| e522c23 | Brian Haas | 27 October 2023, 18:40:42 UTC | fusionfilter update | 27 October 2023, 18:40:42 UTC |
| 27aded2 | Brian Haas | 27 October 2023, 18:12:41 UTC | Merge branch 'devel' of github.com:STAR-Fusion/STAR-Fusion into devel | 27 October 2023, 18:12:41 UTC |
| d24f556 | Brian Haas | 27 October 2023, 18:12:37 UTC | makefile update | 27 October 2023, 18:12:37 UTC |
| cd93624 | Brian Haas | 27 October 2023, 16:44:37 UTC | rebuild w/ lastest FI base docker w/ Trinity support | 27 October 2023, 16:44:37 UTC |
| 87a00ba | Brian Haas | 27 October 2023, 16:32:13 UTC | added numpy to docker for Trinity | 27 October 2023, 16:32:13 UTC |
| 53f05a7 | Brian Haas | 27 October 2023, 16:22:59 UTC | make clean in testing better | 27 October 2023, 16:22:59 UTC |
| 1e12a4e | Brian Haas | 27 October 2023, 15:59:35 UTC | update to fusionfilter module | 27 October 2023, 15:59:35 UTC |
| 5b1a54e | Brian Haas | 27 October 2023, 13:04:45 UTC | changelog updated for v1.13.0 | 27 October 2023, 13:04:45 UTC |
| 321a787 | Brian Haas | 27 October 2023, 13:00:12 UTC | docker update for release v1.13.0 | 27 October 2023, 13:00:12 UTC |
| 54719ec | Brian Haas | 27 October 2023, 12:57:24 UTC | prep for release v1.13.0 | 27 October 2023, 12:57:24 UTC |
| 3fe681d | Brian Haas | 27 October 2023, 11:56:10 UTC | updating to release v1.13.0 | 27 October 2023, 11:56:10 UTC |
| c8ba492 | Brian Haas | 27 October 2023, 11:55:16 UTC | updating submodules | 27 October 2023, 11:55:16 UTC |
| 95345bc | Brian Haas | 27 October 2023, 11:50:09 UTC | Merge branch 'master' of github.com:STAR-Fusion/STAR-Fusion into devel | 27 October 2023, 11:50:09 UTC |
| fff8dbd | Brian Haas | 18 September 2023, 12:49:31 UTC | adding utility for 10x bam to fastq | 18 September 2023, 12:49:31 UTC |
| fea2109 | Brian Haas | 28 August 2023, 15:32:13 UTC | more configuration available for base star-fusion wdl | 28 August 2023, 15:32:13 UTC |
| 65b5f1a | Brian Haas | 08 August 2023, 12:44:03 UTC | Merge pull request #368 from fizwit/exit0 exit 0 for --help and --show_full_usage_info | 08 August 2023, 12:44:03 UTC |
| 78b8ace | fizwit | 07 August 2023, 22:20:27 UTC | exit 0 for --help and --show_full_usage_info | 07 August 2023, 22:20:27 UTC |
| 8a7b039 | Brian Haas | 18 July 2023, 15:41:42 UTC | adding gbio paper | 18 July 2023, 15:41:42 UTC |
| a2b0ec6 | Brian Haas | 15 July 2023, 12:52:47 UTC | key overlap spans on gene_id as well as the earlier gene symbol | 15 July 2023, 12:52:47 UTC |
| bdfc435 | Brian Haas | 29 January 2023, 16:23:58 UTC | added url | 29 January 2023, 16:23:58 UTC |
| 90dd499 | Brian Haas | 29 January 2023, 16:22:54 UTC | adding convert_star_to_bedpe.py | 29 January 2023, 16:22:54 UTC |
| f2eb477 | Brian Haas | 22 January 2023, 17:47:32 UTC | include read name | 22 January 2023, 17:47:32 UTC |
| 9f99350 | Brian Haas | 20 January 2023, 23:43:31 UTC | update | 20 January 2023, 23:43:31 UTC |
| 7f0bb98 | Brian Haas | 20 January 2023, 23:30:23 UTC | add | 20 January 2023, 23:30:23 UTC |
| 8e2fe4e | Brian Haas | 20 January 2023, 22:50:14 UTC | include chimeric read alignments in the main bam | 20 January 2023, 22:50:14 UTC |
| 6431b5d | Brian Haas | 18 January 2023, 14:57:05 UTC | back to devel | 18 January 2023, 14:57:05 UTC |
| be8db5a | Brian Haas | 18 January 2023, 14:23:20 UTC | prep for release v1.12.0 | 18 January 2023, 14:23:20 UTC |
| 0e263b0 | Brian Haas | 16 January 2023, 16:42:39 UTC | adding hg38 kickstart data | 16 January 2023, 16:42:39 UTC |
| 9340e5b | Brian Haas | 16 January 2023, 16:29:57 UTC | make STAR one-pass the default, and set option for twopass as wanted | 16 January 2023, 16:29:57 UTC |
| fa80e52 | Brian Haas | 16 January 2023, 16:21:20 UTC | Merge branch 'devel' of github.com:STAR-Fusion/STAR-Fusion into devel | 16 January 2023, 16:21:20 UTC |
| 5b44ef5 | Brian Haas | 16 January 2023, 16:19:31 UTC | Revert to computing FFPM based on total reads rather than uniquely aligned reads as in v1.11.1 (only release that did that) | 16 January 2023, 16:20:13 UTC |
| 49e764a | Brian Haas | 03 January 2023, 14:49:28 UTC | correction to changelog wrt one-pass option on star-fusion | 03 January 2023, 14:49:28 UTC |
| 62d2b4d | Brian Haas | 03 January 2023, 14:40:45 UTC | updage changelog for v1.11.1 | 03 January 2023, 14:40:45 UTC |
| 023c3d1 | Brian Haas | 10 December 2022, 16:14:16 UTC | making v1.11.1 postdev img | 10 December 2022, 16:14:16 UTC |
| cc164c6 | Brian Haas | 10 December 2022, 16:13:04 UTC | updating ctat-genomebuilder to be more permissive with gtf parsing | 10 December 2022, 16:13:04 UTC |
| 456fa3c | Brian Haas | 07 December 2022, 19:40:00 UTC | Merge pull request #345 from tmooney/add_rgattr_with_long_filenames Pass along the RG line when using params file. | 07 December 2022, 19:40:00 UTC |
| fefaf71 | Thomas Mooney | 29 November 2022, 18:15:08 UTC | Pass along the RG line when using params file. | 29 November 2022, 18:15:08 UTC |
| 4232907 | Brian Haas | 03 October 2022, 15:37:55 UTC | released v1.11.1 | 03 October 2022, 15:37:55 UTC |
| a5f3d82 | Brian Haas | 03 October 2022, 14:57:53 UTC | updating versioning to v1.11.1 | 03 October 2022, 14:57:53 UTC |
| 8cdd3eb | Brian Haas | 03 October 2022, 14:55:07 UTC | erge branch 'master' of github.com:STAR-Fusion/STAR-Fusion into devel | 03 October 2022, 14:55:07 UTC |
| 0cf9248 | Brian Haas | 03 October 2022, 14:53:45 UTC | updating FI to v2.8.0 | 03 October 2022, 14:53:45 UTC |
| 0dc1489 | Brian Haas | 30 September 2022, 18:52:01 UTC | dont compute ffpm or filter based on ffpm if no unique total reads - encountered during testing | 30 September 2022, 18:52:01 UTC |
| fca6037 | Brian Haas | 17 August 2022, 13:07:45 UTC | Update README.md | 17 August 2022, 13:07:45 UTC |
| 774bb31 | Brian Haas | 22 July 2022, 12:36:30 UTC | updatea | 22 July 2022, 12:36:30 UTC |
| 78a9f4e | Brian Haas | 30 June 2022, 19:47:49 UTC | by default, FFPM calculations performed based on uniquely aligned reads. If --no_remove_dups, FFPM calculations performed using total aligned reads (including multi-mapped). For FFPM calculations based on total reads in the sample (original behavior from release 1.11.0 and earlier), set the flag parameter --FFPM_via_total_reads | 30 June 2022, 19:47:49 UTC |
| 7609ea7 | Brian Haas | 13 June 2022, 15:59:31 UTC | updated Changelog for v1.11.0 release | 13 June 2022, 15:59:31 UTC |
| fd68cc8 | Brian Haas | 13 June 2022, 14:18:54 UTC | release for v1.11.0 | 13 June 2022, 14:18:54 UTC |
| 5e80eba | Brian Haas | 13 June 2022, 14:16:14 UTC | Merge branch 'devel' of github.com:STAR-Fusion/STAR-Fusion | 13 June 2022, 14:16:14 UTC |
| 613ed79 | Brian Haas | 13 June 2022, 14:16:00 UTC | updating to latest FI | 13 June 2022, 14:16:00 UTC |
| 3017156 | Brian Haas | 14 May 2022, 10:11:24 UTC | allow for one-pass mode | 14 May 2022, 10:11:24 UTC |
| 667c4bb | Brian Haas | 12 May 2022, 19:03:08 UTC | docker trinityctat/starfusion:pre-1.11.c using devel FI submod | 12 May 2022, 19:03:08 UTC |
| 3414829 | Brian Haas | 12 May 2022, 18:48:33 UTC | FI submod devel | 12 May 2022, 18:48:33 UTC |
| f4fa3e8 | Brian Haas | 26 February 2022, 14:17:07 UTC | utility added for circos support | 26 February 2022, 14:17:07 UTC |
| 8cef78e | Brian Haas | 31 January 2022, 15:50:43 UTC | docker update for pre-1.11.b | 31 January 2022, 15:50:43 UTC |
| 22f37aa | Brian Haas | 31 January 2022, 15:49:44 UTC | added ThreadHelper.pm | 31 January 2022, 15:49:44 UTC |
| 633a496 | Brian Haas | 28 January 2022, 20:35:56 UTC | update | 28 January 2022, 20:35:56 UTC |
| 939deb6 | Brian Haas | 28 January 2022, 20:31:56 UTC | update | 28 January 2022, 20:31:56 UTC |
| 7785f49 | Brian Haas | 28 January 2022, 20:30:18 UTC | updates for improved reproducibility | 28 January 2022, 20:30:18 UTC |
| 7ee35ef | Brian Haas | 28 January 2022, 15:34:22 UTC | allow for zero time | 28 January 2022, 15:34:34 UTC |
| 567e18c | Brian Haas | 21 December 2021, 19:23:10 UTC | test updates for parallel chimJ mapping | 21 December 2021, 19:23:10 UTC |
| c3cbbab | Brian Haas | 21 December 2021, 16:21:16 UTC | include --CPU in make test | 21 December 2021, 16:21:16 UTC |
| 7a7fea8 | Brian Haas | 21 December 2021, 16:18:33 UTC | incorporated --CPU into running STAR-Fusion.map_chimeric_reads_to_genes into starF | 21 December 2021, 16:18:33 UTC |
| 070c3fa | Brian Haas | 21 December 2021, 15:21:37 UTC | beginning to add multithreading to chimeric read to gene mapping step | 21 December 2021, 15:21:37 UTC |
| 676eb48 | Brian Haas | 20 November 2021, 14:32:34 UTC | include --outSAMattrRGline ID:GRPundef in make testing | 20 November 2021, 14:32:34 UTC |
| a4fda76 | Brian Haas | 20 November 2021, 14:25:23 UTC | added --STAR_outSAMattrRGline to allow users to specify read group info to STAR | 20 November 2021, 14:25:23 UTC |
| 9e61966 | Brian Haas | 09 November 2021, 17:12:50 UTC | allow .fq or .fastq extensions for fq files in tar | 09 November 2021, 17:12:50 UTC |
| 625d496 | Brian Haas | 09 November 2021, 16:19:12 UTC | update file tests for tar.gz in wdl | 09 November 2021, 16:19:12 UTC |
| fba43a7 | Brian Haas | 08 November 2021, 20:58:18 UTC | simpler tar exec | 08 November 2021, 20:58:18 UTC |
| 301ee3b | Brian Haas | 08 November 2021, 20:34:00 UTC | adding hg38 specific wdl | 08 November 2021, 20:34:00 UTC |
| 701b33a | Brian Haas | 08 November 2021, 20:26:24 UTC | added help annotations | 08 November 2021, 20:26:24 UTC |
| 2766e6a | Brian Haas | 08 November 2021, 20:16:02 UTC | update to hg19 wdl to match base wdl | 08 November 2021, 20:16:02 UTC |
| 3434743 | Brian Haas | 08 November 2021, 20:14:52 UTC | using boolean for examine_coding_effect param | 08 November 2021, 20:14:52 UTC |
| ca5d3ef | Brian Haas | 08 November 2021, 17:17:22 UTC | revised workflow for simpler star-fusion execution from reads or tar.gz paired fqs | 08 November 2021, 17:17:22 UTC |
| 2a6266c | Brian Haas | 08 November 2021, 16:42:56 UTC | restructured wdl for separate hg19/hg38 configs | 08 November 2021, 16:42:56 UTC |
| 4a77837 | Brian Haas | 08 November 2021, 15:45:13 UTC | prep for Terra-branch wdls | 08 November 2021, 15:45:13 UTC |
| 0de3630 | Brian Haas | 02 November 2021, 23:56:57 UTC | all submod to co master | 02 November 2021, 23:56:57 UTC |
| f587699 | Brian Haas | 02 November 2021, 23:52:33 UTC | was prev missing unintentionally | 02 November 2021, 23:52:33 UTC |
| 90dd0c8 | Brian Haas | 09 September 2021, 20:39:26 UTC | added some documentation | 09 September 2021, 20:39:26 UTC |
| bd4da24 | Brian Haas | 23 July 2021, 16:41:15 UTC | makefile update to separately build plugins from FI | 23 July 2021, 16:41:15 UTC |
| 9bb68a9 | Brian Haas | 23 July 2021, 16:37:46 UTC | docker update for v1.10.1 | 23 July 2021, 16:37:46 UTC |
| b68d4ac | Brian Haas | 23 July 2021, 16:35:26 UTC | build FI during starF build via make | 23 July 2021, 16:35:26 UTC |
| acdc830 | Brian Haas | 23 July 2021, 16:26:09 UTC | using FI base image in docker, updated changelog | 23 July 2021, 16:26:09 UTC |
| 6c15112 | Brian Haas | 23 July 2021, 16:25:00 UTC | prep for release v1.10.1 | 23 July 2021, 16:25:00 UTC |
| 95837ee | Brian Haas | 23 July 2021, 16:16:41 UTC | updating all submodules, including FI v2.6.0 | 23 July 2021, 16:16:41 UTC |
| 63fb833 | Brian Haas | 23 July 2021, 13:46:43 UTC | Merge branch 'master' of github.com:STAR-Fusion/STAR-Fusion into devel | 23 July 2021, 13:46:43 UTC |
| 42e9070 | Brian Haas | 22 July 2021, 13:05:46 UTC | support option --min_pct_MM_nonspecific as advertised | 22 July 2021, 13:05:46 UTC |
| 7a8e3a6 | Brian Haas | 23 June 2021, 18:06:59 UTC | combined star_fusion_tasks.wdl into the main smartseq2 workflow wdl | 23 June 2021, 18:06:59 UTC |
| 898b53d | Brian Haas | 15 May 2021, 00:14:06 UTC | added check for AnnotFilterRule.pm in ctat genome lib | 15 May 2021, 00:14:06 UTC |
| 096d868 | jgould | 19 March 2021, 15:32:47 UTC | capture coding_effect and reads_per_gene outputs | 19 March 2021, 15:32:47 UTC |
| d2e4bf9 | Brian Haas | 06 March 2021, 15:32:31 UTC | back to devel | 06 March 2021, 15:32:31 UTC |
| f6e3833 | Brian Haas | 06 March 2021, 14:33:42 UTC | updated changelog for release v1.10.0 | 06 March 2021, 14:33:42 UTC |
| 04fb425 | Brian Haas | 06 March 2021, 14:21:20 UTC | back to STAR 2.7.8a | 06 March 2021, 14:21:20 UTC |
| 1b13c48 | Brian Haas | 06 March 2021, 13:41:11 UTC | reverting to star 2.7.2b | 06 March 2021, 13:41:11 UTC |
| 62bcf58 | Brian Haas | 05 March 2021, 20:24:21 UTC | updated docker for STAR v2.7.8a | 05 March 2021, 20:24:21 UTC |
| 926760b | Brian Haas | 05 March 2021, 17:03:10 UTC | docker update for release v1.10.0 | 05 March 2021, 17:03:10 UTC |
| 3eec327 | Brian Haas | 05 March 2021, 17:01:42 UTC | prep for release v1.10.0 - docker not ready yet | 05 March 2021, 17:01:42 UTC |
| 25d0ec7 | Brian Haas | 05 March 2021, 16:55:50 UTC | prep for release v1.10.0 | 05 March 2021, 16:55:50 UTC |
| fb38870 | Brian Haas | 01 March 2021, 18:49:45 UTC | upgrade to FI v2.5.0 | 01 March 2021, 18:49:45 UTC |
| b661ea9 | jgould | 23 November 2020, 15:29:33 UTC | Added option to set alignSJDBoverhangMin | 23 November 2020, 15:29:33 UTC |
| e23f51e | Brian Haas | 22 November 2020, 13:04:36 UTC | update to docker for FI integration: 1.10.0-devg | 22 November 2020, 13:04:36 UTC |
