| 575507b | John St John | 04 October 2016, 19:03:16 UTC | add option to not show spinner | 04 October 2016, 19:03:16 UTC |
| 8831f47 | John St John | 04 October 2016, 18:41:43 UTC | change default adapter sequence for read 1 | 04 October 2016, 18:41:43 UTC |
| 8b3b133 | John St John | 04 October 2016, 18:00:08 UTC | merging in master | 04 October 2016, 18:00:08 UTC |
| 9b8d057 | John St John | 04 October 2016, 17:55:10 UTC | removing inline completely | 04 October 2016, 17:55:10 UTC |
| e57a139 | Jason Stajich | 06 May 2016, 13:49:58 UTC | typo optomized -> optimized | 06 May 2016, 13:49:58 UTC |
| bda7a3d | John St. John | 18 March 2016, 17:08:25 UTC | Merge pull request #30 from udo-stenzel/master changed update_spinner to 'static inline' | 18 March 2016, 17:08:25 UTC |
| b670dc6 | John St. John | 18 March 2016, 17:06:49 UTC | Merge pull request #33 from samdemorest/master Specified C99 standard to resolve build issue. | 18 March 2016, 17:06:49 UTC |
| 90b69d2 | samdemorest | 16 March 2016, 17:19:33 UTC | Specified C99 standard to resolve build issue. Build failed with undefined reference to update_spinner unless compiled with -std=c99 using gcc-4.4.7 on RHEL 6.6. Specifying standard resolves this. | 16 March 2016, 17:19:33 UTC |
| 4bad2ab | Udo Stenzel | 05 December 2015, 15:17:10 UTC | changed update_spinner to 'static inline' This makes more sense (it was never used externally), and fixes #24. Also shortened the code while I was at it... | 05 December 2015, 15:17:10 UTC |
| 488ef06 | John St. John | 23 May 2015, 00:11:18 UTC | Merge pull request #28 from alliemacleay/master Fix for masking overlapping adapters | 23 May 2015, 00:11:18 UTC |
| 8923b78 | alliemacleay | 22 May 2015, 22:38:46 UTC | fix README indentation | 22 May 2015, 22:38:46 UTC |
| 96d5754 | alliemacleay | 22 May 2015, 22:25:12 UTC | Fix for masking overlapped adapters | 22 May 2015, 22:25:12 UTC |
| 1a7c44d | John St. John | 19 May 2015, 17:51:59 UTC | Merge pull request #26 from alliemacleay/master Add option for masking instead of trimming | 19 May 2015, 17:51:59 UTC |
| c9dd5ac | alliemacleay | 07 May 2015, 18:12:15 UTC | Fix for Ubuntu not allowing declarations in for loop | 07 May 2015, 18:12:15 UTC |
| 6e5f406 | alliemacleay | 07 May 2015, 15:14:07 UTC | Updated README.md | 07 May 2015, 15:14:07 UTC |
| 8f20654 | alliemacleay | 07 May 2015, 14:58:27 UTC | Added an option for base masking instead of clipping | 07 May 2015, 14:58:27 UTC |
| 70f464a | John St. John | 07 January 2015, 02:35:20 UTC | Merge pull request #21 from alexpreynolds/clang-patch Patches for clang/LLVM 3.5 compilation | 07 January 2015, 02:35:20 UTC |
| 811e088 | Alex Reynolds | 06 January 2015, 20:55:13 UTC | applied patches for clang/LLVM 3.5 compilation | 06 January 2015, 20:55:13 UTC |
| b5efabc | John St John | 10 February 2014, 17:39:10 UTC | adding a tag for the latest version for homebrew | 10 February 2014, 17:39:10 UTC |
| b5606dd | John St John | 31 May 2013, 17:44:45 UTC | added in checks to make sure that quality is above minimal threshold, and below maximal threshold | 31 May 2013, 17:44:45 UTC |
| eb1c078 | John St John | 30 May 2013, 14:14:04 UTC | updates to check for quality scores too low/high during merging | 30 May 2013, 14:14:04 UTC |
| 7d9fd7d | John St. John | 13 May 2013, 04:52:36 UTC | Updates to readme, correction for specificity vs sensitivity. | 13 May 2013, 04:52:36 UTC |
| 11301c4 | John St John | 20 February 2013, 16:33:09 UTC | fixing compiling issues on mac | 20 February 2013, 16:33:09 UTC |
| dd783aa | John St John | 08 September 2012, 19:15:25 UTC | Merge branch 'master' of github.com:jstjohn/SeqPrep | 08 September 2012, 19:15:25 UTC |
| ee567f4 | John St John | 08 September 2012, 19:15:18 UTC | local changes to makefile? | 08 September 2012, 19:15:18 UTC |
| b62f433 | John St. John | 21 March 2012, 18:34:02 UTC | Merge pull request #5 from DarwinAwardWinner/ldflags-fix Place LDFLAGS after OBJECTS in compile command | 21 March 2012, 18:34:02 UTC |
| b879d2a | Ryan C. Thompson | 16 March 2012, 20:09:53 UTC | Place LDFLAGS after OBJECTS in compile command I was getting errors like "undefined reference to `gzopen'", so I found this: http://stackoverflow.com/questions/9145177/undefined-reference-to-gzopen-error which told me to put "-lz" after the object names. I tried making that change in the Makefile, and it fixed things. | 16 March 2012, 20:09:53 UTC |
| b83fd00 | John St. John | 25 October 2011, 18:38:16 UTC | Merge branch 'master' of github.com:jstjohn/SeqPrep | 25 October 2011, 18:38:16 UTC |
| debf184 | John St. John | 25 October 2011, 18:38:11 UTC | local changes to seqlens | 25 October 2011, 18:38:11 UTC |
| 8719a15 | John St. John | 15 September 2011, 23:47:08 UTC | adding fastq-mcf results back into test and mentioning those on the readme | 15 September 2011, 23:47:08 UTC |
| d8c802d | John St. John | 15 September 2011, 23:31:57 UTC | updating README with new test | 15 September 2011, 23:31:57 UTC |
| 6490859 | John St. john | 15 September 2011, 23:13:53 UTC | Updated tests to double check that adapters are being trimmed from reads even when the adapter is only at the last few bases. It appears that the program is working nicely on this case. | 15 September 2011, 23:13:53 UTC |
| 20a8b3b | John St. john | 15 September 2011, 22:22:35 UTC | reformatting README.md | 15 September 2011, 22:22:35 UTC |
| b018207 | John St. john | 15 September 2011, 22:19:58 UTC | Added option to save discarded reads into SeqPrep (Thanks @jdh237!). Also slightly modified default settings for trimming based on further sensitivity/specificity optimization on test data. | 15 September 2011, 22:19:58 UTC |
| 97d5873 | John St. John | 30 August 2011, 22:09:41 UTC | fixed a bug that results in quality scores higher than the maximum allowed quality score, also added a parameter to set the maximum quality that is output by the program when read merging happens | 30 August 2011, 22:09:41 UTC |
| fb9d6b1 | John St. John | 07 July 2011, 23:40:30 UTC | modifying the default parameters, the documentation to reflect those defaults, and posting a link to the website where I post the stats of adapter trimming sensitivity and specificity under different parameter settings (http://hgwdev.cse.ucsc.edu/~jstjohn/seqprep/results2011-07-07.html) | 07 July 2011, 23:40:30 UTC |
| 5235b9b | John St. John | 07 July 2011, 22:13:39 UTC | updating test script to reflect the correct correct reverse adapter sequence | 07 July 2011, 22:13:39 UTC |
| dd96130 | John St. John | 07 July 2011, 21:34:38 UTC | modifying readme to describe my strategy for finding the adapter sequence | 07 July 2011, 21:34:38 UTC |
| cfaafc9 | John St. John | 07 July 2011, 15:32:57 UTC | updating documentation" ; | 07 July 2011, 15:32:57 UTC |
| 6cf1c8b | John St. John | 07 July 2011, 15:29:44 UTC | modification to calculation of sensitivity and specificity in test code, doesn't change much but is more correct now | 07 July 2011, 15:29:44 UTC |
| 918010c | John St. John | 07 July 2011, 15:17:16 UTC | fixing simulated data, and making parameters a little more stringent, the results are the same on the simulated data but it might be a little better with weird cases in real data now | 07 July 2011, 15:17:16 UTC |
| 3e3696c | John St. John | 07 July 2011, 04:45:27 UTC | updating readme | 07 July 2011, 04:45:27 UTC |
| d227da3 | John St. John | 07 July 2011, 04:42:14 UTC | updating readme | 07 July 2011, 04:42:14 UTC |
| 56116c6 | John St. John | 07 July 2011, 04:29:41 UTC | adding in the shorter test files as well | 07 July 2011, 04:29:41 UTC |
| 5ebe23d | John St. John | 07 July 2011, 04:25:13 UTC | adding lots of testing stuff, and updating defaults as a result of those tests | 07 July 2011, 04:25:13 UTC |
| 6d2f669 | John St. John | 06 July 2011, 02:31:27 UTC | fixed a bug where resulting in high probability of discarding reads with low quality bases at the end | 06 July 2011, 02:31:27 UTC |
| 6a7d3aa | John St. John | 05 July 2011, 23:43:06 UTC | now trim parts of reads that do not overlap when performing adapter trimming as well as read merging | 05 July 2011, 23:43:06 UTC |
| 1d97f01 | John St. John | 05 July 2011, 22:26:15 UTC | updating readme to reflect currently available options | 05 July 2011, 22:26:15 UTC |
| 1fbf46f | John St. John | 05 July 2011, 22:25:37 UTC | adding the adapter trim help item back to the help documentation | 05 July 2011, 22:25:37 UTC |
| 9abe976 | John St. John | 05 July 2011, 21:51:02 UTC | making defaults more sensitive to adapters | 05 July 2011, 21:51:02 UTC |
| 2c43662 | John St. John | 05 July 2011, 21:32:08 UTC | changing makefile arguments | 05 July 2011, 21:32:08 UTC |
| 8939962 | John St. John | 05 July 2011, 21:27:46 UTC | fixing a weird index issue that wasn't being handled properly | 05 July 2011, 21:27:46 UTC |
| 76e2126 | John St. John | 05 July 2011, 19:07:25 UTC | adding prettyprint for read overlap even when just doing adapter trimming for user debugging purposes | 05 July 2011, 19:07:25 UTC |
| 96ce1b8 | John St. John | 02 July 2011, 01:18:59 UTC | updating documentation to reflect help, and clarifying which adapters the defaults are in both the help and the program | 02 July 2011, 01:18:59 UTC |
| 2ede58a | John St. John | 02 July 2011, 01:11:44 UTC | adding warning about new line at the end of a file | 02 July 2011, 01:11:44 UTC |
| 0c23eb1 | John St. John | 02 July 2011, 00:13:21 UTC | reverting makefile to 03 optomization flags | 02 July 2011, 00:13:21 UTC |
| 01f7eb4 | John St. John | 01 July 2011, 23:26:18 UTC | fixing issue where sequences could be different length from adapters, and an improvement for detecting more potential adapters through read overlap | 01 July 2011, 23:26:18 UTC |
| ec7b62b | John St. John | 30 June 2011, 03:00:50 UTC | updating test | 30 June 2011, 03:00:50 UTC |
| 288c2ac | John St. John | 29 June 2011, 23:46:06 UTC | updating documentation | 29 June 2011, 23:46:06 UTC |
| fb6129b | John St. John | 29 June 2011, 23:40:27 UTC | cleaning up comments and code a little | 29 June 2011, 23:40:27 UTC |
| 8fed36b | John St. John | 29 June 2011, 23:08:15 UTC | Fixed an important bug with forced overlap after adapter alignment. This will result in more reads passing. Also modifying defaults slightly | 29 June 2011, 23:08:15 UTC |
| 80f75ab | John St. John | 28 June 2011, 23:34:10 UTC | fixed a bug where unsigned ints were used for a minimum score that should have been negative | 28 June 2011, 23:34:10 UTC |
| a0da493 | John St. John | 28 June 2011, 20:14:55 UTC | updated readme | 28 June 2011, 20:14:55 UTC |
| 0609c6b | John St. John | 28 June 2011, 20:13:40 UTC | updated readme | 28 June 2011, 20:13:40 UTC |
| 405ee56 | John St. John | 28 June 2011, 20:05:08 UTC | Switching m and n arguments for consistency | 28 June 2011, 20:05:08 UTC |
| 19d7b9d | John St. John | 27 June 2011, 17:38:34 UTC | fixed error in arguments for 'm' and 'n' when those are supplied they filled the opposite variables. Thanks Chris\! | 27 June 2011, 17:38:34 UTC |
| 7df8f18 | John St. John | 23 June 2011, 17:40:53 UTC | being a little more careful with the length of the sequences | 23 June 2011, 17:40:53 UTC |
| b6c3936 | John St. John | 23 June 2011, 15:52:12 UTC | fix for issue of printing some 0 length sequences | 23 June 2011, 15:52:12 UTC |
| 6871345 | John St. John | 16 June 2011, 06:32:26 UTC | also memsetting the merged sequence just to be safe | 16 June 2011, 06:32:26 UTC |
| e09ee6b | John St. John | 16 June 2011, 05:57:38 UTC | adding in scripts for better testing | 16 June 2011, 05:57:38 UTC |
| 9128cc5 | John St. John | 16 June 2011, 05:54:34 UTC | trying more stringent criteria for printing trimmed reads | 16 June 2011, 05:54:34 UTC |
| 5ba24ab | John St. John | 16 June 2011, 05:44:44 UTC | improved script for running program | 16 June 2011, 05:44:44 UTC |
| 14c694c | John St. John | 16 June 2011, 05:11:32 UTC | adding clean script to quickly clean up test output | 16 June 2011, 05:11:32 UTC |
| 1d37ff4 | John St. John | 16 June 2011, 05:09:23 UTC | fixing test script | 16 June 2011, 05:09:23 UTC |
| 51824b9 | John St. John | 16 June 2011, 05:06:30 UTC | cleaned up test folder | 16 June 2011, 05:06:30 UTC |
| 8cd7a53 | John St. John | 16 June 2011, 04:28:14 UTC | adding in check to switch '.' to 'N' in sequences | 16 June 2011, 04:28:14 UTC |
| 31619f8 | John St. John | 16 June 2011, 04:02:34 UTC | using sequences without trimming this time | 16 June 2011, 04:02:34 UTC |
| 6fee3cc | John St. John | 15 June 2011, 22:32:40 UTC | makking changes, need to fix warning message | 15 June 2011, 22:32:40 UTC |
| 0a73d24 | John St. John | 15 June 2011, 21:51:00 UTC | Merge branch 'master' of git@github.com:jstjohn/SeqPrep | 15 June 2011, 21:51:00 UTC |
| 82cc7e7 | John St. John | 15 June 2011, 21:50:31 UTC | adding test fastqs | 15 June 2011, 21:50:31 UTC |
| 4b1f0a8 | John St. John | 15 June 2011, 21:49:34 UTC | Merge branch 'master' of github.com:jstjohn/SeqPrep | 15 June 2011, 21:49:34 UTC |
| ecfdb05 | John St. John | 15 June 2011, 21:49:16 UTC | fixing issues with choosing trimming position | 15 June 2011, 21:49:16 UTC |
| b3a11da | John St. John | 15 June 2011, 21:44:41 UTC | fixed space problem in test script | 15 June 2011, 21:44:41 UTC |
| 690fecb | John St. John | 15 June 2011, 21:44:03 UTC | adding tests | 15 June 2011, 21:44:03 UTC |
| e84a43e | John St. John | 15 June 2011, 21:34:10 UTC | more sensitive trimming | 15 June 2011, 21:34:10 UTC |
| 9dfd548 | John St. John | 15 June 2011, 21:01:56 UTC | updating with code that prefferres to trim adapters at the beginning of reads if there is a decent match | 15 June 2011, 21:01:56 UTC |
| 2d17492 | John St. John | 15 June 2011, 20:11:34 UTC | Merge branches 'devel' and 'master' | 15 June 2011, 20:11:34 UTC |
| 4458fdc | John St. John | 15 June 2011, 20:10:10 UTC | updating to full smith-waterman search for adapters | 15 June 2011, 20:10:10 UTC |
| bf56d51 | John St. John | 15 June 2011, 20:08:12 UTC | adding in smith-waterman adapter search | 15 June 2011, 20:08:12 UTC |
| 8b4cf61 | John St. John | 11 June 2011, 16:39:24 UTC | making adapter matching more sensitive | 11 June 2011, 16:39:24 UTC |
| cba26fa | John St. John | 31 May 2011, 18:22:43 UTC | should now handle cases where adapter appears before start of read | 31 May 2011, 18:22:43 UTC |
| 6f0a86b | John St. John | 25 May 2011, 06:52:43 UTC | fixed a bug I just introduced | 25 May 2011, 06:52:43 UTC |
| c2e6c5b | John St. John | 25 May 2011, 06:18:19 UTC | fixed a bug I just introduced | 25 May 2011, 06:18:19 UTC |
| 2f3c469 | John St. John | 25 May 2011, 05:30:58 UTC | fixed a bug I just introduced | 25 May 2011, 05:30:58 UTC |
| b2368e7 | John St. John | 25 May 2011, 05:05:11 UTC | attempting some changes | 25 May 2011, 05:05:11 UTC |
| 7b46025 | John St. John | 25 May 2011, 03:14:52 UTC | try to get case where only a little adapter is present at ends of reads | 25 May 2011, 03:14:52 UTC |
| 1447ecc | John St. John | 30 April 2011, 22:38:32 UTC | Fixed compiling bug | 30 April 2011, 22:38:32 UTC |
| 8291940 | John St. John | 30 April 2011, 22:32:58 UTC | Gives an error message about fastq id's not matching. | 30 April 2011, 22:32:58 UTC |
| 3ce79f8 | John St. John | 30 April 2011, 22:21:56 UTC | Include notes on two most common questions in the help text | 30 April 2011, 22:21:56 UTC |
| b01743e | John St. John | 30 April 2011, 22:08:59 UTC | Just warn once about non-standard base characters | 30 April 2011, 22:08:59 UTC |
