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https://github.com/OpenGene/fastp
31 October 2022, 10:53:24 UTC
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Revision Author Date Message Commit Date
fbe796a Shifu Chen 16 May 2018, 07:28:12 UTC set version to 0.14.1 16 May 2018, 07:28:12 UTC
00bdece Shifu Chen 16 May 2018, 07:27:23 UTC bug fix for buffer queue 16 May 2018, 07:27:23 UTC
3a6ab05 Shifu Chen 04 May 2018, 06:59:50 UTC support limit the number of reads to process 04 May 2018, 06:59:50 UTC
31fa236 Shifu Chen 04 May 2018, 05:41:29 UTC set version to v0.14.0 04 May 2018, 05:41:29 UTC
c3c370f Shifu Chen 04 May 2018, 05:39:20 UTC Merge pull request #55 from OpenGene/add-index-filter Add index filter 04 May 2018, 05:39:20 UTC
a209dc4 Shifu Chen 24 April 2018, 03:43:07 UTC output debug info for index filtering 24 April 2018, 03:43:07 UTC
4e29695 Shifu Chen 24 April 2018, 03:18:03 UTC fix Linux compile 24 April 2018, 03:18:03 UTC
88c393f Shifu Chen 24 April 2018, 03:14:23 UTC fix index filter 24 April 2018, 03:14:23 UTC
701fcdf Shifu Chen 24 April 2018, 01:57:20 UTC support index filtering 24 April 2018, 01:57:20 UTC
f943e6a Shifu Chen 23 April 2018, 10:04:42 UTC skip some bases after UMI to trim the UMI separator and A/T tailing. Specify `--umi_skip` to enable the number of bases to skip. By default it is not enabled. 23 April 2018, 10:04:42 UTC
139e23e Shifu Chen 17 April 2018, 13:31:26 UTC comment check_file_writable since it is always different in different OS 17 April 2018, 13:31:26 UTC
0a1738b Shifu Chen 17 April 2018, 11:49:27 UTC set version to v0.13.0 17 April 2018, 11:49:27 UTC
027ca19 Shifu Chen 17 April 2018, 11:43:21 UTC fix the issue of check_file_writable for some Linux systems https://github.com/OpenGene/fastp/issues/50wq 17 April 2018, 11:43:21 UTC
14b0fce Shifu Chen 17 April 2018, 05:50:45 UTC WAR for check_file_writable bug 17 April 2018, 05:50:45 UTC
a9dc9fd Shifu Chen 17 April 2018, 01:51:02 UTC disable check_file_writable temporarily For its bug on Linux systems 17 April 2018, 01:51:02 UTC
9fb320d Shifu Chen 16 April 2018, 09:28:51 UTC check folder exist for output 16 April 2018, 09:28:51 UTC
e85dd68 Shifu Chen 16 April 2018, 08:47:33 UTC code refactoring for stats and filtering 16 April 2018, 08:47:33 UTC
c53afc2 Shifu Chen 16 April 2018, 06:39:10 UTC revise quality filtering https://github.com/OpenGene/fastp/issues/49 16 April 2018, 06:39:10 UTC
e4467e5 Shifu Chen 08 April 2018, 14:09:18 UTC fix potential mem leak 08 April 2018, 14:09:18 UTC
da047e7 Shifu Chen 08 April 2018, 13:50:39 UTC apply nucleotide tree based adapter detection 08 April 2018, 13:50:39 UTC
f562144 Shifu Chen 04 April 2018, 13:56:02 UTC add nucleotidetree 04 April 2018, 13:56:02 UTC
ed514e7 Shifu Chen 29 March 2018, 01:01:34 UTC use merged UMI for both R1/R2 for per_index and per_read mode To keep read names identical for R1/R2 https://github.com/OpenGene/fastp/issues/46 29 March 2018, 01:01:34 UTC
0578f45 Shifu Chen 22 March 2018, 07:16:17 UTC Add travis build status to README 22 March 2018, 07:16:17 UTC
9270bc8 Shifu Chen 22 March 2018, 07:11:50 UTC revise low complexity filter 22 March 2018, 07:11:50 UTC
8e9309e Shifu Chen 22 March 2018, 07:08:32 UTC add .travis.yml 22 March 2018, 07:09:13 UTC
bc5b8be Shifu Chen 16 March 2018, 10:11:38 UTC Update README.md 16 March 2018, 10:11:38 UTC
dbd9920 Shifu Chen 16 March 2018, 10:09:22 UTC Update README.md 16 March 2018, 10:09:22 UTC
3eecb26 Shifu Chen 16 March 2018, 02:37:59 UTC Update README.md 16 March 2018, 02:37:59 UTC
ccb1dc7 Shifu Chen 14 March 2018, 14:38:00 UTC support low complexity filtering 14 March 2018, 14:38:00 UTC
5215aa8 Shifu Chen 14 March 2018, 04:05:20 UTC filter zero-length reads even when length filter is not enabled 14 March 2018, 04:05:20 UTC
a0e7738 Shifu Chen 13 March 2018, 06:54:51 UTC fix the issue of lowercase UMI https://github.com/OpenGene/fastp/issues/41 13 March 2018, 06:54:51 UTC
5093f17 Shifu Chen 12 March 2018, 09:20:23 UTC Merge pull request #38 from bgruening/patch-1 use https instead of http 12 March 2018, 09:20:23 UTC
a8861db Björn Grüning 12 March 2018, 08:57:25 UTC use https instead of http 12 March 2018, 08:57:25 UTC
82eb296 Shifu Chen 09 March 2018, 02:01:55 UTC Update README.md 09 March 2018, 02:01:55 UTC
078ebc0 Shifu Chen 09 March 2018, 01:59:17 UTC Update README.md 09 March 2018, 01:59:17 UTC
aeb7c32 Shifu Chen 09 March 2018, 00:49:41 UTC Perform polyG --> polyX trimming in 3'ends when they are both enabled 09 March 2018, 00:49:41 UTC
1d20ad1 Shifu Chen 07 March 2018, 03:33:06 UTC trim the polyX having a different last base in 3' end https://github.com/OpenGene/fastp/issues/33 07 March 2018, 03:33:06 UTC
986bd76 Shifu Chen 06 March 2018, 14:35:58 UTC support polyX trimming in 3' ends https://github.com/OpenGene/fastp/issues/33 06 March 2018, 14:35:58 UTC
f1c0ac0 Shifu Chen 06 March 2018, 06:45:17 UTC change default overlap length requirement for overlap based PE adapter trimming 06 March 2018, 06:45:17 UTC
7b788c9 Shifu Chen 06 March 2018, 06:44:23 UTC change trimBySequence from backward method to forward method 06 March 2018, 06:44:23 UTC
8746036 Shifu Chen 04 March 2018, 07:09:55 UTC improve quality cutting in 5' and 3' ends 04 March 2018, 07:09:55 UTC
b7e120f Shifu Chen 02 March 2018, 00:37:27 UTC Update README.md 02 March 2018, 00:37:27 UTC
9780591 Shifu Chen 02 March 2018, 00:36:01 UTC Update README.md 02 March 2018, 00:36:01 UTC
64898d5 Shifu Chen 04 February 2018, 09:19:06 UTC Update README.md 04 February 2018, 09:19:06 UTC
a9c5b64 Shifu Chen 04 February 2018, 09:15:24 UTC Update README.md 04 February 2018, 09:15:24 UTC
f874201 Shifu Chen 04 February 2018, 09:07:11 UTC add poly_g_min_len option https://github.com/OpenGene/fastp/issues/25 04 February 2018, 09:07:11 UTC
8d146e9 Shifu Chen 04 February 2018, 08:43:50 UTC add -v/--version to show version info https://github.com/OpenGene/fastp/issues/21 04 February 2018, 08:43:50 UTC
5ce9b6a Shifu Chen 04 February 2018, 08:22:02 UTC support R1 adapter, R2 adapter given respectively for PE data 04 February 2018, 08:22:02 UTC
ddfc3af Shifu Chen 04 February 2018, 07:26:37 UTC use adapter sequence to trim adapter for PE data when failed to find overlap 04 February 2018, 07:26:37 UTC
0e61ca4 Shifu Chen 11 January 2018, 02:45:44 UTC Update README.md 11 January 2018, 02:45:44 UTC
775ffe9 Shifu Chen 11 January 2018, 02:41:27 UTC Add Conda information to README 11 January 2018, 02:41:27 UTC
4c5fa30 Shifu Chen 19 December 2017, 02:35:06 UTC fix crash caused by returning NULL from trimAndCut 19 December 2017, 02:35:06 UTC
1e0b626 Shifu Chen 14 December 2017, 08:58:45 UTC set default length requirement from 30 to 15 for miRNA sequencing 14 December 2017, 08:58:45 UTC
161299b Shifu Chen 14 December 2017, 08:44:01 UTC for SE adapter trimming, continue to search when the adapter sequence is wholely contained 14 December 2017, 08:44:01 UTC
05a04a6 Shifu Chen 13 December 2017, 03:56:06 UTC set version to v12.0 13 December 2017, 03:56:06 UTC
a53aa21 Shifu Chen 13 December 2017, 03:52:37 UTC support hide/show 13 December 2017, 03:52:37 UTC
666e5dc Shifu Chen 12 December 2017, 13:25:53 UTC minor revision for report 12 December 2017, 13:26:30 UTC
61b79dd Shifu Chen 12 December 2017, 12:29:39 UTC Update README.md 12 December 2017, 12:29:39 UTC
b897ded Shifu Chen 12 December 2017, 12:28:22 UTC update readme for overrepresented sequence analysis 12 December 2017, 12:28:22 UTC
5c12797 Shifu Chen 12 December 2017, 10:18:00 UTC update README for overrepresented sequence analysis 12 December 2017, 10:18:00 UTC
2f213f8 Shifu Chen 12 December 2017, 10:04:05 UTC overrepresented sequence analyss completed 12 December 2017, 10:04:05 UTC
d89c3df Shifu Chen 12 December 2017, 07:31:13 UTC add overrepresentation analysis 12 December 2017, 07:31:13 UTC
589188c Shifu Chen 10 December 2017, 06:38:25 UTC add seqlen evaluator 10 December 2017, 06:38:25 UTC
eeaa34b Shifu Chen 10 December 2017, 05:35:24 UTC add evaluateOverRepSeqs 10 December 2017, 05:35:24 UTC
04dfaee Shifu Chen 07 December 2017, 13:09:08 UTC set version to v0.11.0 07 December 2017, 13:09:08 UTC
a50468c Shifu Chen 07 December 2017, 13:02:51 UTC show GC content in summary table https://github.com/OpenGene/fastp/issues/15 07 December 2017, 13:02:51 UTC
58c8636 Shifu Chen 07 December 2017, 10:06:08 UTC Show base content percentage in base content graph 07 December 2017, 10:06:08 UTC
fb3fae8 Shifu Chen 07 December 2017, 06:46:23 UTC report kmer counting in JSON 07 December 2017, 06:46:23 UTC
c7d8c33 Shifu Chen 07 December 2017, 06:20:43 UTC add kmer counting and display 07 December 2017, 06:21:07 UTC
1f42298 Shifu Chen 05 December 2017, 06:43:52 UTC Update README.md 05 December 2017, 06:43:52 UTC
1369f95 Shifu Chen 05 December 2017, 06:21:52 UTC add polyG tail trimming 05 December 2017, 06:21:52 UTC
9c3207b Shifu Chen 01 December 2017, 01:46:11 UTC revise UMI example 01 December 2017, 01:46:11 UTC
2dc4a98 Shifu Chen 01 December 2017, 01:41:22 UTC make prefix configurable for UMI, and no prefix for default 01 December 2017, 01:41:22 UTC
c2413a5 Shifu Chen 30 November 2017, 03:05:47 UTC set version to v0.9.1 30 November 2017, 03:05:47 UTC
f6739da Shifu Chen 30 November 2017, 03:05:11 UTC limit base numbers in evaluation for the long read cases 30 November 2017, 03:05:11 UTC
842207e Shifu Chen 30 November 2017, 02:58:43 UTC revise read number evaluation 30 November 2017, 02:58:43 UTC
9fda5c5 Shifu Chen 30 November 2017, 02:22:47 UTC change K/M/G/T carry from 1024 to 1000 30 November 2017, 02:22:47 UTC
abfe9bb Shifu Chen 29 November 2017, 09:00:41 UTC Update README.md 29 November 2017, 09:00:41 UTC
22487b8 Shifu Chen 29 November 2017, 03:28:57 UTC support per_index / per_read for UMI processing 29 November 2017, 03:28:57 UTC
31989da Shifu Chen 29 November 2017, 03:04:08 UTC Update README.md 29 November 2017, 03:04:08 UTC
951ad84 Shifu Chen 29 November 2017, 02:59:23 UTC Update README.md 29 November 2017, 02:59:23 UTC
1e5eb32 Shifu Chen 29 November 2017, 02:52:14 UTC Update README.md 29 November 2017, 02:52:14 UTC
979d416 Shifu Chen 29 November 2017, 02:38:45 UTC Update README.md 29 November 2017, 02:38:45 UTC
2d17d67 Shifu Chen 29 November 2017, 02:17:18 UTC Update README.md 29 November 2017, 02:17:18 UTC
6865e2c Shifu Chen 29 November 2017, 02:08:41 UTC Update README.md 29 November 2017, 02:08:41 UTC
191daf1 Shifu Chen 29 November 2017, 01:57:09 UTC Update README.md 29 November 2017, 01:57:09 UTC
207816d Shifu Chen 29 November 2017, 01:42:13 UTC Update README.md 29 November 2017, 01:42:13 UTC
ee65540 Shifu Chen 29 November 2017, 01:17:18 UTC Update README.md 29 November 2017, 01:17:18 UTC
0fdd5f7 Shifu Chen 29 November 2017, 01:15:21 UTC Update README.md 29 November 2017, 01:15:21 UTC
9a532da Shifu Chen 28 November 2017, 13:57:03 UTC set version to v0.9.0 28 November 2017, 13:57:03 UTC
7c9acd2 Shifu Chen 28 November 2017, 13:43:40 UTC update read number evaluation 28 November 2017, 13:43:40 UTC
4c5dde2 Shifu Chen 28 November 2017, 13:18:50 UTC update README 28 November 2017, 13:18:50 UTC
ae4ff32 Shifu Chen 28 November 2017, 12:40:10 UTC add option to change the report title https://github.com/OpenGene/fastp/issues/4 28 November 2017, 12:40:10 UTC
5ebd686 Shifu Chen 28 November 2017, 10:53:56 UTC update README 28 November 2017, 10:53:56 UTC
d43f9e9 Shifu Chen 28 November 2017, 10:51:02 UTC fix trimFront 28 November 2017, 10:51:02 UTC
f8c5d5a Shifu Chen 28 November 2017, 10:44:49 UTC add UMI processing 28 November 2017, 10:44:49 UTC
7ac1e68 Shifu Chen 26 November 2017, 13:22:34 UTC fix a typo of split 26 November 2017, 13:22:34 UTC
e780193 Shifu Chen 26 November 2017, 13:15:13 UTC set version to v0.8.0 26 November 2017, 13:15:13 UTC
5065f3b Shifu Chen 26 November 2017, 13:12:47 UTC Update README.md 26 November 2017, 13:12:47 UTC
1513189 Shifu Chen 26 November 2017, 13:11:05 UTC Update README.md 26 November 2017, 13:11:05 UTC
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