summarylogtreecommitdiffstats
AgeCommit message (Collapse)Author
2024-10-05Update to 2.18.4Rhinoceros
* Upstream changelogs * v2.18.2_actual * Simplify genome selection dialog * Single select * Remove "download sequence" option * v2.18.3 * update batch test script * v2.18.4 * Update macos launcher -- possible Sentinel One fix?
2024-08-16Update to 2.18.1-1Rhinoceros
* Upstream changelog: "Clarify zoom in instructions for whole genome view. Fixes #1539"
2024-08-04Update to 2.18.0Rhinoceros
* Upstream changelog: "Cleanup git ignore"
2024-04-05Update to 2.17.4Rhinoceros
* Upstream changelog: "Add base modification options to alignment track preferences (defaults)"
2024-03-08Update to 2.17.3-1Rhinoceros
* Upstream changelog: "Genome menu changes (GenArk)" * Also chage _github_pkgver to track _pkgver
2024-02-12Update to 2.17.2-1Rhinoceros
* Github not updated, so use old licence and icon. * Upstream changlog: * Bug fixes * BAM/CRAM files with malformed SA tags were not viewable. * Validation of base modification tag (MM) was sometimes incorrect for reverse strand alignments. GitHub issue #1476. * The alignment track "copy clipped sequence" menu item incorrectly copied reverse complement sequence for reverse strand alignments. GitHub issue #1487.
2024-01-24Update to 2.17.1-1Rhinoceros
* Upstream change log * v2.17.1: Fix alignment block drawing bug. Fixes #1470 * Fix problem with copy-to-clipboard from popup text
2024-01-08Update to 2.17.0Rhinoceros
* From the IGV website, this is the stable version. From Github, this is _rc1 * Needed to change Java dependency from v11 to v17 (major.minor version 61.0) * Update *.sh scripts to reflect this change * Fix source of licence from master to versioned tag * Remove hardcoded IGV version from *.desktop files
2023-07-14Update to 2.16.2-1Rhinoceros
* Upstream changelog: "Add test session for 10X MM bug (#1305)"
2023-06-13Update to 2.16.1-2Rhinoceros
* Update licence
2023-04-19Update to 2.16.1Rhinoceros
* Upstream changelog: "remove broken tests -- test files no longer available"
2023-01-26Update to 2.16.0-1Rhinoceros
* Upstream changelogs: * https://software.broadinstitute.org/software/igv/2.16.x#LatestVersion * https://github.com/igvteam/igv/releases/tag/v2.16.0
2023-01-21Update to 2.15.5-1Rhinoceros
* Upstream changelog: https://github.com/igvteam/igv/releases/tag/v2.15.5
2022-12-09Update to 2.15.4-1Rhinoceros
Upstream changelog: "Add NPE protection to alignment sort method."
2022-11-30Update to 2.15.3-1Rhinoceros
Upstream changelog: "update batch scripts"
2022-11-09Update to 2.15.2-1Rhinoceros
* Upstream changelog: Fixes [https://github.com/igvteam/igv/issues/1252](#1252), [https://github.com/igvteam/igv/pull/1245](#1245)
2022-10-26Update to 2.15.1-1Rhinoceros
* Upstream changelog: * Fix Sahshimi [sic] plot gene track SVG peformance bug
2022-10-25Update to 2.15.0-1Rhinoceros
* Upstream changelog: * v2.15.0: Splice junction track scaling issues (fixes #1015) * Autoscale correctly in expanded mode * Refresh view on scaling state change * Add menu item to explicitly set depth * Save autoscale & maxDepth state to session
2022-09-03Update to 2.14.1-1Rhinoceros
* Upstream changelog: "Adjust treatment of indels for backwards compatibility -- SNPs have precedence over indels"
2022-08-09Update to 2.14.0-1Rhinoceros
* Upstream changelog: "add test xml"
2022-07-12Update to 2.13.2-2Rhinoceros
* New licence
2022-07-09Update to 2.13.2-1Rhinoceros
* Upstream changelog: "This release fixes a problem with Sashimi plots - they were not displaying any splice junctions, only the annotation track."
2022-06-16Update to 2.13.1-1Rhinoceros
* Upstream changelog: * Apply "group by" menu option to selected alignment track only, not all alignment tracks. Fixes #1045
2022-05-17Update to 2.13.0Rhinoceros
* Upstream changelog: "Update README" :/
2022-03-05Update to 2.12.3-1Rhinoceros
Upstream changelog: "Enable port by default"
2022-02-11Update to 2.12.2Rhinoceros
* Upstream changelog: * v2.12.2: Disable "feature jumping" from annotation tracks when typing gene name in search text field. Otherwise, genes containing "f" or "r" will cause an unwanted feature jump.
2022-02-10Update to 2.12.1-1Rhinoceros
* Upstream changelog: "Account for data range thresholding when coloring coverage tracks by allele fractions -- fixes #1100"
2022-02-01Update checksumRhinoceros
2022-02-01Update to 2.12.0-1Rhinoceros
* Upstream changelog: * bug fix -- cytoband "red box" does not move. Fixes #1096
2021-12-22Update to 2.11.9-1Rhinoceros
* Upstream changelog: This release includes the following updates: The Log4j dependency has been removed from IGV and replaced with java.util.logging. Note, if you have customized Log4j settings in previous versions of IGV, these customized settings are now ignored. Open an issue in the IGV GitHub repo if you need customized log settings. Loading of BAM files has been optimized to alleviate bottlenecks affecting large 3rd gen seqencing files and very deep coverage files. The function to Move the IGV Directory, which is invoked from View > Preferences > Advanced, now moves the IGV directory to the target directory, rather than moving the contents of the IGV directory to the target directory.
2021-12-17Update to 2.11.7-1Rhinoceros
* Upstream changelog: By default, the port listener is disabled on IGV startup. Change the setting in View > Preferences > Advanced. To use web links to IGV or control IGV from other programs, you must enable the port. Update to use Log4j version 2.16.0. Note however, we do not believe any version of IGV is impacted by the vulnerability of earlier Log4j versions because IGV is a desktop application and does not expose any input forms to users over the web, and it does not log any user input. Remove the "Color by insert size" option for RNA-Seq alignment tracks. This option cannot be meaningfully implemented or interpreted for RNA-Seq data. Allow symbolically linked launch scripts. (Git Issue #1060) Save the sequence for BLAT tracks in session files. (Git Issue #1065)
2021-12-16Fix incorrect url for iconRhinoceros
* Previous was the html page
2021-12-16Fix bad checksumRhinoceros
* No need to update pkgver if it didn't install previously
2021-12-15Update to 2.11.6-1Rhinoceros
* Upstream changelog: * By default, the port listener is disabled on IGV startup. Change the setting in View > Preferences > Advanced. Note that to use oAuth for Google or Amazon AWS access you must enable the port. * Update to use Log4j version 2.16.0. Note however, we do not believe any version of IGV is impacted by the vulnerability of earlier Log4j versions because IGV is a desktop application and does not expose any input forms to users over the web, and it does not log any user input. * Main download no longer bundles icon, so explicitly download from GitHub repository * Remove commented png that was unused * Fix whitespace indentations for consistency
2021-11-23Update to 2.11.4Rhinoceros
* Upstream changelog: * Ignore "f" and "b" keys if no tracks are selected, do not popup dialog.
2021-11-06Update to 2.11.3Rhinoceros
* Upstream changelog: * Bind "f" and "b" keystrokes to next feature and previous feature, in addition to "ctrl-f" and "ctrl-b". Also "shift-f" and "shift-b" to next/prev exon, in addition to "ctrl-shift-f/b". Fixes #1046
2021-10-08Update to 2.11.2-1Rhinoceros
* Upstream changelog: "Taking scrolling into account when exporting images. Fixes #1033"
2021-09-11Update to 2.11.1-1Rhinoceros
* Upstream changelog: "v2.11.1: Bug fix -- preference overrides from batch script were being stored persistently"
2021-08-25Update to 2.11.0-1Rhinoceros
* Upstream changelog: "Changed to use sha512 for signing Windows installers"
2021-08-02Update to .SRCINFO to 2.10.3-1Rhinoceros
2021-08-02Update to 2.10.3Rhinoceros
* Upstream changelog: "Fix broken paired end alignment popup text. Fixes #1003"
2021-07-15Update to 2.10.2-1Rhinoceros
* Upstream changelog: This bug fix release includes the following improvements: Fixed a problem with displaying extra large chromosomes (1024^3 bp). (Git issue #977 - initial issue) Fixed a problem with loading BAM files that do not store read sequence. (Git issue #977 - part 2) Tracks generated via Tools > Find Motif are now correctly saved in sessions. (Git issue #988) Fixed a problem in alignment tracks that caused the right-click popup menu command Copy read details to the clipboard to fail. Fixed a problem that sometimes occurred when reloading tracks (via File > Reload Tracks) if using a local reference genome.
2021-07-13Update to 2.10.1-1Rhinoceros
Upstream changelog: > v2.10.1: Use full height of track to render features in "COLLAPSED" mode. Fixes #990
2021-06-04Merge branch 'master' of aur:igvRhinoceros
2021-06-04Update to 2.10.0Rhinoceros
* Upstream changelog: * v2.10.0: remove unused code * fix module definition
2021-03-18Update to 2.9.4-1Rhinoceros
* Upstream changelog: "code cleanup"
2021-03-13Update to 2.9.3-1Rhinoceros
Upstream changelog: "Read stats optimization (alignment experiment type heuristics)"
2021-02-17Update to 2.9.2-1Rhinoceros
* Upstream changelog: "batch test files"
2021-02-11Update to 2.9.1-1Rhinoceros
* Upstream changelog: "blat refresh fix"
2021-02-02Update to 2.9.0-1Rhinoceros
* Upstream changelog: "color unit test"