v347

Code changes:

• Added Proxy support for HTTPS and FTP. Can configure 4 new settings in hg.conf. Also supports corresponding environment variables. Can configure an exception list of things not to proxy. Can turn on logging for proxy troubleshooting. Updated documentation (#19124). Galt
• Fixed udcCache to allow HIPAA-compliant Amazon Storage securely signed URL redirects by using GET with byterange=0-0 instead of HEAD to find the last-modified date and file size (#19158). Galt
• Changed internal script, bedJoinTabOffset, to append offsets of tab-sep lines to bed file. Max
• Added "filter activated" to labels for All GENCODE, mRNA and EST tracks if filters are configured. Mark
• Added HGVS terms as variant input option in Variant Annotation Integrator (#11460). Angie
• Fixed a small problem in Table Browser: summary/stats for mrna, est tables (#19111). Angie
• Fixed VAI to allow 2-bit-finding to work on both old nib assemblies and remote GBiB (#19113). Angie
• Corrected DECIPHER track details page to display correct mean ratio and pathogenicity; previously it sometimes showed the values for another variant from the same patient (#19129). Jonathan
• Added logic to hgLogin. Doing a password change with now automatically logs you in at the conclusion (#8351). Jonathan
• Added functionality to the bottleneck server. Now it can impose a fraction of the standard penalty value; hgTracks, hgTrackUi, and hgBlat now use this to permit more frequent non-programmatic use (#19019, #18461). Jonathan
• Transitioned makePushQSql.pl script to output redmine listings (#10146). Hiram
• Fixed version info tag on details page of NCBI Other gene track (#19079). Hiram
• Ongoing work to support snakes in bigPsl format. Brian
• Ongoing work on blat custom track support (#2811). Brian
• Fixed a few bugs in coverage graphs, added support for chains (#19031). Brian
• Fixed a problem with searching for items in tracks (#19117). Brian

Data changes:

• Fixed CRISPR track. It was missing "palindromic" guides (those flanked on both sides by an NGG motif) (#19167). Max
• Added star-rating of variants to ClinVar track (#17970). Max
• Created SNP v149 track for human assemblies: hg19, hg38 (#18330). Angie
• Edited Rhesus (rheMac8) description page to clarify reference. Angie
• Finished assembly browsers for Bison (bisBis1), Chinese pangolin (manPen1), and Tibetan Frog (nanPar1) (#15056 #15388 #15515). Hiram
• Created cytoBand track for rat (rn6) with data from NCBI (#14583). Hiram
• Updated phylogenetic tree to include 213 species (#17545). Hiram