All File Changes
v305_preview2 to v305_base (2014-08-25 to 2014-09-02) v305
- src/hg/encode3/eap/eapSchedule/eapSchedule.c
- lines changed 8, context: html, text, full: html, text
Removing sponge-force kludge and allowing hg38 to happen.
- src/hg/encode3/eap/inc/eapGraph.h
- src/hg/encode3/eap/lib/eapGraph.c
- src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
- lines changed 3, context: html, text, full: html, text
Only doing replicate comparisons on same assembly.
- src/hg/expData/expData.c
- lines changed 276, context: html, text, full: html, text
ExpData.c takes in a matrix of data and a corresponding matrix of names.The output is a .json file which can be used for visualizations.
forceLayout.html is a d3 visualization that is generated with a .json file.
radialDend.html is a d3 visualization that is generated with a .json
file.
hacTree.c, refactored the code slightly to remove uneccesary merge
calls.
bigWigCluster.c
runs on a list of bigWig files, uses the hacTree library to cluster the
bigWigs into a binary tree. The output is a .json file which can be used
for visualizations
- lines changed 2, context: html, text, full: html, text
Fixing comments, normalizing output values
- src/hg/expData/forceLayout.json
- lines changed 247, context: html, text, full: html, text
ExpData.c takes in a matrix of data and a corresponding matrix of names.The output is a .json file which can be used for visualizations.
forceLayout.html is a d3 visualization that is generated with a .json file.
radialDend.html is a d3 visualization that is generated with a .json
file.
hacTree.c, refactored the code slightly to remove uneccesary merge
calls.
bigWigCluster.c
runs on a list of bigWig files, uses the hacTree library to cluster the
bigWigs into a binary tree. The output is a .json file which can be used
for visualizations
- src/hg/expData/radialDend.html
- lines changed 109, context: html, text, full: html, text
ExpData.c takes in a matrix of data and a corresponding matrix of names.The output is a .json file which can be used for visualizations.
forceLayout.html is a d3 visualization that is generated with a .json file.
radialDend.html is a d3 visualization that is generated with a .json
file.
hacTree.c, refactored the code slightly to remove uneccesary merge
calls.
bigWigCluster.c
runs on a list of bigWig files, uses the hacTree library to cluster the
bigWigs into a binary tree. The output is a .json file which can be used
for visualizations
- src/hg/hgBlat/hgBlat.c
- lines changed 2, context: html, text, full: html, text
Fixes #13850. use oneSize instead of seq->size to reflect stripped out Ns and Xs
- src/hg/hgTables/hgTables.c
- lines changed 1, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- lines changed 4, context: html, text, full: html, text
In doOutHyperlinks, no attempt was made to find a tdb for table2 whenintersecting, but we can find it for cheap in fullTrackList.
Meanwhile, passing NULL into ensureVisibility caused a call to
hTrackDbForTrackAndAncestors which doesn't work for custom tracks
anyway (and used to SEGV when given a custom track). Thanks Matt for finding!
refs #13776
- src/hg/hgTables/seqOut.c
- lines changed 1, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- src/hg/hgTracks/bigBedTrack.c
- lines changed 43, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- src/hg/hgc/bigBedClick.c
- lines changed 24, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- src/hg/hgc/hgc.c
- lines changed 127, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- src/hg/htdocs/ENCODE/aboutScaleup.html
- lines changed 5, context: html, text, full: html, text
Minor cleanup of ENCODE 'relic' page (not linked to current site)
- src/hg/htdocs/ENCODE/cellTypes.html
- lines changed 1, context: html, text, full: html, text
Add notice to top of relic NHGRI ENCODE pages
- lines changed 5, context: html, text, full: html, text
Adding width 100% to style of iframes for archived ENCODE cell type pages, and small html changes refs #13616
- src/hg/htdocs/ENCODE/cellTypesMouse.html
- lines changed 1, context: html, text, full: html, text
Adding width 100% to style of iframes for archived ENCODE cell type pages, and small html changes refs #13616
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
- lines changed 2, context: html, text, full: html, text
Add notice to top of relic NHGRI ENCODE pages
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 3, context: html, text, full: html, text
Small CSS cleanup. refs #13616
- src/hg/htdocs/ENCODE/downloadsMouse.html
- lines changed 2, context: html, text, full: html, text
Small CSS cleanup. refs #13616
- src/hg/htdocs/ENCODE/index.html
- lines changed 2, context: html, text, full: html, text
Add link to news archive. refs #13616
- lines changed 32, context: html, text, full: html, text
Adding images with old ENCODE logo instead of DNA bridge, updating news on ENCODE index about portal change refs #13616
- lines changed 17, context: html, text, full: html, text
Trimmed and wordsmithing to News. Fixed an errant table table tag. refs #13616
- src/hg/htdocs/ENCODE/newsarch.html
- lines changed 20, context: html, text, full: html, text
Adding images with old ENCODE logo instead of DNA bridge, updating news on ENCODE index about portal change refs #13616
- lines changed 14, context: html, text, full: html, text
Updating ENCODE/newsarch to match change in index.html news refs #13616
- src/hg/htdocs/ENCODE/qualityMetrics.html
- lines changed 1, context: html, text, full: html, text
Add notice to top of relic NHGRI ENCODE pages
- src/hg/htdocs/goldenPath/help/hubQuickStart.html
- lines changed 168, context: html, text, full: html, text
Just removing old table markup, no real content changes, per Code Review Recommendation #13366
- lines changed 9, context: html, text, full: html, text
Small html tag edits to Hub Quick Start guide, no content changes, CR #13366
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
- lines changed 1, context: html, text, full: html, text
Updating hub/trackDb doc changing dragAndDrop ...on to ...subTracks refs #13893
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
- lines changed 1, context: html, text, full: html, text
Updating hub/trackDb doc changing dragAndDrop ...on to ...subTracks refs #13893
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 2, context: html, text, full: html, text
Updating hub/trackDb doc changing dragAndDrop ...on to ...subTracks refs #13893
- src/hg/htdocs/images/encode/browser.png
- lines changed 0, context: html, text, full: html, text
Adding images with old ENCODE logo instead of DNA bridge, updating news on ENCODE index about portal change refs #13616
- src/hg/htdocs/images/encode/dataMatrix.png
- lines changed 0, context: html, text, full: html, text
Adding images with old ENCODE logo instead of DNA bridge, updating news on ENCODE index about portal change refs #13616
- src/hg/htdocs/images/gbLogoOnly.png
- lines changed 0, context: html, text, full: html, text
Adding images with old ENCODE logo instead of DNA bridge, updating news on ENCODE index about portal change refs #13616
- src/hg/htdocs/inc/encodeProject.newportal.html
- lines changed 7, context: html, text, full: html, text
Add notice to NHGRI ENCODE relic pages. refs #13616
- src/hg/htdocs/style/encodeProject.css
- lines changed 22, context: html, text, full: html, text
Small CSS cleanup. refs #13616
- src/hg/htdocs/training.html
- lines changed 13, context: html, text, full: html, text
split out local from external training pages. Refs #13712
- src/hg/inc/genePred.h
- lines changed 3, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- src/hg/inc/hdb.h
- lines changed 1, context: html, text, full: html, text
Added a missing NULL check to hTrackDbForTrackAndAncestors, which was SEGV'ing in #13776.I also noticed that it doesn't support custom tracks, but the right way to add that
functionality would be more disruptive, and there are only 4 places that call
hTrackDbForTrackAndAncestors. So I added a comment warning to the declaration and
an error message in case I'm wrong about custom tracks not being passed into this.
refs #13776
- src/hg/inc/trackDb.h
- lines changed 1, context: html, text, full: html, text
another place where bigGenePred should be treated like bigBed
- src/hg/inc/versionInfo.h
- src/hg/lib/cart.c
- lines changed 3, context: html, text, full: html, text
Prevent segv triggered by blank line in user's settings URL.refs #13669
- src/hg/lib/genePred.c
- lines changed 44, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- src/hg/lib/hdb.c
- lines changed 12, context: html, text, full: html, text
Added a missing NULL check to hTrackDbForTrackAndAncestors, which was SEGV'ing in #13776.I also noticed that it doesn't support custom tracks, but the right way to add that
functionality would be more disruptive, and there are only 4 places that call
hTrackDbForTrackAndAncestors. So I added a comment warning to the declaration and
an error message in case I'm wrong about custom tracks not being passed into this.
refs #13776
- src/hg/lib/hgSeq.c
- lines changed 10, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- src/hg/makeDb/doc/dm6.txt
- lines changed 429, context: html, text, full: html, text
rebuild with genbank sequence refs #4049
- lines changed 105, context: html, text, full: html, text
genscan done ucscToINSDC search rule for gold table and default position set refs #4049
- lines changed 341, context: html, text, full: html, text
running up all lastz runs refs #4049
- src/hg/makeDb/doc/hg19.txt
- lines changed 59, context: html, text, full: html, text
Methylation scores (bed 9 for color scale similar to HAIB Methyl RRBS tracks) for Neandertal and Denisova.refs #13439
- src/hg/makeDb/doc/hg38.txt
- lines changed 44, context: html, text, full: html, text
Added SIB Genes and SIB Alt-Splicing tracks; refs #13681
- src/hg/makeDb/doc/mm10.txt
- lines changed 54, context: html, text, full: html, text
import mouse GENCODE VM3
- lines changed 338, context: html, text, full: html, text
Added details for constructing NCBI Ends track; refs #10083
- lines changed 393, context: html, text, full: html, text
Added details for constructing NCBI Ends track; refs #10083
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 14, context: html, text, full: html, text
adding dm6 fly refs #4049
- src/hg/makeDb/schema/all.joiner
- lines changed 80, context: html, text, full: html, text
import mouse GENCODE VM3
- lines changed 2, context: html, text, full: html, text
Methylation scores (bed 9 for color scale similar to HAIB Methyl RRBS tracks) for Neandertal and Denisova.refs #13439
- src/hg/makeDb/trackDb/drosophila/dm6/description.html
- lines changed 14, context: html, text, full: html, text
updated text for new assembly from genbank refs #4049
- src/hg/makeDb/trackDb/human/hg19/denisovaMethylation.html
- lines changed 31, context: html, text, full: html, text
Methylation scores (bed 9 for color scale similar to HAIB Methyl RRBS tracks) for Neandertal and Denisova.refs #13439
- src/hg/makeDb/trackDb/human/hg19/neandertalMethylation.html
- lines changed 31, context: html, text, full: html, text
Methylation scores (bed 9 for color scale similar to HAIB Methyl RRBS tracks) for Neandertal and Denisova.refs #13439
- src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
- lines changed 7, context: html, text, full: html, text
Methylation scores (bed 9 for color scale similar to HAIB Methyl RRBS tracks) for Neandertal and Denisova.refs #13439
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 7, context: html, text, full: html, text
Added SIB Genes and SIB Alt-Splicing tracks; refs #13681
- src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
- lines changed 7, context: html, text, full: html, text
add ensembl version to gencode label
- src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV20.ra
- lines changed 5, context: html, text, full: html, text
add ensembl version to gencode label
- src/hg/makeDb/trackDb/human/trackDb.nt.ra
- lines changed 8, context: html, text, full: html, text
Methylation scores (bed 9 for color scale similar to HAIB Methyl RRBS tracks) for Neandertal and Denisova.refs #13439
- src/hg/makeDb/trackDb/mouse/cloneEnd.trackDb.ra
- lines changed 30, context: html, text, full: html, text
Updated visibility settings; refs #10083
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM3.html
- lines changed 311, context: html, text, full: html, text
import mouse GENCODE VM3
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM3.ra
- lines changed 263, context: html, text, full: html, text
import mouse GENCODE VM3
- src/hg/oneShot/freen/freen.c
- lines changed 226, context: html, text, full: html, text
First cut of parallelizing seems to work.
- lines changed 220, context: html, text, full: html, text
Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
- src/hg/pslCDnaFilter/cDnaStats.c
- lines changed 25, context: html, text, full: html, text
add option to save filtering statistics to file rather then writing to stderr
- src/hg/pslCDnaFilter/cDnaStats.h
- lines changed 2, context: html, text, full: html, text
add option to save filtering statistics to file rather then writing to stderr
- src/hg/pslCDnaFilter/pslCDnaFilter.c
- lines changed 11, context: html, text, full: html, text
add option to save filtering statistics to file rather then writing to stderr
- src/hg/pslCDnaFilter/tests/expected/blackListTest/keep.psl
- lines changed 15, context: html, text, full: html, text
for some reason expected test order was wrong
- lines changed 79, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/keep.psl
- lines changed 2, context: html, text, full: html, text
for some reason expected test order was wrong
- lines changed 31, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/globalBestTest/keep.psl
- lines changed 4, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/keep.psl
- lines changed 6, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/hapLocalTest/keep.psl
- lines changed 6, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/localBestTest/keep.psl
- lines changed 8, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/maxAlignTest/keep.psl
- lines changed 2, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/minSpan10Test/keep.psl
- lines changed 2, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/noopTest/keep.psl
- lines changed 2, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/noopTest/weird.psl
- lines changed 2, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/overlapTest/weird.psl
- lines changed 2, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/uniqueMappedHapTest/keep.psl
- lines changed 4, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/weird.psl
- lines changed 2, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/tests/makefile
- lines changed 2, context: html, text, full: html, text
add option to save filtering statistics to file rather then writing to stderr
- lines changed 1, context: html, text, full: html, text
fix problem with sort order of pslCDnaFilter test results being non-deterministic in some cases
- src/hg/pslCDnaFilter/usage.txt
- lines changed 3, context: html, text, full: html, text
add option to save filtering statistics to file rather then writing to stderr
- src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
- lines changed 1, context: html, text, full: html, text
adding more support for bigGenePred in hgc and hgTables.
- src/inc/hacTree.h
- lines changed 6, context: html, text, full: html, text
Adding hacTreeMultiThread.
- lines changed 18, context: html, text, full: html, text
Adding possibility to include precalculated distances to hacTreeMultiThread and improving commenting.
- lines changed 12, context: html, text, full: html, text
Removing hacTreeExpensiveMerges and simplifying hacTreeMultiThread
- src/inc/pthreadDoList.h
- lines changed 67, context: html, text, full: html, text
Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
- src/lib/hacTree.c
- lines changed 17, context: html, text, full: html, text
ExpData.c takes in a matrix of data and a corresponding matrix of names.The output is a .json file which can be used for visualizations.
forceLayout.html is a d3 visualization that is generated with a .json file.
radialDend.html is a d3 visualization that is generated with a .json
file.
hacTree.c, refactored the code slightly to remove uneccesary merge
calls.
bigWigCluster.c
runs on a list of bigWig files, uses the hacTree library to cluster the
bigWigs into a binary tree. The output is a .json file which can be used
for visualizations
- lines changed 20, context: html, text, full: html, text
Reversing ordering, and refactoring to set up for parallelization of distance calcs.
- lines changed 126, context: html, text, full: html, text
Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
- lines changed 37, context: html, text, full: html, text
Adding possibility to include precalculated distances to hacTreeMultiThread and improving commenting.
- lines changed 15, context: html, text, full: html, text
Changing the new hacTree code so that it creates trees in same order (I hope) as old code. Previously it was inverting some branches.
- lines changed 198, context: html, text, full: html, text
Removing hacTreeExpensiveMerges and simplifying hacTreeMultiThread
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
- src/lib/pthreadDoList.c
- lines changed 109, context: html, text, full: html, text
Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
- lines changed 5, context: html, text, full: html, text
Adding empty list short-cut and threadCount error checking.
- src/oneShot/bigWigCluster/bigWigCluster.c
- lines changed 318, context: html, text, full: html, text
Parallelized bigWig clustering via hacTree to produce a json graph seems to work.
- lines changed 131, context: html, text, full: html, text
Adding tabular output. Commenting and cleaning up code.
- src/oneShot/bigWigCluster/makefile
- lines changed 3, context: html, text, full: html, text
Parallelized bigWig clustering via hacTree to produce a json graph seems to work.
- src/oneShot/hacTreeTest/hacTreeTest.c
- lines changed 118, context: html, text, full: html, text
Adding a little test program.
- src/oneShot/hacTreeTest/makefile
- lines changed 3, context: html, text, full: html, text
Adding a little test program.
- src/oneShot/hacTreeTest/testIt
- lines changed 3, context: html, text, full: html, text
Adding a little test program.
- src/oneShot/orderMiddle/makefile
- lines changed 7, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/oneShot/orderMiddle/orderMiddle.c
- lines changed 145, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/oneShot/orderMiddle/test.expected
- lines changed 6, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/oneShot/orderMiddle/test.lst
- lines changed 6, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/oneShot/orderMiddle/test.pair
- lines changed 15, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/utils/bigWigCluster/bigWigCluster.c
- lines changed 195, context: html, text, full: html, text
ExpData.c takes in a matrix of data and a corresponding matrix of names.The output is a .json file which can be used for visualizations.
forceLayout.html is a d3 visualization that is generated with a .json file.
radialDend.html is a d3 visualization that is generated with a .json
file.
hacTree.c, refactored the code slightly to remove uneccesary merge
calls.
bigWigCluster.c
runs on a list of bigWig files, uses the hacTree library to cluster the
bigWigs into a binary tree. The output is a .json file which can be used
for visualizations
- lines changed 93, context: html, text, full: html, text
Fixing comments, normalizing output values
- lines changed 243, context: html, text, full: html, text
Swapping in Jim's version which fixes some parallelization issues and adds a new tabular output.
- src/utils/bigWigCluster/makefile
- lines changed 3, context: html, text, full: html, text
ExpData.c takes in a matrix of data and a corresponding matrix of names.The output is a .json file which can be used for visualizations.
forceLayout.html is a d3 visualization that is generated with a .json file.
radialDend.html is a d3 visualization that is generated with a .json
file.
hacTree.c, refactored the code slightly to remove uneccesary merge
calls.
bigWigCluster.c
runs on a list of bigWig files, uses the hacTree library to cluster the
bigWigs into a binary tree. The output is a .json file which can be used
for visualizations
- src/utils/bigWigCorrelate/bigWigCorrelate.c
- lines changed 11, context: html, text, full: html, text
Adding -rootNames option, and making by default system output complete input file name instead of just root name.
- src/utils/orderMiddle/makefile
- lines changed 7, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/utils/orderMiddle/orderMiddle.c
- lines changed 145, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/utils/orderMiddle/test.expected
- lines changed 6, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/utils/orderMiddle/test.lst
- lines changed 6, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/utils/orderMiddle/test.pair
- lines changed 15, context: html, text, full: html, text
Moving utility that doesn't really work to oneShot.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 3, context: html, text, full: html, text
v305 final build refs #13703
- lines changed: 6603
- files changed: 130