| 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 |
| edd7fee | John St. John | 09 April 2011, 16:59:08 UTC | making the cutoff for good quality 90% | 09 April 2011, 16:59:08 UTC |
| b37b915 | John St. John | 08 April 2011, 23:52:09 UTC | making defaults for read merging a little more stringent | 08 April 2011, 23:52:09 UTC |
| becec69 | John St. John | 08 April 2011, 23:50:14 UTC | making defaults for read merging a little more stringent | 08 April 2011, 23:50:14 UTC |
| 8499bd9 | John St. John | 15 March 2011, 16:14:54 UTC | tamed the spinner a little, no changes to the code otherwise | 15 March 2011, 16:14:54 UTC |
| a1e1d38 | John St. John | 14 March 2011, 22:31:21 UTC | fixing issue where when one read is shorter than the other before trimming | 14 March 2011, 22:31:21 UTC |
| 9c396b6 | John St. John | 13 March 2011, 05:42:47 UTC | updating README to properly display list | 13 March 2011, 05:42:47 UTC |
| 3322dd5 | John St. John | 13 March 2011, 05:41:35 UTC | updating README to properly display list | 13 March 2011, 05:41:35 UTC |
| bf20265 | John St. John | 13 March 2011, 05:34:15 UTC | updating readme and changing a floor to ceil for the min_match array | 13 March 2011, 05:34:15 UTC |
| 8c963fe | John St. John | 13 March 2011, 05:19:52 UTC | updating README file | 13 March 2011, 05:19:52 UTC |
| 8652e8b | John St. John | 13 March 2011, 05:17:07 UTC | updating README file | 13 March 2011, 05:17:07 UTC |
| 305d94b | John St. John | 13 March 2011, 05:06:51 UTC | making spinner go a little faster, two revolutions per 5000 reads | 13 March 2011, 05:06:51 UTC |
| 7e5608f | John St. John | 13 March 2011, 04:54:05 UTC | replacing dots with much more interesting spinner | 13 March 2011, 04:54:05 UTC |
| 20eecc7 | John St. John | 13 March 2011, 02:36:16 UTC | Trying a slightly more conservative paired end merging default | 13 March 2011, 02:36:16 UTC |
| 6ca6c32 | John St. John | 13 March 2011, 01:28:34 UTC | Fixed issue where last completely overlapping match positionw wasn't checked for forced adapter merge reads | 13 March 2011, 01:28:34 UTC |
| e522d73 | John St. John | 13 March 2011, 01:02:36 UTC | Fixed bug where human readable dump file wasn't closed on program exit, resulting in a malformed gzipped file | 13 March 2011, 01:02:36 UTC |
| de5480b | John St. John | 12 March 2011, 23:50:50 UTC | adding method to dump human readable alignments for qualitative checking | 12 March 2011, 23:50:50 UTC |
| 4fbfdda | John St. John | 12 March 2011, 20:58:23 UTC | tested and works on some simple cases now | 12 March 2011, 20:58:23 UTC |
| 6ffdfc9 | John St. John | 12 March 2011, 08:38:29 UTC | Merge branch 'master' of github.com:jstjohn/SeqPrep | 12 March 2011, 08:38:29 UTC |
| f3f6829 | John St. John | 12 March 2011, 08:37:49 UTC | removing the initial program output to save space | 12 March 2011, 08:37:49 UTC |
| fc61823 | John St. John | 12 March 2011, 08:37:11 UTC | adding some test files | 12 March 2011, 08:37:11 UTC |
| 92b7776 | John St. John | 12 March 2011, 08:35:59 UTC | fixing issue with trimming | 12 March 2011, 08:35:59 UTC |
| f44ab27 | John St. John | 12 March 2011, 08:31:26 UTC | fixing issue with not writing one of output files | 12 March 2011, 08:31:26 UTC |
| 81ebc6a | John St. John | 12 March 2011, 08:30:19 UTC | closing output files | 12 March 2011, 08:30:19 UTC |
| bac183d | John St. John | 12 March 2011, 08:25:00 UTC | fixing issue poorly passed variables | 12 March 2011, 08:25:00 UTC |
| a867fb6 | John St. John | 12 March 2011, 08:23:29 UTC | fixing issue with unallocated ints | 12 March 2011, 08:23:29 UTC |
| e629495 | John St. John | 12 March 2011, 08:10:24 UTC | fixed makefile issue | 12 March 2011, 08:10:24 UTC |
| 6e19452 | John St. John | 12 March 2011, 08:05:30 UTC | adding tag for compile success, messing with default values, and adding a little to the README | 12 March 2011, 08:05:30 UTC |
| e0d7cfe | John St. John | 12 March 2011, 06:02:04 UTC | made the help screen look a little nicer | 12 March 2011, 06:02:04 UTC |
| f394570 | John St. John | 12 March 2011, 06:00:26 UTC | it compiles properly now, it is still untested though | 12 March 2011, 06:00:26 UTC |
| 7c51bba | John St. John | 11 March 2011, 09:48:56 UTC | finished up user options, and added a few high level TODOs to the code | 11 March 2011, 09:48:56 UTC |
| 5a1da32 | John St. John | 11 March 2011, 09:22:13 UTC | verified and set default illumina PE primer sequences, filling in usage message and working on option parsing | 11 March 2011, 09:22:13 UTC |
| a972947 | John St. John | 11 March 2011, 05:52:09 UTC | pushing work for the evening, starting to add in user options, and set up the loop over reads | 11 March 2011, 05:52:09 UTC |
| 148d1ad | John St. John | 11 March 2011, 04:36:51 UTC | filling in makefile, getting closer to working program... | 11 March 2011, 04:36:51 UTC |
| 853936f | John St. John | 10 March 2011, 17:18:36 UTC | adding logic to avoid cases where no good quality bases are present | 10 March 2011, 17:18:36 UTC |
| 3a2abcf | John St. John | 10 March 2011, 17:09:04 UTC | adding LICENSE | 10 March 2011, 17:09:04 UTC |
| 3150030 | John St. John | 10 March 2011, 17:04:05 UTC | changing name | 10 March 2011, 17:04:05 UTC |
| 3506380 | John St. John | 10 March 2011, 17:03:51 UTC | changing name | 10 March 2011, 17:03:51 UTC |
| 70c9b71 | John St. John | 10 March 2011, 09:06:21 UTC | adding shell of a makefile | 10 March 2011, 09:06:21 UTC |
| 2205b33 | John St. John | 10 March 2011, 08:23:14 UTC | Adding README | 10 March 2011, 08:23:14 UTC |
| f8771c5 | John St. John | 10 March 2011, 08:16:27 UTC | getting closer to something that works, have a decent ungapped overlapper now | 10 March 2011, 08:16:27 UTC |
| f6f64b3 | John St. John | 10 March 2011, 02:39:20 UTC | in the middle of making this work for my task | 10 March 2011, 02:39:20 UTC |
