Commits for galt

v492_base to v493_preview (2025-12-15 to 2026-01-12) v493

4cf72ff67368e864c7e80b8918245689d22264f6 Mon Dec 15 17:06:21 2025 -0800

• Reapply "Little patch for udc.localDir and trackHub security for local bigDataUrl disallowed for non-local hubUrl. We have to double check the cached trackDb data. fixes #34544" This reverts commit b1d12cdd8bea10895a0ff1b787f5c0549cb76d7a. Revert the reversion!
  • src/hg/lib/trackHub.c - lines changed 7, context: html, text, full: html, text

e028ddcac656a6b6e3e923b00d3e6233059d79e7 Mon Dec 15 17:07:09 2025 -0800

• Reapply "freeMem was crashing for settings values, cannot do that for settings returned from trackDbCache. refs #34544, #36835, #36834" This reverts commit 648f90bb5f2bbbf365a7005a69fdfa82c37057e0. Revert the reversion!
  • src/hg/lib/trackHub.c - lines changed 6, context: html, text, full: html, text

f7f5b164d6bacfd8da9b8f7772497ef971f2b0f8 Fri Dec 19 11:37:31 2025 -0800

• Add options -chrom -start -end -range -bed -positions -udcDir to bigMafToMaf. Adds -positions to bigBedToBed. Moved parsePosition and parseRange routines into common.c so they could be shared with these and other utilities. -range has one 0-based start on commandline. -positions is a file with a list of 1-based starts. fixes #28109
  • src/hg/hgc/hgc.c - lines changed 27, context: html, text, full: html, text
  • src/hg/lib/genbank.c - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 26, context: html, text, full: html, text
  • src/hg/utils/bigMafToMaf/bigMafToMaf.c - lines changed 115, context: html, text, full: html, text
  • src/inc/common.h - lines changed 11, context: html, text, full: html, text
  • src/lib/common.c - lines changed 54, context: html, text, full: html, text
  • src/utils/bigBedToBed/bigBedToBed.c - lines changed 58, context: html, text, full: html, text

168f1d98aebcb04463c0a90e2249aa4414530e8a Fri Dec 19 13:34:48 2025 -0800

• Revert "Reapply "freeMem was crashing for settings values, cannot do that for settings returned from trackDbCache. refs #34544, #36835, #36834"" This reverts commit e028ddcac656a6b6e3e923b00d3e6233059d79e7. We can use touch single file hub.txt or rm -rf $cacheTrackDbDir to force updating the trackDb cache and still allow udc.localDir to be used.
  • src/hg/lib/trackHub.c - lines changed 6, context: html, text, full: html, text

e95fa927a040a8d89ac8e63e0cf0622c4efd1374 Fri Dec 19 13:36:23 2025 -0800

• Revert "Reapply "Little patch for udc.localDir and trackHub security for local bigDataUrl disallowed for non-local hubUrl. We have to double check the cached trackDb data. fixes #34544"" This reverts commit 4cf72ff67368e864c7e80b8918245689d22264f6. We can use touch single file hub.txt or rm -rf $cacheTrackDbDir to force updating the trackDb cache and still allow udc.localDir to be used.
  • src/hg/lib/trackHub.c - lines changed 7, context: html, text, full: html, text

a9389f2c0af99f64b1f32353499fb48b4aca0872 Thu Jan 8 13:15:09 2026 -0800

• whitelist genark in localUrl paths in isValidBigDataUrl() in customFactory.c
  • src/hg/lib/customFactory.c - lines changed 7, context: html, text, full: html, text