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
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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/aladdin/aladdin/aladdin.c
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removing execute permissions from .c files
- src/aladdin/aladdin/makefile
- lines changed 0, context: html, text, full: html, text
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
- lines changed 0, context: html, text, full: html, text
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
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/cdnaAli/findCdna/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/cdnaAli/g2cCheck/makefile
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fixing exec perms on makefiles
- src/cdnaAli/introns/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/cdnaAli/pairClo/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/cdnaAli/patCount/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/cdnaAli/patSpace/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/cdnaAli/refineAli/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/cdnaAli/sortFilt/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/cdnaAli/stitchea/makefile
- lines changed 0, context: html, text, full: html, text
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.
- 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.
- 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 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
- lines changed 0, context: html, text, full: html, text
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
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/hg/ffaToFa/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/hg/gigAssembler/goldToAgp/makefile
- lines changed 0, context: html, text, full: html, text
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
- 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/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
- 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/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
- lines changed 0, context: html, text, full: html, text
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
- 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/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.
- lines changed 5, 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/index/fofFa/fofFa.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/index/fofFa/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/indexRa/indexRa.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/index/indexRa/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/indexfa/indexfa.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/index/indexfa/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/indexgl/indexgl.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/index/indexgl/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/ixali/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/ixword1/ixword1.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/index/ixword1/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/ixword3/ixword3.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/index/ixword3/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/ixxenost/ixxenost.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/index/ixxenost/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/makepgo/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/makepgo/makepgo.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/index/stToXao/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/index/stToXao/stToXao.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/intronerator/idb/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/lib/alpha/placeHolder.c
- lines changed 0, context: html, text, full: html, text
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
- lines changed 0, context: html, text, full: html, text
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
- 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/metaReformat/metaReformat.c
- lines changed 5, context: html, text, full: html, text
Adding maxDepth parameter to metaWriteAll. Adding depth command line option to metaReformat which uses this.
- src/oneShot/badbad/badbad.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/cbCountOver/cbCountOver.c
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removing execute permissions from .c files
- src/oneShot/cdnalen/cdnalen.c
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removing execute permissions from .c files
- src/oneShot/chkGlue/forChuck.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/chkGlue/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/oneShot/ck3and5/ck3and5.c
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removing execute permissions from .c files
- src/oneShot/cmpfa/cmpfa.c
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removing execute permissions from .c files
- src/oneShot/cntGlue/cntGlue.c
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removing execute permissions from .c files
- src/oneShot/cntGlue/makefile
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fixing exec perms on makefiles
- src/oneShot/conrand/conrand.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/conrand/foo.c
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removing execute permissions from .c files
- src/oneShot/cosmoCtr/cosmoCtr.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/coverage/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/oneShot/deEns/makefile
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fixing exec perms on makefiles
- src/oneShot/debog/debog.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/doublea/doublea.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/dynAlign/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/oneShot/faends/faends.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/filterdb/filterdb.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/fixInfo/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/oneShot/foo/foo.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/forChuck/forChuck.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/geneFreq/geneFreq.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/grokGff/makefile
- lines changed 0, context: html, text, full: html, text
fixing exec perms on makefiles
- src/oneShot/intersect/intersect.c
- lines changed 0, context: html, text, full: html, text
removing execute permissions from .c files
- src/oneShot/invert/invert.c
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removing execute permissions from .c files
- src/oneShot/invert/makefile
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fixing exec perms on makefiles
- src/oneShot/jimgrep/jimgrep.c
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removing execute permissions from .c files
- src/oneShot/killRabbit/makefile
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fixing exec perms on makefiles
- src/oneShot/leaders/leaders.c
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removing execute permissions from .c files
- src/oneShot/m22dirs/makefile
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fixing exec perms on makefiles
- src/oneShot/memeint/memeint.c
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removing execute permissions from .c files
- src/oneShot/noali/noali.c
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removing execute permissions from .c files
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removing execute permissions from .c files
- src/oneShot/ooRev/makefile
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fixing exec perms on makefiles
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fixing exec perms on makefiles
- src/oneShot/passHi/passHi.c
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removing execute permissions from .c files
- src/oneShot/patJobs/makefile
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fixing exec perms on makefiles
- src/oneShot/patJobs/patJobs.c
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removing execute permissions from .c files
- src/oneShot/shorten/makefile
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fixing exec perms on makefiles
- src/oneShot/shorten/shorten.c
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removing execute permissions from .c files
- src/oneShot/sizeSplitFa/sizeSplitFa.c
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removing execute permissions from .c files
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removing execute permissions from .c files
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fixing exec perms on makefiles
- src/oneShot/sources/sources.c
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removing execute permissions from .c files
- src/oneShot/splitSql/makefile
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fixing exec perms on makefiles
- src/oneShot/splitSql/splitSql.c
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removing execute permissions from .c files
- src/oneShot/splitTxt/splitTxt.c
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removing execute permissions from .c files
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removing execute permissions from .c files
- src/oneShot/tabTable/makefile
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fixing exec perms on makefiles
- src/oneShot/testTagStorm/makefile
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New variant of meta tags starting to work.
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Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
- src/oneShot/testTagStorm/testTagStorm.c
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New variant of meta tags starting to work.
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Streamlining interface and moving tagStorm code to src/lib.
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Adding flattened ra output and reworking standard write a bit.
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Adding tagStormWriteAsFlatTab
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Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
- src/oneShot/truncat/truncat.c
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removing execute permissions from .c files
- src/oneShot/uniqSize/makefile
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fixing exec perms on makefiles
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fixing exec perms on makefiles
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fixing exec perms on makefiles
- src/oneShot/wormPromo/wormpromo.c
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removing execute permissions from .c files
- src/reformat/fa4blast/makefile
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fixing exec perms on makefiles
- src/reformat/fatont4/fatont4.c
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removing execute permissions from .c files
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fixing exec perms on makefiles
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removing execute permissions from .c files
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fixing exec perms on makefiles
- src/reformat/gb2cdi/gb2cdi.c
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removing execute permissions from .c files
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fixing exec perms on makefiles
- src/reformat/gbNoDna/gbNoDna.c
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removing execute permissions from .c files
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removing execute permissions from .c files
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removing execute permissions from .c files
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fixing exec perms on makefiles
- src/reformat/gbtofa/gbtofa.c
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removing execute permissions from .c files
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fixing exec perms on makefiles
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removing execute permissions from .c files
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fixing exec perms on makefiles
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removing execute permissions from .c files
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fixing exec perms on makefiles
- src/reformat/makec2c/makec2c.c
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removing execute permissions from .c files
- src/reformat/makefont/common.h
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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/reformat/makefont/fnt2c.c
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removing execute permissions from .c files
- src/reformat/makefont/gemfont.h
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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/reformat/makefont/makefile
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fixing exec perms on makefiles
- src/reformat/moresyn/makefile
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fixing exec perms on makefiles
- src/reformat/moresyn/moresyn.c
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removing execute permissions from .c files
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removing execute permissions from .c files
- src/stats/codons/codons.c
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removing execute permissions from .c files
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removing execute permissions from .c files
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removing execute permissions from .c files
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removing execute permissions from .c files
- src/tagStorm/makefile
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Adopting metaHoist to tagStorm.
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A few parts working, but the whole is not.
- src/tagStorm/tagStormFromTab/tagStormFromTab.c
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A few parts working, but the whole is not.
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Refactoring, and creating a yet unused function.
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Refactoring so it fills in metadata stanza from parting fields info rather than table.
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Doing the recursive bits. It still needs to do leaf output.
- src/tagStorm/tagStormHoist/makefile
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Adopting metaHoist to tagStorm.
- src/tagStorm/tagStormHoist/tagStormHoist.c
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Adopting metaHoist to tagStorm.
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Renaming tagStormAddTag to tagStormUpdate tag.
- src/tagStorm/tagStormInfo/makefile
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Utility to look for info about a tag storm seems to work.
- src/tagStorm/tagStormInfo/tagStormInfo.c
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Utility to look for info about a tag storm seems to work.
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Making the names output default rather than an option.
- src/tagStorm/tagStormInfo/test.in
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Utility to look for info about a tag storm seems to work.
- src/tagStorm/tagStormJoinTab/expected.tags
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Tag storm to tab-sep joiner seems to work.
- src/tagStorm/tagStormJoinTab/makefile
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Tag storm to tab-sep joiner seems to work.
- src/tagStorm/tagStormJoinTab/tagStormJoinTab.c
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Tag storm to tab-sep joiner seems to work.
- src/tagStorm/tagStormJoinTab/test.tab
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Tag storm to tab-sep joiner seems to work.
- src/tagStorm/tagStormJoinTab/test.tags
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Tag storm to tab-sep joiner seems to work.
- src/tagStorm/tagStormQuery/makefile
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Tag storm file sql-like query utility seems to work.
- src/tagStorm/tagStormQuery/tagStormQuery.c
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Tag storm file sql-like query utility seems to work.
- src/tagStorm/tagStormQuery/test.tags
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Tag storm file sql-like query utility seems to work.
- src/tagStorm/tagStormReformat/expected.files
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Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
- src/tagStorm/tagStormReformat/expected.ra
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Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
- src/tagStorm/tagStormReformat/expected.tab
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Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
- src/tagStorm/tagStormReformat/makefile
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Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
- src/tagStorm/tagStormReformat/tagStormReformat.c
- lines changed 81, context: html, text, full: html, text
Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
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Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
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Adding flatten option to usage message.
- src/tagStorm/tagStormReformat/test.in
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Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
- src/utils/catUncomment/makefile
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fixing exec perms on makefiles
- src/utils/faFrag/makefile
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fixing exec perms on makefiles
- src/utils/faNoise/makefile
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fixing exec perms on makefiles
- src/utils/faOneRecord/makefile
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fixing exec perms on makefiles
- src/utils/faSplit/makefile
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fixing exec perms on makefiles
- src/utils/geneStarts/makefile
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fixing exec perms on makefiles
- src/utils/gitTools/makefile
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fixing exec perms on makefiles
- src/utils/jkShell/pipeTest.c
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removing execute permissions from .c files
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fixing exec perms on makefiles
- src/utils/paraMd5/makefile
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Utility for multithreaded md5 calculation seems to work.
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Utility for multithreaded md5 calculation seems to work.
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Improving name of subroutine.
- src/utils/pslPosTarget/makefile
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eliminate non-standard makefile to fix broken build refs #14648
- src/utils/pslPosTarget/pslPosTarget.c
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fixed memory leak in pslPosTarget
- src/utils/qa/weeklybld/buildEnv.csh
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v312 preview2 refs #14768
- src/utils/scaffoldFaToAgp/makefile
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fixing exec perms on makefiles
- src/utils/toLower/makefile
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fixing exec perms on makefiles
- src/utils/toUpper/makefile
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fixing exec perms on makefiles
- src/utils/upper/makefile
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fixing exec perms on makefiles
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removing execute permissions from .c files
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removing execute permissions from .c files
- src/xenoAli/bwana/makefile
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fixing exec perms on makefiles
- src/xenoAli/cbAli/makefile
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fixing exec perms on makefiles
- src/xenoAli/dynAlign/makefile
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fixing exec perms on makefiles
- src/xenoAli/stitcher/makefile
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fixing exec perms on makefiles
- src/xenoAli/waba/makefile
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fixing exec perms on makefiles
- src/xenoAli/xaShow/makefile
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fixing exec perms on makefiles
- src/xenoAli/xenWorm/makefile
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fixing exec perms on makefiles
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