commit 32f93dee599af2b7e4844943309c9db62923d01b Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Tue Mar 5 13:34:31 2024 -0800 Genome menu changes (GenArk) commit a716f73168f41372eb6ecefc150a5691ee817cd2 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Tue Mar 5 10:11:36 2024 -0800 Support chromosome pulldown for GenArk assemblies commit 55d25f383a314ab9aa8b31a8b7ab9b817c20d9db Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Mon Mar 4 19:52:18 2024 -0800 Fix bug caused by calculating genomic range of a reference frame prior to frame having a width in pixels. commit 54606776bad9c1b674d579517ba2bd0db8bb478b Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Fri Mar 1 09:29:14 2024 -0800 Searchable table - correct tooltip text, code cleanup commit d827f74fc3d24821bdce8fac4d87199f66451d22 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Feb 29 22:12:50 2024 -0800 typo commit cf8469f73ca863799dc1ba6bec4dd36d6e8f4e99 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Feb 29 22:11:58 2024 -0800 Rename GenArk menu item commit 18616bfc48e83fc93c90f3cfd92f77f9f0a6031b Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Feb 29 22:02:42 2024 -0800 Create "psuedo" cytoband to enable ideogram navigation for assemblies with no cytoband file. Maintains pre 2.17 compatibility. Fixes #1498 commit 455dc004d8781db80bb6c63a1128fe8382b600c8 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Feb 29 21:48:50 2024 -0800 Fix logic validating MM tags on negative strand alignments. See #1476 commit f77a27f837175470549794f06c199771036a0fe6 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Sun Feb 25 20:43:30 2024 -0800 Sashimi plot layout changes. commit 2feb7e2595b7b2e7ecc68c13b22fbf03871413ea Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed Feb 21 21:12:47 2024 -0800 Fix performance issue with sashimi plot SVG output. commit ff5f7f4545f917832a1aa39000d318df444fa83a Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Mon Feb 19 18:02:44 2024 -0800 Add UCSC GenArk search widget commit cb33d0551e5bcf7459957696ff2873f9013fad70 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Feb 8 08:06:26 2024 -0800 Array index check. See #1488 commit 8f79f06bd3863a996813e3d0bedf919070eef260 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Feb 8 00:11:10 2024 -0800 Fix broken unit tests (T2T hub down or moved) commit df442b9b322e57646b3929c384b30b96d9bbd71f Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed Feb 7 23:48:47 2024 -0800 Bug fix -- copied clipped sequences were reverse complemented for (-) strand alignments. This is inconsistent with copy read sequence, and the SAM/BAM conventions. Fixes #1487 commit bc3addca6180285575fd64b1a692b1d4c5e7f4aa Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed Feb 7 19:47:20 2024 -0800 account for alignment strand in MM validation. See issue #1476 commit 52332ed09ca4ec7c8a58bbee46bb4e27cfe2e3d5 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed Feb 7 15:23:46 2024 -0800 Simplify gct probe mapping error message commit 958c1196fd4feb5e3b1d3b7b0ef18b101b517870 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed Feb 7 15:11:28 2024 -0800 Remove "bam" files from ENCODE lists, they aren't indexed. commit f3444ed51b548c50a18d9070c1387bba7366e553 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed Feb 7 13:58:18 2024 -0800 auto trim entries to track hub dialog. Fixes #1485 commit dc0eb955e00532aa9514c4f8075826b10892c8ff Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Fri Feb 2 12:17:48 2024 -0800 validate base mod counts by default commit 2820304e23ad48a85cde8b4b9e39665be68689c0 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Feb 1 11:14:45 2024 -0800 Turn base modes "group by strand" off by default. See #1478 commit a37413edcacf809ae931a01ee3084a50bc8dc1f3 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed Jan 31 14:24:10 2024 -0800 Set validate basemod calls to off by default. See issue #1476 commit 25baf759bde702742ac6bff27d3f8e5d6779abaa Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Mon Jan 29 17:11:52 2024 -0800 Update script message commit 3cd649c6f72363361e8a6b03fedc9e8d30a21929 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Jan 25 11:59:14 2024 -0800 rollback whitespace changes commit d8a1fe76b7fa20db205422f677e67042e9d739ef Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Jan 25 11:17:08 2024 -0800 Catch errors parsing supplementary alignments commit 5d0fe7b4c68dfcfa9e8b8f8fc6885d6342579209 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Jan 25 21:54:56 2024 -0800 Echo required version number in startup script. commit 7a15e48a01c4c50f6232e6409f8b2165ebcb7ee8 Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Jan 25 21:19:02 2024 -0800 Add java version printout to shell scripts to aid diagnosis of startup problems. See #1475 commit d78ba9954a3973f0af75f5819809a662079f64af Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Jan 25 17:02:43 2024 -0800 Update README to specify Java 17 commit a5c27e535f5fefd0ff5b6975bc154ad5f6c21f5d Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Thu Jan 25 11:16:19 2024 -0800 Remove print statement commit ce9a88f47e984324b0740436ba9eefc00dabca9f Author: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Tue Jan 23 18:12:05 2024 -0800 blat - remove validation of genome ID from the response, the blat server might return an alternate ID.