin Murray at 2014-04-14T06:33:16Z
further optimisations which reduce num of allocs

Basically trying to remove the number of calls to alloc by preserving
the score array for the duration of the call to find_best_match

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369cd64b by Kevin Murray at 2014-04-14T06:41:46Z
[scythe.c] fix to fclose output_fp w/ -o option

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7c497837 by Kevin Murray at 2014-04-14T06:48:58Z
update tests w/ optimised score_sequence API

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8ffdb67f by Vince Buffalo at 2014-04-19T19:53:08Z
Merge pull request #18 from kdmurray91/optimised

Further optimisations
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2aad12e0 by Vince Buffalo at 2014-04-19T19:53:14Z
Merge pull request #19 from kdmurray91/fix-fclose

Call fclose on output_fp when -o option is given
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c128b19c by Vince Buffalo at 2014-04-19T19:59:24Z
version bump; removed paper, this will go into separate repository

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20d3cff7 by Vince Buffalo at 2014-10-17T21:11:49Z
fixed error in readme, thanks to @kbradnam

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bf847cba by Andreas Tille at 2018-08-24T14:25:55Z
New upstream version 0.994+git20141017.20d3cff
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e5a8da6b by Andreas Tille at 2018-08-24T15:49:05Z
use git mode

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122ccade by Andreas Tille at 2018-08-24T15:49:41Z
New upstream version 0.994+git20141017.20d3cff
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b5103f93 by Andreas Tille at 2018-08-24T15:49:43Z
Update upstream source from tag 'upstream/0.994+git20141017.20d3cff'

Update to upstream version '0.994+git20141017.20d3cff'
with Debian dir 4b8ec7504aaa2a6119c2b2049cb1ef77b4071394
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caac4ccc by Andreas Tille at 2018-08-24T15:50:07Z
Drop unneeded get-orig-source target

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119f4895 by Andreas Tille at 2018-08-24T15:50:40Z
debhelper 11

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09055c8b by Andreas Tille at 2018-08-24T15:50:50Z
Point Vcs fields to salsa.debian.org

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420c15fb by Andreas Tille at 2018-08-24T15:50:50Z
Standards-Version: 4.2.0

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409da38f by Andreas Tille at 2018-08-24T15:51:49Z
Upload to unstable

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6 changed files:

- .gitignore
- debian/changelog
- debian/compat
- debian/control
- debian/rules
- debian/watch


Changes:

=====================================
.gitignore
=====================================
--- a/.gitignore
+++ b/.gitignore
@@ -42,12 +42,5 @@ tramp
 *.out
 
 scythe
-test-scythe
 
 *.gch
-
-# debian stuff
-debian/files
-debian/scythe.substvars
-debian/scythe.debhelper.log
-README.html


=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+scythe (0.994+git20141017.20d3cff-1) unstable; urgency=medium
+
+  * d/watch: use git mode
+  * Drop unneeded get-orig-source target
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.0
+
+ -- Andreas Tille <tille at debian.org>  Fri, 24 Aug 2018 17:50:51 +0200
+
 scythe (0.994-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,18 +3,19 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Kevin Murray <spam at kdmurray.id.au>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                zlib1g-dev,
                python-markdown,
                check
-Standards-Version: 3.9.7
-Vcs-Browser: https://anonscm.debian.org/git/debian-med/scythe.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/scythe.git
+Standards-Version: 4.2.0
+Vcs-Browser: https://salsa.debian.org/med-team/scythe
+Vcs-Git: https://salsa.debian.org/med-team/scythe.git
 Homepage: https://github.com/vsbuffalo/scythe
 
 Package: scythe
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
 Description: Bayesian adaptor trimmer for sequencing reads
  Scythe uses a Naive Bayesian approach to classify contaminant substrings in
  sequence reads. It considers quality information, which can make it robust in


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -6,7 +6,3 @@
 override_dh_auto_build:
 	dh_auto_build
 	markdown_py -f README.html README.md
-
-get-orig-source:
-	@echo "Downloading source from GitHub"
-	wget -O scythe_0.994.orig.tar.gz https://api.github.com/repos/vsbuffalo/scythe/tarball/20d3cff7d7f483bd779aff75f861e93708c0a2b5


=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,4 @@
-#version=3
-#https://github.com/vsbuffalo/scythe/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+version=4
+
+opts="mode=git,pretty=0.994+git%cd.%h" \
+    https://github.com/vsbuffalo/scythe.git HEAD



View it on GitLab: https://salsa.debian.org/med-team/scythe/compare/fa6b295a9f96ce44a5773e7e90e593dd7071c8fa...409da38feb6eebfaa307f0bc4448f783db030997

-- 
View it on GitLab: https://salsa.debian.org/med-team/scythe/compare/fa6b295a9f96ce44a5773e7e90e593dd7071c8fa...409da38feb6eebfaa307f0bc4448f783db030997
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