All File Changes

v312_preview to v312_preview2 (2015-02-02 to 2015-02-09) v312

• java/src/edu/ucsc/genome/qa/linkCheck/LinkCheck.java
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/aladdin/aladdin/aladdin.c
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    removing execute permissions from .c files
    
• src/aladdin/aladdin/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/ali2alx/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/aliGlue/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/binGood/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/cdnaOff/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/cluster/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/exonAli/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/findCdna/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/g2cCheck/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/introns/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/pairClo/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/patCount/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/patSpace/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/refineAli/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/sortFilt/makefile
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    fixing exec perms on makefiles
    
• src/cdnaAli/stitchea/makefile
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    fixing exec perms on makefiles
    
• src/checkUmask.sh
  • lines changed 12, context: html, text, full: html, text
    check umask for local hgwdev users refs #14507
    
• src/hg/cirm/cdw/cdwFakeManifestFromSubmit/cdwFakeManifestFromSubmit.c
  • lines changed 2, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 1, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c
  • lines changed 1, context: html, text, full: html, text
    Fixed edwSamPairedEndStats/cdwSamPairedEndStats mixup.
    
• src/hg/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c
  • lines changed 1, context: html, text, full: html, text
    Fixed cdwSamRepeatAnalysis/edwSamRepeatAnalysis mixup.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 9, context: html, text, full: html, text
    Filling in cdwSubmit.fileCount field in database.
    
  • lines changed 32, context: html, text, full: html, text
    Adding validations for vcf and pdf files.
    
• src/hg/cirm/cdw/cdwQuery/cdwQuery.c
  • lines changed 158, context: html, text, full: html, text
    SQL-like query for files matching tags seems to work.
    
• src/hg/cirm/cdw/cdwQuery/makefile
  • lines changed 4, context: html, text, full: html, text
    SQL-like query for files matching tags seems to work.
    
• src/hg/cirm/cdw/cdwRunDaemon/cdwRunDaemon.c
  • lines changed 20, context: html, text, full: html, text
    Sanitizing stderr a bit before putting it into database with SQL.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 17, context: html, text, full: html, text
    A small step in adapting to submissions being on local file system.
    
  • lines changed 245, context: html, text, full: html, text
    It compiles but still is very much in development, not working.
    
  • lines changed 379, context: html, text, full: html, text
    Getting a bit closer to working.
    
  • lines changed 48, context: html, text, full: html, text
    Actually storing manifest and metadata files.
    
  • lines changed 4, context: html, text, full: html, text
    Filling in cdwSubmit.fileCount field in database.
    
  • lines changed 22, context: html, text, full: html, text
    Saving userId in cdwFile table.
    
  • lines changed 48, context: html, text, full: html, text
    Adding option to get md5 sums from a precomputed file. Also will take md5 sum from database if it is there and file name, size, and update time match. Adding support for .pdf and .vcf files.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 3, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 5, context: html, text, full: html, text
    Adding userId to file record and swapping submitFileId for manifestFileId and metaFileId in submit record.
    
  • lines changed 2, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 3, context: html, text, full: html, text
    Adding a PDF file recognizer/minimal validator.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 1, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 3, context: html, text, full: html, text
    Adding userId to file record and swapping submitFileId for manifestFileId and metaFileId in submit record.
    
  • lines changed 1, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 7, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 66, context: html, text, full: html, text
    Adding userId to file record and swapping submitFileId for manifestFileId and metaFileId in submit record.
    
  • lines changed 45, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 3, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 6, context: html, text, full: html, text
    Adding userId to file record and swapping submitFileId for manifestFileId and metaFileId in submit record.
    
  • lines changed 1, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 6, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 4, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
  • lines changed 2, context: html, text, full: html, text
    Changing experiment column to meta and fixing edwBamStats name typo.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 7, context: html, text, full: html, text
    Adding a PDF file recognizer/minimal validator.
    
• src/hg/cirm/quakeLab/djangoModels/take3/models.as
  • lines changed 99, context: html, text, full: html, text
    New version of django models from quake lab.
    
• src/hg/cirm/quakeLab/djangoModels/take3/models.py
  • lines changed 148, context: html, text, full: html, text
    New version of django models from quake lab.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/makefile
  • lines changed 4, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/models.as
  • lines changed 51, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
  • lines changed 1, context: html, text, full: html, text
    Adding meta output.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/models.c
  • lines changed 594, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
  • lines changed 6, context: html, text, full: html, text
    Adding meta output.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/models.h
  • lines changed 201, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
  • lines changed 1, context: html, text, full: html, text
    Defining unknown2 as something real.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/quakeFakeMouseManifest.c
  • lines changed 149, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
  • lines changed 41, context: html, text, full: html, text
    Adding meta output.
    
  • lines changed 15, context: html, text, full: html, text
    Changing some uglyfs to verboses. Making a missing SampleSheet a logged error rather than an aborting error.
    
• src/hg/ctgFaToFa/makefile
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    fixing exec perms on makefiles
    
• src/hg/encode/encodeValidate/test/input/duke/DukeDNase.PIF
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/encode/encodeValidate/test/input/duke/Duke_GM12878_DNase.DDF
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/fakeOut/makefile
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    fixing exec perms on makefiles
    
• src/hg/ffaToFa/makefile
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    fixing exec perms on makefiles
    
• src/hg/gigAssembler/goldToAgp/makefile
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    fixing exec perms on makefiles
    
• src/hg/gigAssembler/qaGold/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/hgTables/bigBed.c
  • lines changed 3, context: html, text, full: html, text
    fix a bug where "show schema" doesn't work in the table browser for
    custom tracks, or track hubs
    
• src/hg/hgTables/bigWig.c
  • lines changed 2, context: html, text, full: html, text
    add hgc and hgTables support for bigGenePred in custom tracks. #13861
    
• src/hg/hgTracks/expRatioTracks.h
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 40, context: html, text, full: html, text
    turning off the new full mode and back to the three mode track refs #9741
    
• src/hg/hgc/hgc.c
  • lines changed 58, context: html, text, full: html, text
    add hgc and hgTables support for bigGenePred in custom tracks. #13861
    
• src/hg/hgc/rmskJoinedClick.c
  • lines changed 3, context: html, text, full: html, text
    fixup get DNA hgc click refs #13706
    
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 1, context: html, text, full: html, text
    changed the text a bit so a google search on _make link_ will pick up this page
    
  • lines changed 2, context: html, text, full: html, text
    changed the text a bit so a google search on _make link_ will pick up this page
    
• src/hg/htdocs/README
  • lines changed 14, context: html, text, full: html, text
    adding some reminders about htdocsExtra repository.
    
• src/hg/htdocs/geneExtra/lepre1.gif
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/htdocs/goldenPath/ftLauderdale.pdf
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    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 13, context: html, text, full: html, text
    added box to search whole site. Refs #14807
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 2, context: html, text, full: html, text
    Correcting gfserver to gfServer, code review refs #14769
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    minor tweaks suggested by Angie in codereview.
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    Adding announcements for re-launch of training intake survey. refs #14714
    
  • lines changed 3, context: html, text, full: html, text
    Fixing repetitive wording. refs #14714
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 3, context: html, text, full: html, text
    Removing aberrant space found in code review and extra dash that was throwing off my syntax highlighting. refs #14771
    
• src/hg/htdocs/images/dot_clear.gif
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/htdocs/images/platypus.jpg
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/htdocs/indexNews.html
  • lines changed 29, context: html, text, full: html, text
    Adding announcements for re-launch of training intake survey. refs #14714
    
  • lines changed 2, context: html, text, full: html, text
    Fixing repetitive wording. refs #14714
    
  • lines changed 19, context: html, text, full: html, text
    Fixing up some formatting issues in staged archives
    
• src/hg/htdocs/makefile
  • lines changed 6, context: html, text, full: html, text
    adding some reminders about htdocsExtra repository.
    
• src/hg/htdocs/mirror.html
  • lines changed 13, context: html, text, full: html, text
    Adam moved himself and his mirror from Cornell to CSHL
    
• src/hg/htdocs/training/index.html
  • lines changed 11, context: html, text, full: html, text
    Adding announcements for re-launch of training intake survey. refs #14714
    
  • lines changed 1, context: html, text, full: html, text
    Extra exclamation mark made the announcement seem repetitive. refs #14714
    
  • lines changed 2, context: html, text, full: html, text
    Fixing repetitive wording. refs #14714
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 133, context: html, text, full: html, text
    Staging sections for upcoming training videos 6 and 7. refs #13969 #14239
    
• src/hg/inc/encode/wgEncodeGencodeEntrezGene.h
  • lines changed 64, context: html, text, full: html, text
    Added GENCODE Entrez gene id metadata
    
• src/hg/js/jshintrc.json
  • lines changed 16, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/js/model/hgAi/hgAiModel.js
  • lines changed 3, context: html, text, full: html, text
    Code review feedback from Brian Craft: use _. functions instead of Object.keys(thing).forEach.
    
  • lines changed 58, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/js/model/hgAi/makefile
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/js/model/hgChooseDb/hgChooseDbModel.js
  • lines changed 14, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/js/model/hgChooseDb/makefile
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/js/model/lib/CladeOrgDbMixin.js
  • lines changed 10, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
  • lines changed 8, context: html, text, full: html, text
    Better workaround for jshint warning about unused file-module variable: bogus assignment instead of disabling the check.
    
• src/hg/js/model/lib/ImModel.js
  • lines changed 2, context: html, text, full: html, text
    Code review feedback from Brian Craft: use _. functions instead of Object.keys(thing).forEach.
    
  • lines changed 50, context: html, text, full: html, text
    Code review feedback from Brian C: separate out the logic that traverses
    the uiHandlers tree from the code that installs or executes handler functions.
    
  • lines changed 18, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/js/model/lib/PositionSearchMixin.js
  • lines changed 16, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
  • lines changed 7, context: html, text, full: html, text
    Better workaround for jshint warning about unused file-module variable: bogus assignment instead of disabling the check.
    
• src/hg/js/model/lib/cart.js
  • lines changed 22, context: html, text, full: html, text
    Code review feedback from Brian Craft: use _. functions instead of Object.keys(thing).forEach.
    
  • lines changed 6, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
  • lines changed 8, context: html, text, full: html, text
    Better workaround for jshint warning about unused file-module variable: bogus assignment instead of disabling the check.
    
• src/hg/js/model/lib/makefile
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/js/react/hgAi/hgAi.jsx
  • lines changed 15, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/hgAi/makefile
  • lines changed 4, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/hgChooseDb/hgChooseDb.jsx
  • lines changed 17, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/hgChooseDb/makefile
  • lines changed 4, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/CheckboxLabel.jsx
  • lines changed 4, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/CladeOrgDb.jsx
  • lines changed 5, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/Icon.jsx
  • lines changed 6, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/LabeledSelect.jsx
  • lines changed 8, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/LoadingImage.jsx
  • lines changed 6, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/Modal.jsx
  • lines changed 6, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/PositionSearch.jsx
  • lines changed 11, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/Section.jsx
  • lines changed 3, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/SetClearButtons.jsx
  • lines changed 4, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/Sortable.jsx
  • lines changed 6, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/TextInput.jsx
  • lines changed 4, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/react/mixins/ImmutableUpdate.js
  • lines changed 9, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
  • lines changed 5, context: html, text, full: html, text
    Better workaround for jshint warning about unused file-module variable: bogus assignment instead of disabling the check.
    
• src/hg/js/react/mixins/PathUpdate.js
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
  • lines changed 7, context: html, text, full: html, text
    Better workaround for jshint warning about unused file-module variable: bogus assignment instead of disabling the check.
    
• src/hg/js/react/mixins/PathUpdateOptional.js
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
  • lines changed 7, context: html, text, full: html, text
    Better workaround for jshint warning about unused file-module variable: bogus assignment instead of disabling the check.
    
• src/hg/js/react/mixins/makefile
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/js/react/react.mk
  • lines changed 1, context: html, text, full: html, text
    Hooked in stricter jshint config to jsxhint for React/JSX *.jsx files.
    
• src/hg/js/simple.mk
  • lines changed 1, context: html, text, full: html, text
    Code review feedback from Brian C:
    1. Making a temporary this.mutState that all handlers implicitly have
    access to via this is almost as bad as using a global variable.
    Instead, pass mutState as a function arg so it's very clear where
    it's coming from.
    Brian suggested going a step farther and returning mutState from
    every handler so that the handler functions could be _.compose'd,
    but I'll be stubborn and stick with explicit side effects and _.forEach.
    2. Tighten up jshint warnings -- it is very lax by default.
    I should have done #2 first and then embarked on #1 as a separate commit,
    but after doing #1 I wanted jshint checks to help me find places I forgot
    to update so it's all mashed together, sorry.
    
• src/hg/lib/codeBlastScore.as
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/lib/codeBlastScore.sql
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/lib/encode/wgEncodeGencodeEntrezGene.as
  • lines changed 6, context: html, text, full: html, text
    Added GENCODE Entrez gene id metadata
    
• src/hg/lib/encode/wgEncodeGencodeEntrezGene.c
  • lines changed 123, context: html, text, full: html, text
    Added GENCODE Entrez gene id metadata
    
• src/hg/lib/encode/wgEncodeGencodeEntrezGene.sql
  • lines changed 12, context: html, text, full: html, text
    Added GENCODE Entrez gene id metadata
    
• src/hg/lib/gbRNAs.as
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/lib/hgSeq.c
  • lines changed 1, context: html, text, full: html, text
    add hgc and hgTables support for bigGenePred in custom tracks. #13861
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added GENCODE Entrez gene id metadata
    
• src/hg/lib/protHomolog.as
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/lib/rnaGenes.as
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    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/lib/rnaHybridization.as
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/lib/samSubdir.as
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/lib/snoRNAs.as
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/lib/tRNAs.as
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/danRer10/initialBuild.txt
  • lines changed 4, context: html, text, full: html, text
    in the pushQ 007479 refs #14017
    
• src/hg/makeDb/doc/go.txt
  • lines changed 46, context: html, text, full: html, text
    finished building GO database
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 1, context: html, text, full: html, text
    Added GENCODE Entrez gene id metadata
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 364, context: html, text, full: html, text
    finished oviAri3 running up oryLat2 anoCar2 cheMyd1 chrPic2 refs #14560
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 1, context: html, text, full: html, text
    Added GENCODE Entrez gene id metadata
    
• src/hg/makeDb/doc/proteins/090821.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/proteins/101005.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/proteins/111004.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/proteins/120806.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/proteins/121210.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/proteins/140122.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/proteins/150115.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp080707.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp090821.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp100331.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp101005.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp110315.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp111004.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp120323.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp121210.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp140122.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/doc/uniProt/sp150115.txt
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    fix tarSyr2 to not have ests, since it has no ests
    
• src/hg/makeDb/outside/ensembl/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 407, context: html, text, full: html, text
    Added GENCODE Entrez gene id metadata
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 7, context: html, text, full: html, text
    clean up papAnu2 refs #14462
    
• src/hg/makeDb/tfbsConsLoc/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    Removing old clinvar trackDb stanza in prep for release of new clinvar track, refs #14045
    
  • lines changed 10, context: html, text, full: html, text
    Added trackDb entry for new COSMIC track; refs #14461
    
• src/hg/makeDb/trackDb/joinedRmskComposite.ra
  • lines changed 1, context: html, text, full: html, text
    back to the three mode type of track refs #13706
    
• src/hg/oneShot/doEvoFold/doEvoFold.c
  • lines changed 0, context: html, text, full: html, text
    removing execute permissions from .c files
    
• src/hg/oneShot/doEvoFoldV2/doEvoFoldV2.c
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    removing execute permissions from .c files
    
• src/hg/oneShot/doOmimDisorders/doOmimDisorders.c
  • lines changed 0, context: html, text, full: html, text
    removing execute permissions from .c files
    
• src/hg/oneShot/freen/freen.c
  • lines changed 39, context: html, text, full: html, text
    Freen generates a big sample metadata file
    
• src/hg/oneShot/missingTable/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/oneShot/rmDupCol1/rmDupCol1.c
  • lines changed 0, context: html, text, full: html, text
    removing execute permissions from .c files
    
• src/hg/oneShot/spanRaft/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/qaToQac/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/qacAgpLift/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/qacToQa/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/qacToWig/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/splitFa/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/uniqSize/makefile
  • lines changed 0, context: html, text, full: html, text
    fixing exec perms on makefiles
    
• src/hg/utils/pslMap/README
  • lines changed 7, context: html, text, full: html, text
    updated pslMap README instuctions to explain chains correctly
    
• src/hg/zoo/analyze4d/Makefile
  • lines changed 0, context: html, text, full: html, text
    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/hg/zoo/transitivityCheck/Makefile
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    removing unwanted exec permission on 38 files of various types including pdf java h gif jpg as sql txt Makefile PIF DDF
    
• src/inc/meta.h
  • lines changed 4, context: html, text, full: html, text
    Adding maxDepth parameter to metaWriteAll.
    
  • lines changed 2, context: html, text, full: html, text
    Adding note that this line of development is moving to tagStorm.
    
• src/inc/ra.h
  • lines changed 13, context: html, text, full: html, text
    Implementing a raNextTagValWithIndent function.
    
  • lines changed 4, context: html, text, full: html, text
    Removing INLINE from raNextTagVal since it was causeing compile problems.
    
• src/inc/tagStorm.h
  • lines changed 68, context: html, text, full: html, text
    Streamlining interface and moving tagStorm code to src/lib.
    
  • lines changed 9, context: html, text, full: html, text
    Adding flattened ra output and reworking standard write a bit.
    
  • lines changed 20, context: html, text, full: html, text
    Adding routines that allow you to build up a tagStorm in memory.
    
  • lines changed 5, context: html, text, full: html, text
    Adding tagStormUniqueIndex.
    
  • lines changed 25, context: html, text, full: html, text
    Adding stuff for finding tags within a stanza.
    
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    Adding new method to add stanza that puts it at end of existing stanzas rather than at beginning.
    
• src/index/fofFa/fofFa.c
  • lines changed 0, context: html, text, full: html, text
    removing execute permissions from .c files
    
• src/index/fofFa/makefile
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    fixing exec perms on makefiles
    
• src/index/indexRa/indexRa.c
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    removing execute permissions from .c files
    
• src/index/indexRa/makefile
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    fixing exec perms on makefiles
    
• src/index/indexfa/indexfa.c
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    removing execute permissions from .c files
    
• src/index/indexfa/makefile
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    fixing exec perms on makefiles
    
• src/index/indexgl/indexgl.c
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    removing execute permissions from .c files
    
• src/index/indexgl/makefile
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    fixing exec perms on makefiles
    
• src/index/ixali/makefile
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    fixing exec perms on makefiles
    
• src/index/ixword1/ixword1.c
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    removing execute permissions from .c files
    
• src/index/ixword1/makefile
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    fixing exec perms on makefiles
    
• src/index/ixword3/ixword3.c
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    removing execute permissions from .c files
    
• src/index/ixword3/makefile
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    fixing exec perms on makefiles
    
• src/index/ixxenost/ixxenost.c
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    removing execute permissions from .c files
    
• src/index/ixxenost/makefile
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    fixing exec perms on makefiles
    
• src/index/makepgo/makefile
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    fixing exec perms on makefiles
    
• src/index/makepgo/makepgo.c
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    removing execute permissions from .c files
    
• src/index/stToXao/makefile
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    fixing exec perms on makefiles
    
• src/index/stToXao/stToXao.c
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    removing execute permissions from .c files
    
• src/intronerator/idb/makefile
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    fixing exec perms on makefiles
    
• src/lib/alpha/placeHolder.c
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    removing execute permissions from .c files
    
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    Removing stray blank line.
    
• src/lib/hash.c
  • lines changed 5, context: html, text, full: html, text
    don't crash if the maximum size of a hash table is reached.
    
• src/lib/i386/placeHolder.c
  • lines changed 0, context: html, text, full: html, text
    removing execute permissions from .c files
    
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Streamlining interface and moving tagStorm code to src/lib.
    
• src/lib/meta.c
  • lines changed 11, context: html, text, full: html, text
    Adding maxDepth parameter to metaWriteAll.
    
  • lines changed 2, context: html, text, full: html, text
    Adding note that this line of development is moving to tagStorm.
    
• src/lib/ppc/placeHolder.c
  • lines changed 0, context: html, text, full: html, text
    removing execute permissions from .c files
    
• src/lib/ra.c
  • lines changed 25, context: html, text, full: html, text
    Implementing a raNextTagValWithIndent function.
    
  • lines changed 11, context: html, text, full: html, text
    Removing INLINE from raNextTagVal since it was causeing compile problems.
    
• src/lib/sparc/placeHolder.c
  • lines changed 0, context: html, text, full: html, text
    removing execute permissions from .c files
    
• src/lib/tagStorm.c
  • lines changed 245, context: html, text, full: html, text
    Streamlining interface and moving tagStorm code to src/lib.
    
  • lines changed 65, context: html, text, full: html, text
    Adding flattened ra output and reworking standard write a bit.
    
  • lines changed 105, context: html, text, full: html, text
    Adding tagStormWriteAsFlatTab
    
  • lines changed 1, context: html, text, full: html, text
    Removing some debugging code.
    
  • lines changed 56, context: html, text, full: html, text
    Adding routines that allow you to build up a tagStorm in memory.
    
  • lines changed 22, context: html, text, full: html, text
    Adding tagStormUniqueIndex.
    
  • lines changed 33, context: html, text, full: html, text
    Adding stuff for finding tags within a stanza.
    
  • lines changed 20, context: html, text, full: html, text
    Adding new method to add stanza that puts it at end of existing stanzas rather than at beginning.
    
• src/lib/vcf.c
  • lines changed 53, context: html, text, full: html, text
    Making it so that there can be warning messages as well as errors for VCF files. Changing message 'missing ##fileformat= header line? Assuming 4.1.' to a warning and indeed making it assume 4.1. Also having a missing #CHROM POS type header also just a warning.
    
• src/lib/x86_64/placeHolder.c
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    removing execute permissions from .c files
    
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    check umask for local hgwdev users refs #14507
    
  • lines changed 1, context: html, text, full: html, text
    Adding tagStorm dir to compile targets.
    
• src/meta/metaFlatten/metaFlatten.c
  • lines changed 1, context: html, text, full: html, text
    Adding maxDepth parameter to metaWriteAll. Adding depth command line option to metaReformat which uses this.
    
• src/meta/metaHoist/metaHoist.c
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