All File Changes
v290_preview to v290_preview2 (2013-09-16 to 2013-09-23) v290
- src/README
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Adding section about preventing sqli to src/README
- src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
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Making paraFetch retry an extra time. Making it only hit database once a second when checking for interrupts.
- src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
- lines changed 2, context: html, text, full: html, text
Making pooled replicates not try to find a mate.
- src/hg/hgTracks/simpleTracks.c
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code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/hgVai/hgVai.c
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Fixing a URL (copy-paste error).
- src/hg/htdocs/ENCODE/FAQ/index.html
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Making corrections per code review refs #11759
- src/hg/htdocs/ENCODE/index.html
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Making corrections per code review refs #11759
- lines changed 1, context: html, text, full: html, text
Adding back link to newsarchives code review 11759
- src/hg/htdocs/ENCODE/newsarch.html
- lines changed 3, context: html, text, full: html, text
Making corrections per code review refs #11759
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Updating per code review refs #11759
- src/hg/htdocs/ENCODE/pubsEncode.html
- lines changed 296, context: html, text, full: html, text
Publication/requested specific updates from Mike Pazin (per document) for ENCODE, RM at Stanford #562
- lines changed 7, context: html, text, full: html, text
Removing misplaced reference in Mike Pazin's document, refs Stanford RM #562
- src/hg/htdocs/ENCODE/pubsOther.html
- lines changed 769, context: html, text, full: html, text
Publication/requested specific updates from Mike Pazin (per document) for ENCODE, RM at Stanford #562
- src/hg/htdocs/FAQ/FAQformat.html
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Adding a frameshift SNP to pgSNP format example per request of Bob
- src/hg/htdocs/admin/mirror.html
- src/hg/htdocs/conditions.html
- lines changed 32, context: html, text, full: html, text
Made some changes to conditions.html per ref #8699. Also removed some duplicate info from indexInfo.html, but not all of it. This will improve once we revamp the static pages, but I think it's OK for now.
- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
- lines changed 1, context: html, text, full: html, text
Fixing link to information on PSL format, refs #11307
- src/hg/htdocs/indexInfo.html
- lines changed 51, context: html, text, full: html, text
Made some changes to conditions.html per ref #8699. Also removed some duplicate info from indexInfo.html, but not all of it. This will improve once we revamp the static pages, but I think it's OK for now.
- src/hg/lib/annoFormatVep.c
- lines changed 2, context: html, text, full: html, text
Avoid double-linebreak in VEP header when dbSNP is not included.
- src/hg/lib/haplotypes.c
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Corrected a typo that Donna noticed.
- src/hg/lib/jsHelper.c
- lines changed 12, context: html, text, full: html, text
Handle IE's unique behavior of window.location.replace when the newURL (including stuff after '?') is the same as the current URL.
fixes #11443
- src/hg/lib/tests/expected/annoGrator/gpFx.txt
- lines changed 4, context: html, text, full: html, text
Oops, forgot to correct test file after fixing intron off-by-one in 099102d. Too bad I didn't notice it in the test file to begin with...
- src/hg/makeDb/doc/hg19.txt
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panTig1 lastz done starting letCam1 lastz refs #10272
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the 100-way procedure included refs #10272
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swapping hg19 letCam1 lastz and constructing downloads for 100-way refs #10272
- src/hg/makeDb/doc/makeEnsembl.txt
- lines changed 1276, context: html, text, full: html, text
adding v73 build sequences refs #11675
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 29, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/etc/ignore.idx
- lines changed 5, context: html, text, full: html, text
add more lines to this file ignore.idx which is a list of lines
- src/hg/makeDb/genbank/src/dbload/dbLoadOptions.h
- lines changed 1, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/src/dbload/dbLoadPartitions.c
- lines changed 2, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/src/dbload/gbAlignData.c
- lines changed 2, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
- lines changed 4, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c
- lines changed 9, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/src/dbload/gbGeneTbl.h
- lines changed 2, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
- lines changed 8, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/src/dbload/gbMetaData.c
- lines changed 5, context: html, text, full: html, text
oops, a little fix to updating metadata to track whether to keep theversion #
- src/hg/makeDb/genbank/src/inc/gbDefs.h
- lines changed 1, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- lines changed 1, context: html, text, full: html, text
code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
Adding all dgv* tracks to tablesIgnored.
- lines changed 1, context: html, text, full: html, text
avoid duplicate ensGene.name errors on gadMor1 refs #11675
- src/hg/makeDb/trackDb/chicken/bgiCov.html
- lines changed 2, context: html, text, full: html, text
Fixing broken links on some chicken track description pages
- src/hg/makeDb/trackDb/chicken/bgiSnp.html
- lines changed 2, context: html, text, full: html, text
Fixing broken links on some chicken track description pages
- src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
- lines changed 12, context: html, text, full: html, text
added the panTro2 to panTro4 over chains as a separate track as requested by Adam/David, they want to compare the assemblies
- src/hg/makeDb/trackDb/human/dgvPlus.html
- lines changed 9, context: html, text, full: html, text
Incorporating corrections from Jeff MacDonald.refs #11200
- src/hg/makeDb/trackDb/human/hg19/cons100way.html
- lines changed 108, context: html, text, full: html, text
updated genome list for this set of 100 refs #10272
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case and name updates updated refs #10272
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
- lines changed 440, context: html, text, full: html, text
Added searchable termRegex cg######## probe items to HAIB Methyl track, with BRaney's help, refs #11754
- lines changed 434, context: html, text, full: html, text
bringing down search results for wgEncodeHaibMethyl450.ra to just one table of Tier1 cell line per feedback from Steve & BrianR refs #11754
- src/hg/makeDb/trackDb/human/hg19/wgRna.html
- lines changed 11, context: html, text, full: html, text
Fixing links to miRBase, refs #11280
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 2, context: html, text, full: html, text
Incorporating corrections from Jeff MacDonald.refs #11200
- src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
- lines changed 2, context: html, text, full: html, text
Fixing broken download links on lamprey conservation description page
- src/hg/pslCDnaFilter/algo.txt
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add new option -maxAlignsDrop=N to pslCDnaFilter that drops all thealignments of a query that aligns more than N times.
- src/hg/pslCDnaFilter/cDnaAligns.h
- lines changed 2, context: html, text, full: html, text
add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
- src/hg/pslCDnaFilter/cDnaReader.c
- lines changed 6, context: html, text, full: html, text
add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
- src/hg/pslCDnaFilter/pslCDnaFilter.c
- lines changed 37, context: html, text, full: html, text
add new option -maxAlignsDrop=N to pslCDnaFilter that drops all thealignments of a query that aligns more than N times.
- lines changed 3, context: html, text, full: html, text
add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
- src/hg/pslCDnaFilter/usage.txt
- lines changed 4, context: html, text, full: html, text
add new option -maxAlignsDrop=N to pslCDnaFilter that drops all thealignments of a query that aligns more than N times.
- lines changed 2, context: html, text, full: html, text
add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
- src/hg/utils/phyloTrees/benchMark100.commonNames.nh
- lines changed 100, context: html, text, full: html, text
updated distances from 4D measurement on the 100-way MAF files refs #10272
- src/hg/utils/phyloTrees/benchMark100.nh
- lines changed 100, context: html, text, full: html, text
updated distances from 4D measurement on the 100-way MAF files refs #10272
- src/hg/utils/phyloTrees/benchMark100.scientificNames.nh
- lines changed 100, context: html, text, full: html, text
updated distances from 4D measurement on the 100-way MAF files refs #10272
- src/hg/utils/phyloTrees/commonNames.sh
- lines changed 12, context: html, text, full: html, text
cleaning up the commonNames.sh name listing refs #10272
- src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
- lines changed 115, context: html, text, full: html, text
tab separated listing for dbDb entries refs #10272
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correct clade from the clade table in hgcentral refs #10272
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update case and naming consistency refs #10272
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cleaning up the commonNames.sh name listing refs #10272
- src/hg/utils/pslMap/tests/expected/mrnaChainMapBug.mapinfo
- lines changed 2, context: html, text, full: html, text
fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
- src/hg/utils/pslMap/tests/expected/mrnaChainMapBug.psl
- lines changed 1, context: html, text, full: html, text
fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
- src/hg/utils/pslMap/tests/input/mrnaChainMapRefSeq.chain
- lines changed 610956, context: html, text, full: html, text
fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
- src/hg/utils/pslMap/tests/input/mrnaChainMapRefSeq.psl
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fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
- src/lib/annoStreamVcf.c
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Yikes, when querying at the cart position instead of the whole genome,annoStreamVcf was skipping rows that it shouldn't have!
- lines changed 149, context: html, text, full: html, text
Fixing bug reported by user in MLQ #11775: VCF that is sorted bystart position might not be sorted by UCSC-start position, specifically
when at the same VCF start position there is an indel followed by a
substitution. VCF start coords for indels are actually one base to
the left of the actual inserted or deleted bases. So we internally
adjust those to be one base to the right, which can make them out-of-order
when followed by a non-indel variant.
To restore sorting order, indels are now saved aside in a queue until
we know it's safe to let them out because either
a) we got a substitution whose start is greater than the indel start
b) we got an indel whose start is greater than the queued indel start
c) we hit EOF.
When condition (a) or (b) is met, we have to do something with the
new record while the indel queue drains, so it's saved aside in the
nextPosQ (which never holds more than one row). If it's (b), then
when indelQ is empty, we move the nextPosQ indel to indelQ because
we can't let that indel out until one of the 3 conditions is met.
fixes #11787
- src/lib/paraFetch.c
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fixing progress indicator
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removed return FALSE that was unneeded and just causing it to be unable to retry
- lines changed 6, context: html, text, full: html, text
improving timeout and retry handling based in Jims suggestions
- src/product/ex.hg.conf
- lines changed 9, context: html, text, full: html, text
adding documentation for db.neverLocal
- src/utils/git-reports/git-reports.c
- lines changed 24, context: html, text, full: html, text
I am reverting Hirams changes and doing the same thing a different way. Fixes the double-free error.
- lines changed 7, context: html, text, full: html, text
Changing the plain text diffs to add file/link extension ".txt" which seems to help more than hurt, as most browsers support the .txt as text automatically. Of course there is a small chance that some software somewhere did automatically recognize the .diff extension properly and show it nicely colored in that way.
- src/utils/qa/2bitCompare
- lines changed 175, context: html, text, full: html, text
New script to compare md5sums of assembly 2bit files (redmine #6508)
- lines changed 24, context: html, text, full: html, text
Modified the script to also output the date and filesize of all 2bit files if applicable (redmine #6508)
- src/utils/qa/makefile
- lines changed 1, context: html, text, full: html, text
Modified makefile to include new 2bitCompare script (redmine #6508)
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/raToStructGen/testOut/test.as
- lines changed 1, context: html, text, full: html, text
eliminate duplicate sql definition to src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as refs #11756
- lines changed: 617465
- files changed: 84