All File Changes

v321_preview to v321_preview2 (2015-08-10 to 2015-08-17) v321

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    Adding a temporary hgwbeta.hg.conf setting enabling hot keys refs #15370
    
• src/blat/version.doc
  • lines changed 4, context: html, text, full: html, text
    Bumping version number
    
• src/hg/cirm/cdw/cdwAddStep/cdwAddStep.c
  • lines changed 46, context: html, text, full: html, text
    Command line utility to load a cdwStepDef.
    
• src/hg/cirm/cdw/cdwAddStep/makefile
  • lines changed 4, context: html, text, full: html, text
    Command line utility to load a cdwStepDef.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 21, context: html, text, full: html, text
    Changing image on main page and bumping version number. Adding color picker widget to test page.
    
• src/hg/cirm/cdw/inc/cdwStep.h
  • lines changed 288, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/lib/cdwStep.as
  • lines changed 38, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/lib/cdwStep.c
  • lines changed 640, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/lib/cdwStep.sql
  • lines changed 47, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 4, context: html, text, full: html, text
    Making it so that all tags starting with 'GEO_' are allowed. Also added cell_type, submission_date, and update_date to the allowed tags.
    
• src/hg/cirm/cdw/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/oneShot/cdwSnyderomeStepLink/cdwSnyderomeStepLink.c
  • lines changed 139, context: html, text, full: html, text
    Program that helps load Snyderome file graph seems to work for WGS data.
    
  • lines changed 139, context: html, text, full: html, text
    Moving from oneShot to wrangling directory
    
• src/hg/cirm/cdw/oneShot/cdwSnyderomeStepLink/makefile
  • lines changed 4, context: html, text, full: html, text
    Program that helps load Snyderome file graph seems to work for WGS data.
    
  • lines changed 4, context: html, text, full: html, text
    Moving from oneShot to wrangling directory
    
• src/hg/cirm/cdw/wrangle/cdwSnyderomeStepLink/cdwSnyderomeStepLink.c
  • lines changed 139, context: html, text, full: html, text
    Moving from oneShot to wrangling directory
    
• src/hg/cirm/cdw/wrangle/cdwSnyderomeStepLink/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving from oneShot to wrangling directory
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/manifest.txt
  • lines changed 933, context: html, text, full: html, text
    Checking in program generated manifest.
    
  • lines changed 1, context: html, text, full: html, text
    Adding # to first line
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/meta.txt
  • lines changed 3944, context: html, text, full: html, text
    Initial cut of quake brain PNAS paper metadata.
    
  • lines changed 544, context: html, text, full: html, text
    Adding cell_type field, access field, and starting to unpack age-related fields from GEO tag.
    
  • lines changed 42, context: html, text, full: html, text
    Unpacking GEO_Sample_age into age/age-units/life_stage fields
    
  • lines changed 89, context: html, text, full: html, text
    Removing extranious third level GEO_Sample_c1_chip_id tag
    
  • lines changed 22, context: html, text, full: html, text
    Removing a bunch of uninformative or incorrect GEO fields.
    
  • lines changed 36, context: html, text, full: html, text
    Adding donor and cell_count tag. Reworking body_part tag to be at finer level. Getting rid of some GEO tags that contained no new info.
    
  • lines changed 434, context: html, text, full: html, text
    Removing now redundand GEO_Sample_cell_type.
    
  • lines changed 16, context: html, text, full: html, text
    Fixed age_units/age_unit typo
    
  • lines changed 1, context: html, text, full: html, text
    Adding data_set_id tag
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/quakeRnaPipeline2.txt
  • lines changed 1, context: html, text, full: html, text
    First cut of the pipeline description.
    
• src/hg/das/das.c
  • lines changed 8, context: html, text, full: html, text
    Making help text not appear as XML to the browser.
    
  • lines changed 14, context: html, text, full: html, text
    Fixing crash on fetching ctgPos2 features.
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 10, context: html, text, full: html, text
    short match switch to pack automatically, refs #15871
    
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    implement the suggestion in note-18 of #6551. Default track visibilities
    are now stored in the cart. The defaults are reloaded from trackDb on a
    new cart, when the assembly is changed, or when "default tracks" is
    pressed.
    
• src/hg/hgTracks/extTools.c
  • lines changed 11, context: html, text, full: html, text
    oops, forgot to strip off hgsid when sending current URL to external site
    
  • lines changed 61, context: html, text, full: html, text
    adding email display during redirect, GET urls, adding onlyDbs/notDbs tags to support hg38, refs #15113.
    
• src/hg/hgTracks/extTools.h
  • lines changed 3, context: html, text, full: html, text
    adding email display during redirect, GET urls, adding onlyDbs/notDbs tags to support hg38, refs #15113.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 37, context: html, text, full: html, text
    implement the suggestion in note-18 of #6551. Default track visibilities
    are now stored in the cart. The defaults are reloaded from trackDb on a
    new cart, when the assembly is changed, or when "default tracks" is
    pressed.
    
• src/hg/hgTracks/menu.c
  • lines changed 8, context: html, text, full: html, text
    adding email display during redirect, GET urls, adding onlyDbs/notDbs tags to support hg38, refs #15113.
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 1, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    fixing null pointer problem found in code review by Angie, as usual. refs #15850
    
• src/hg/hgsqlLocal/hgsqlLocal.c
  • lines changed 41, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/hgsqlLocal/makefile
  • lines changed 3, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/hgsqlTableDate/hgsqlTableDate.c
  • lines changed 2, context: html, text, full: html, text
    trivial cleanup to hgsqlTableDate
    
• src/hg/hgsqldumpLocal/hgsqldumpLocal.c
  • lines changed 39, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/hgsqldumpLocal/makefile
  • lines changed 3, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/htdocs/style/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding style to support a color picker jquery widget.
    
• src/hg/inc/annoGrateWigDb.h
  • lines changed 3, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/inc/cart.h
  • lines changed 1, context: html, text, full: html, text
    implement the suggestion in note-18 of #6551. Default track visibilities
    are now stored in the cart. The defaults are reloaded from trackDb on a
    new cart, when the assembly is changed, or when "default tracks" is
    pressed.
    
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    changing oligomatch default seq, refs #15871
    
• src/hg/js/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding d3pie.js 3rd party module for current CIRM use, and colorPicker in anticipation of future use.
    
  • lines changed 5, context: html, text, full: html, text
    Fixing simple merge conflict.
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 1, context: html, text, full: html, text
    Oops, need to include maf along with wigMaf in order to exclude MAF custom tracks.
    fixes #15857
    
• src/hg/lib/annoFormatVep.c
  • lines changed 29, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/lib/annoGrateWigDb.c
  • lines changed 5, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/lib/annoStreamDb.c
  • lines changed 2, context: html, text, full: html, text
    Fixing corner-case that caused the last item(s) to be lost when merge-sorting
    large-bin items and all items are in large bins.
    fixes #15867
    
• src/hg/lib/annoStreamWig.c
  • lines changed 2, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/lib/cart.c
  • lines changed 5, context: html, text, full: html, text
    implement the suggestion in note-18 of #6551. Default track visibilities
    are now stored in the cart. The defaults are reloaded from trackDb on a
    new cart, when the assembly is changed, or when "default tracks" is
    pressed.
    
• src/hg/lib/cartJson.c
  • lines changed 2, context: html, text, full: html, text
    Work around some hgcentraltest genome values that unintentionally include extra whitespace.
    
• src/hg/lib/hAnno.c
  • lines changed 3, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/lib/jksql.c
  • lines changed 6, context: html, text, full: html, text
    oops compile-time mysql version checking
    
• src/hg/lib/sqlProg.c
  • lines changed 2, context: html, text, full: html, text
    cleaning up commented lines from unused vars
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 8, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/makeDb/doc/ce11/lastzRuns.txt
  • lines changed 24, context: html, text, full: html, text
    rerun oncVol1 and bruMal2 with wolbachia sequence refs #15209
    
• src/hg/makeDb/doc/ce11/multiz26way.txt
  • lines changed 120, context: html, text, full: html, text
    rerun with new oncVol1 and bruMal2 sequence and run as full chromosomes refs #15209
    
• src/hg/makeDb/doc/hg38/hg19MassiveLift.txt
  • lines changed 4, context: html, text, full: html, text
    RID 15518 Doumentation for the IKMC lift from hg19 to hg38
    
• src/hg/makeDb/doc/microsat.txt
  • lines changed 19, context: html, text, full: html, text
    generic construction procedure for microstat track refs #15398
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh
  • lines changed 4, context: html, text, full: html, text
    malacards update, refs #14417
    
• src/hg/makeDb/doc/worms/lastzRuns.txt
  • lines changed 58, context: html, text, full: html, text
    lastz with bruMal2 and oncVol1 both have wolbachia refs #15209
    
• src/hg/makeDb/doc/worms/oncVol1.txt
  • lines changed 70, context: html, text, full: html, text
    rebuild with wolbachia sequence included refs #15209
    
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 4, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/makeDb/trackDb/checkMetaDb
  • lines changed 4, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra
  • lines changed 50, context: html, text, full: html, text
    eliminate underscore in the track/table names refs #13713
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Disabling pop-up configuration for exacVariants subtrack because the js pop-up config code
    mangles the cart's multishad & value of checkbox group items.
    refs #14379, #15873
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 2, context: html, text, full: html, text
    change long label per #14639
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    RID 15518 Adding the lifted from hg19 icon to the track
    
  • lines changed 2, context: html, text, full: html, text
    Addint release tag to two experimental tracks that were causing errors on the RR, no redmine
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Shortening longLabels to fit our conventions, refs #15767
    
• src/hg/makeDb/trackDb/loadTracks
  • lines changed 11, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/makeDb/trackDb/makeMetaDb
  • lines changed 4, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/makeDb/trackDb/makeTrixLinks
  • lines changed 4, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 4, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/makeDb/trackDb/mouse/cloneEnd.trackDb.ra
  • lines changed 28, context: html, text, full: html, text
    eliminate underscore in the track/table names refs #13713
    
• src/hg/makeDb/trackDb/trackDb.chainNet.nematode.ra
  • lines changed 527, context: html, text, full: html, text
    rearranging orders and adding ce11 refs #15209
    
  • lines changed 9, context: html, text, full: html, text
    fixup correct o_Organism names on a couple refs #15209
    
• src/hg/makeDb/trackDb/worm/bruMal2/gold.html
  • lines changed 1, context: html, text, full: html, text
    added wolbachia/AE017321.1 note refs #15209
    
• src/hg/makeDb/trackDb/worm/bruMal2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    up[date gold search table rule to find wolbachia refs #15209
    
• src/hg/makeDb/trackDb/worm/oncVol1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    add wolbachia to gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    adding ws245Genes track definition refs #15209
    
• src/hg/makeDb/trackDb/worm/ws245Genes.html
  • lines changed 36, context: html, text, full: html, text
    adding ws245Genes track definition refs #15209
    
• src/hg/makefile
  • lines changed 2, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/hg/utils/automation/runLastzChain.sh
  • lines changed 3, context: html, text, full: html, text
    Removed B=0 from lastz parameters, refs #15710
    
• src/hg/utils/hubCrawl/hubCrawl.c
  • lines changed 112, context: html, text, full: html, text
    new utility, hubCrawl, to output strings useful for finding a hub.
    
• src/hg/utils/hubCrawl/makefile
  • lines changed 3, context: html, text, full: html, text
    new utility, hubCrawl, to output strings useful for finding a hub.
    
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 6, context: html, text, full: html, text
    Every 2-3 releases of ClinVar introduce a new type of error. Skipping
    lines on chrUn for now until they fix this one.
    
• src/inc/annoGrateWig.h
  • lines changed 12, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/inc/annoRow.h
  • lines changed 13, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    This makes it easier to include the kent code from outside the tree.
    
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    Bumping version number
    
• src/inc/jsonWrite.h
  • lines changed 12, context: html, text, full: html, text
    Improving opening module level comment.
    
• src/inc/net.h
  • lines changed 4, context: html, text, full: html, text
    increase some buffers in the net connection layer to allow user names
    and passwords longer than 128 characters long (no redmine)
    
• src/inc/psl.h
  • lines changed 3, context: html, text, full: html, text
    added function to clone a psl
    
  • lines changed 11, context: html, text, full: html, text
    converted macro to access PSL strands to inline functions to improve code reliablity (no redmine)
    
  • lines changed 12, context: html, text, full: html, text
    added inline function to get PSL block starts to match ones to get block ends (no redmine)
    
• src/inc/tagStorm.h
  • lines changed 6, context: html, text, full: html, text
    Improving documentation a little.
    
• src/isPcr/isPcr/tests/input/in.fa
  • lines changed 2001, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/input/in.primers
  • lines changed 1, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/input/testFlip.in
  • lines changed 1, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/simple/in.fa
  • lines changed 2001, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/simple/in.primers
  • lines changed 1, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/simple/testFlip.in
  • lines changed 1, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/jkOwnLib/ffSeedExtend.c
  • lines changed 22, context: html, text, full: html, text
    Removing some unused code.
    
• src/jkOwnLib/gfBlatLib.c
  • lines changed 2, context: html, text, full: html, text
    Fixing fastMap bogus double-sided gaps redmine #15317
    
• src/jkOwnLib/gfPcrLib.c
  • lines changed 9, context: html, text, full: html, text
    Think I fixed #15643
    
• src/lib/annoFormatTab.c
  • lines changed 72, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/lib/annoGrateWig.c
  • lines changed 5, context: html, text, full: html, text
    Use isnan instead of comparing to NAN, which does not work!
    
  • lines changed 105, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/lib/annoRow.c
  • lines changed 25, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/lib/annoStreamBigWig.c
  • lines changed 4, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/lib/psl.c
  • lines changed 18, context: html, text, full: html, text
    added function to clone a psl
    
  • lines changed 2, context: html, text, full: html, text
    pslClone needs to check if qSequence/tSequence fields are allocated before referencing (no redmine)
    
  • lines changed 2, context: html, text, full: html, text
    premature command of bug fix in pslClone (no redmine)
    
  • lines changed 1, context: html, text, full: html, text
    found yet another bug in pslClone. Sorry for committing prematurely (no redmine)
    
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    Removing some encode3 stuff from build.
    
• src/product/README.mysql.setup
  • lines changed 4, context: html, text, full: html, text
    documenting a new mysql5.7 option to require all connections to be encrypted. Also fixed a couple of errors noticed in the text regarding profile config.
    
• src/product/ex.hg.conf
  • lines changed 2, context: html, text, full: html, text
    Fixed a couple of errors noticed in the text regarding profile config.
    
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
  • lines changed 72, context: html, text, full: html, text
    Adding div option.
    
• src/userApps/fetchKentSource.sh
  • lines changed 2, context: html, text, full: html, text
    Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option. Jing says it is OK to nuke this old junk. Of course it will live in history as it should.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 1, context: html, text, full: html, text
    correct date on preview1 refs #15836
    
  • lines changed 2, context: html, text, full: html, text
    v321 preview2 refs #15836
    

• lines changed: 13486
• files changed: 129