All File Changes

v281_preview2 to v281_base (2013-03-19 to 2013-03-25) v281

• src/hg/encode3/importEncode2/README
  • lines changed 17, context: html, text, full: html, text
    Describing encode2Meta database and how to build it some.
• src/hg/encode3/importEncode2/encode2BedDoctor/encode2BedDoctor.c
  • lines changed 78, context: html, text, full: html, text
    Starting to write program to fix problems in ENCODE2 beds.
  • lines changed 42, context: html, text, full: html, text
    Making doctor strip track and browser lines.
  • lines changed 6, context: html, text, full: html, text
    Turning floating point scores into integers.
  • lines changed 12, context: html, text, full: html, text
    Fixing up a few more encode2 beds - this one with '.' in the thickStart/thickEnd fields.
  • lines changed 3, context: html, text, full: html, text
    Fixed a place where doctor was actually munging things up.
• src/hg/encode3/importEncode2/encode2BedDoctor/expected.bed
  • lines changed 0, context: html, text, full: html, text
    Starting to write program to fix problems in ENCODE2 beds.
  • lines changed 10, context: html, text, full: html, text
    Adding test case to source tree and make system.
• src/hg/encode3/importEncode2/encode2BedDoctor/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting to write program to fix problems in ENCODE2 beds.
  • lines changed 5, context: html, text, full: html, text
    Adding test case to source tree and make system.
  • lines changed 1, context: html, text, full: html, text
    Copying executables to San Diego, where they will be run, in makefiles. A temporary measure.
• src/hg/encode3/importEncode2/encode2BedDoctor/test.bed
  • lines changed 10, context: html, text, full: html, text
    Starting to write program to fix problems in ENCODE2 beds.
  • lines changed 1, context: html, text, full: html, text
    Adding to test case.
• src/hg/encode3/importEncode2/encode2BedPlusDoctor/encode2BedPlusDoctor.c
  • lines changed 113, context: html, text, full: html, text
    Adding new encode2 doctor - for bed files with a .as file.
  • lines changed 12, context: html, text, full: html, text
    Fixing integer overflows.
• src/hg/encode3/importEncode2/encode2BedPlusDoctor/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding new encode2 doctor - for bed files with a .as file.
  • lines changed 1, context: html, text, full: html, text
    Copying executables to San Diego, where they will be run, in makefiles. A temporary measure.
• src/hg/encode3/importEncode2/encode2CmpMd5/encode2CmpMd5.c
  • lines changed 124, context: html, text, full: html, text
    Utility to compare md5 sums lists generated by two methods.
• src/hg/encode3/importEncode2/encode2CmpMd5/go
  • lines changed 1, context: html, text, full: html, text
    Utility to compare md5 sums lists generated by two methods.
• src/hg/encode3/importEncode2/encode2CmpMd5/makefile
  • lines changed 18, context: html, text, full: html, text
    Utility to compare md5 sums lists generated by two methods.
• src/hg/encode3/importEncode2/encode2CopyManifest/encode2CopyManifest.c
  • lines changed 281, context: html, text, full: html, text
    Starting on a program to copy over files selectively and unpack some of the tgz fastq's in the process.
  • lines changed 103, context: html, text, full: html, text
    Making it convert narrowPeak into a particular bigBed.
  • lines changed 310, context: html, text, full: html, text
    A little paranoid fastq directory rearranger for encode conversion. Probably a way to do this with a 10 line shell script, but what's another 100 line C program?
• src/hg/encode3/importEncode2/encode2CopyManifest/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting on a program to copy over files selectively and unpack some of the tgz fastq's in the process.
  • lines changed 18, context: html, text, full: html, text
    A little paranoid fastq directory rearranger for encode conversion. Probably a way to do this with a 10 line shell script, but what's another 100 line C program?
• src/hg/encode3/importEncode2/encode2ExpDumpFlat/encode2ExpDumpFlat.c
  • lines changed 81, context: html, text, full: html, text
    Making this generate a SQL table creation statement and a view creation statement as well. The view doesn't seem to really work, just hands on MySQL.
• src/hg/encode3/importEncode2/encode2FastqSubdirsInManifest/encode2FastqSubdirsInManifest.c
  • lines changed 61, context: html, text, full: html, text
    Starting to work on program work expanded fastq tarballs back into manifest
  • lines changed 12, context: html, text, full: html, text
    Patching in tarball contents. Md5sums/sizes/vkeys still need update, but will do that with a separate program.
• src/hg/encode3/importEncode2/encode2FastqSubdirsInManifest/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting to work on program work expanded fastq tarballs back into manifest
• src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/encode2FlattenFastqSubdirs.c
  • lines changed 111, context: html, text, full: html, text
    A little paranoid fastq directory rearranger for encode conversion. Probably a way to do this with a 10 line shell script, but what's another 100 line C program?
  • lines changed 4, context: html, text, full: html, text
    Avoiding making renames to self in simple case with no subdirs.
  • lines changed 25, context: html, text, full: html, text
    If fileName doesn't end in .fastq, actually look at file before giving up.
  • lines changed 8, context: html, text, full: html, text
    Catching abort inside isFastq when file is gzipped.
• src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/makefile
  • lines changed 19, context: html, text, full: html, text
    Copying executables to San Diego, where they will be run, in makefiles. A temporary measure.
• src/hg/encode3/importEncode2/encode2GffDoctor/encode2GffDoctor.c
  • lines changed 99, context: html, text, full: html, text
    Making program to help smooth out some of those ugly cufflinks gffs.
  • lines changed 36, context: html, text, full: html, text
    Fixing a few more tweaked encode2 gffs.
  • lines changed 18, context: html, text, full: html, text
    Abbreviating more long things that might end up in bed->name field.
  • lines changed 4, context: html, text, full: html, text
    Removing some rouge transcript type lines in gff doctor.
  • lines changed 11, context: html, text, full: html, text
    Fixing a bug in subForSmaller that caused garbled output. Leaving transcript lines after all - the fix for that problem was better done at a lower level.
• src/hg/encode3/importEncode2/encode2GffDoctor/makefile
  • lines changed 18, context: html, text, full: html, text
    Making program to help smooth out some of those ugly cufflinks gffs.
  • lines changed 1, context: html, text, full: html, text
    Copying executables to San Diego, where they will be run, in makefiles. A temporary measure.
• src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c
  • lines changed 310, context: html, text, full: html, text
    A little paranoid fastq directory rearranger for encode conversion. Probably a way to do this with a 10 line shell script, but what's another 100 line C program?
  • lines changed 204, context: html, text, full: html, text
    Adding more specific file types, especially to convert to big bed.
  • lines changed 73, context: html, text, full: html, text
    Adding a bunch more bigBed variant outputs, improving gff/gtf handling, and adding to the list of things to just copy.
  • lines changed 73, context: html, text, full: html, text
    Ignoring files that are in manifest but don't exist on file system. Making some things labeled bed into more specific formats.
  • lines changed 9, context: html, text, full: html, text
    Adding new encode2 doctor - for bed files with a .as file.
  • lines changed 2, context: html, text, full: html, text
    Fixing up a few more encode2 beds - this one with '.' in the thickStart/thickEnd fields.
  • lines changed 108, context: html, text, full: html, text
    Starting to make manifest.new output. A bunch of little fixes for strange input.
  • lines changed 11, context: html, text, full: html, text
    Improving manifest.new output.
  • lines changed 13, context: html, text, full: html, text
    Coping with new outputType and size fields.
  • lines changed 76, context: html, text, full: html, text
    Moving manifestInfo to library as encode2Manifest.
• src/hg/encode3/importEncode2/encode2MakeEncode3/makefile
  • lines changed 18, context: html, text, full: html, text
    A little paranoid fastq directory rearranger for encode conversion. Probably a way to do this with a 10 line shell script, but what's another 100 line C program?
  • lines changed 3, context: html, text, full: html, text
    Adding more specific file types, especially to convert to big bed.
  • lines changed 3, context: html, text, full: html, text
    Copying executables to San Diego, where they will be run, in makefiles. A temporary measure.
• src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c
  • lines changed 225, context: html, text, full: html, text
    Initial cut at program to make manifest file from Encode2 data.
  • lines changed 17, context: html, text, full: html, text
    Adding md5sum column. Polishing a few other fields\n
  • lines changed 32, context: html, text, full: html, text
    Adding size and output_type fields.
  • lines changed 14, context: html, text, full: html, text
    Dealing with addition of several new fields to manifest.
  • lines changed 49, context: html, text, full: html, text
    Removing some unused code. Making it load mdbs for all databases up front.
• src/hg/encode3/importEncode2/encode2Manifest/makefile
  • lines changed 18, context: html, text, full: html, text
    Initial cut at program to make manifest file from Encode2 data.
• src/hg/encode3/importEncode2/encode2Md5UpdateManifest/encode2Md5UpdateManifest.c
  • lines changed 88, context: html, text, full: html, text
    Making an encode2 manifest.tab patcher that updates the md5sum and other fields for files that have changed.
• src/hg/encode3/importEncode2/encode2Md5UpdateManifest/go
  • lines changed 1, context: html, text, full: html, text
    Making an encode2 manifest.tab patcher that updates the md5sum and other fields for files that have changed.
• src/hg/encode3/importEncode2/encode2Md5UpdateManifest/makefile
  • lines changed 19, context: html, text, full: html, text
    Making an encode2 manifest.tab patcher that updates the md5sum and other fields for files that have changed.
• src/hg/encode3/importEncode2/encode2Meta.as
  • lines changed 434, context: html, text, full: html, text
    Describing encode2Meta database and how to build it some.
  • lines changed 434, context: html, text, full: html, text
    Moving .as file to .as.txt since it is just for documentation and it is screwing up automatic table documenter.
• src/hg/encode3/importEncode2/encode2Meta.as.txt
  • lines changed 434, context: html, text, full: html, text
    Moving .as file to .as.txt since it is just for documentation and it is screwing up automatic table documenter.
• src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c
  • lines changed 428, context: html, text, full: html, text
    An interesting first cut.
  • lines changed 26, context: html, text, full: html, text
    Suppressing output of some fields.
  • lines changed 121, context: html, text, full: html, text
    Separating file from other metadata output. Slimming down what is written a bit.
  • lines changed 26, context: html, text, full: html, text
    Commenting each suppressed tag. Sorting and polishing output.
  • lines changed 12, context: html, text, full: html, text
    making close enough hoisting attempts on a few more fields. Cutting out sort of meaningless highest level tag
  • lines changed 29, context: html, text, full: html, text
    fixing bug where composite meta objects got entered twice into tree.
  • lines changed 3, context: html, text, full: html, text
    Adding hg19/ or mm9/ to file names.
  • lines changed 22, context: html, text, full: html, text
    Making whether it puts out the parent field or not a command line option. Also only outputting files that are in manifest.
• src/hg/encode3/importEncode2/encode2Meta/makefile
  • lines changed 18, context: html, text, full: html, text
    An interesting first cut.
• src/hg/encode3/importEncode2/encodeCvToDb/README
  • lines changed 2, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/encodeCvToDb/encodeCvToDb.c
  • lines changed 967, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/encodeCvToDb/makefile
  • lines changed 18, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
  • lines changed 3, context: html, text, full: html, text
    Updating makefile to cope with move of source code.
• src/hg/encode3/importEncode2/encodeCvToDb/splitAntibody.ra
  • lines changed 7, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
  • lines changed 1, context: html, text, full: html, text
    Updating a bit to cope with ENCODE changes in last year.
• src/hg/encode3/importEncode2/encodeCvToDb/splitAntibody.sql
  • lines changed 34, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/encodeCvToDb/splitAntibodyModel.py
  • lines changed 49, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
  • lines changed 4, context: html, text, full: html, text
    Updating a bit to cope with ENCODE changes in last year.
• src/hg/encode3/importEncode2/encodeCvToDb/tryIt
  • lines changed 37, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
  • lines changed 10, context: html, text, full: html, text
    Updating a bit to cope with ENCODE changes in last year.
• src/hg/encode3/importEncode2/encodeExpToCvDb/encodeExpToCvDb.c
  • lines changed 35, context: html, text, full: html, text
    No longer splitting out antibody and target, since Cricket is doing that by hand.
  • lines changed 6, context: html, text, full: html, text
    Cutting out bam index md5sums. Making output for table as well as file rows.
• src/hg/encode3/importEncode2/encodeExpToCvDb/experiment.sql
  • lines changed 2, context: html, text, full: html, text
    No longer splitting out antibody and target, since Cricket is doing that by hand.
• src/hg/encode3/importEncode2/encodeExpToCvDb/go
  • lines changed 4, context: html, text, full: html, text
    No longer splitting out antibody and target, since Cricket is doing that by hand.
• src/hg/encode3/importEncode2/makefile
  • lines changed 38, context: html, text, full: html, text
    Adding makefile to call make in all subdirectories that need it.
• src/hg/encode3/importEncode2/testCvToSql/README
  • lines changed 2, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/testCvToSql/makefile
  • lines changed 18, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/testCvToSql/splitAntibody.ra
  • lines changed 7, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/testCvToSql/splitAntibody.sql
  • lines changed 34, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/testCvToSql/splitAntibodyModel.py
  • lines changed 49, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/testCvToSql/testCvToSql.c
  • lines changed 967, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/importEncode2/testCvToSql/tryIt
  • lines changed 37, context: html, text, full: html, text
    Renaming testCvToSql to encodeCvToDb
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 22, context: html, text, full: html, text
    Moving calcValidKey function to library.
• src/hg/genePredToBed/expected.bed
  • lines changed 100, context: html, text, full: html, text
    Making C version of genePredToBed so as to have somewhat better error reporting.
• src/hg/genePredToBed/genePredToBed.c
  • lines changed 69, context: html, text, full: html, text
    Making C version of genePredToBed so as to have somewhat better error reporting.
• src/hg/genePredToBed/makefile
  • lines changed 22, context: html, text, full: html, text
    Making C version of genePredToBed so as to have somewhat better error reporting.
• src/hg/genePredToBed/test.genePred
  • lines changed 100, context: html, text, full: html, text
    Making C version of genePredToBed so as to have somewhat better error reporting.
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    fold back in the changes Angie made in the commit before my last commit. Change cartCopyCustomTracks() to not take a database argument since it's interation over all the "ctfile_*" in the cart anyway.All of this is to fix the problem that now loading a cart and connecting to hubs is what should be an atomic act. As it was, there were some hdb routines called after a new cart was loaded, but before the referenced hubs were loaded.
    As it is now, hgSession will load new carts without reloading the associated hubs. This would only be a problem with assembly hubs, and I don't think it matters since hgSession isn't displaying hub data anyway.
    
• src/hg/hgTracks/multiWig.c
  • lines changed 1, context: html, text, full: html, text
    Improving comment.
• src/hg/hgc/hgc.c
  • lines changed 14, context: html, text, full: html, text
    Making extended case and coloring options dialog check boxes and radio buttons sticky. fixes #10325
  • lines changed 3, context: html, text, full: html, text
    commented out a link from COSMIC track details that goes only to their main site. It is redundant with a link in Description. Also repaired the link so it works in case we want to add it back ever. Fixed spelling of Tumour to Tumor
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 544, context: html, text, full: html, text
    Adding ENCODE FAQ directory and index.html page, RM#9712
  • lines changed 35, context: html, text, full: html, text
    Correcting directory links to place page in FAQ/ directory and a few typos, RM#9712
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 47, context: html, text, full: html, text
    Finished genome-euro help doc. Commented out line from hgTracksHelp that points to the genome-euro doc. When we go live with genome-euro, it can be un-commented. (redmine #9767)
  • lines changed 7, context: html, text, full: html, text
    Removed the paragraph about moving custom tracks. Bob, Brooke and I decided not to address that for now. (redmine #9767)
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    Finished genome-euro help doc. Commented out line from hgTracksHelp that points to the genome-euro doc. When we go live with genome-euro, it can be un-commented. (redmine #9767)
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 33, context: html, text, full: html, text
    added a paper of Kate's from 2010 that was missing
• src/hg/inc/cart.h
  • lines changed 2, context: html, text, full: html, text
    oops.... forgot to update this declaration
  • lines changed 3, context: html, text, full: html, text
    fold back in the changes Angie made in the commit before my last commit. Change cartCopyCustomTracks() to not take a database argument since it's interation over all the "ctfile_*" in the cart anyway.All of this is to fix the problem that now loading a cart and connecting to hubs is what should be an atomic act. As it was, there were some hdb routines called after a new cart was loaded, but before the referenced hubs were loaded.
    As it is now, hgSession will load new carts without reloading the associated hubs. This would only be a problem with assembly hubs, and I don't think it matters since hgSession isn't displaying hub data anyway.
    
• src/hg/inc/encode3/encode2Manifest.h
  • lines changed 35, context: html, text, full: html, text
    Moving encode2Manifest to a library.
• src/hg/inc/encode3/encode3Valid.h
  • lines changed 10, context: html, text, full: html, text
    Making a place for shared code among encode3 programs.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v281
• src/hg/lib/cart.c
  • lines changed 24, context: html, text, full: html, text
    fold back in the changes Angie made in the commit before my last commit. Change cartCopyCustomTracks() to not take a database argument since it's interation over all the "ctfile_*" in the cart anyway.All of this is to fix the problem that now loading a cart and connecting to hubs is what should be an atomic act. As it was, there were some hdb routines called after a new cart was loaded, but before the referenced hubs were loaded.
    As it is now, hgSession will load new carts without reloading the associated hubs. This would only be a problem with assembly hubs, and I don't think it matters since hgSession isn't displaying hub data anyway.
    
• src/hg/lib/ceBlastTab.as
  • lines changed 17, context: html, text, full: html, text
    add an as file for seven of the blastTab tables so the decription will be more clear as to their contents fixes #9363
• src/hg/lib/dbNsfpInterPro.as
  • lines changed 8, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/lib/dbNsfpLrt.as
  • lines changed 21, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/lib/dbNsfpMutationAssessor.as
  • lines changed 18, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/lib/dbNsfpMutationTaster.as
  • lines changed 18, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/lib/dbNsfpPolyPhen2.as
  • lines changed 24, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/lib/dbNsfpSeqChange.as
  • lines changed 21, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/lib/dbNsfpSift.as
  • lines changed 15, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/lib/dbNsfpUniProt.as
  • lines changed 9, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/lib/dmBlastTab.as
  • lines changed 17, context: html, text, full: html, text
    add an as file for seven of the blastTab tables so the decription will be more clear as to their contents fixes #9363
• src/hg/lib/drBlastTab.as
  • lines changed 17, context: html, text, full: html, text
    add an as file for seven of the blastTab tables so the decription will be more clear as to their contents fixes #9363
• src/hg/lib/encode/narrowPeak.as
  • lines changed 1, context: html, text, full: html, text
    Changing peak field to int, so it can take the -1 missing data value.
• src/hg/lib/encode/openChromCombinedPeaks.as
  • lines changed 0, context: html, text, full: html, text
    Fixed indentation.
  • lines changed 2, context: html, text, full: html, text
    Fixes to get bigBed to accept this .as file.
• src/hg/lib/encode/shortFrags.as
  • lines changed 31, context: html, text, full: html, text
    Adding placeholder for shortFrags.as.
  • lines changed 5, context: html, text, full: html, text
    Making shortFrags.as work with ENCODE files. I still don't have better names for the fields, but there's long comma-separated lists in some of them so I made those lstrings. It looks like in most cases a field I named arraySize describes the # of items in the comma separated lists, but there are exceptions in files which may have other problems too.
• src/hg/lib/encode3/encode2Manifest.c
  • lines changed 60, context: html, text, full: html, text
    Moving encode2Manifest to a library.
• src/hg/lib/encode3/encode3Valid.c
  • lines changed 27, context: html, text, full: html, text
    Making a place for shared code among encode3 programs.
• src/hg/lib/genePred.c
  • lines changed 22, context: html, text, full: html, text
    When turning GFF to gene pred, calculate start/end from exons and cds only, not from every possible type.
• src/hg/lib/hgBlastTab.as
  • lines changed 17, context: html, text, full: html, text
    add an as file for seven of the blastTab tables so the decription will be more clear as to their contents fixes #9363
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding module for shared encode3 validation routines.
  • lines changed 1, context: html, text, full: html, text
    Moving encode2Manifest to a library.
• src/hg/lib/mmBlastTab.as
  • lines changed 17, context: html, text, full: html, text
    add an as file for seven of the blastTab tables so the decription will be more clear as to their contents fixes #9363
• src/hg/lib/rnBlastTab.as
  • lines changed 17, context: html, text, full: html, text
    add an as file for seven of the blastTab tables so the decription will be more clear as to their contents fixes #9363
• src/hg/lib/scBlastTab.as
  • lines changed 17, context: html, text, full: html, text
    add an as file for seven of the blastTab tables so the decription will be more clear as to their contents fixes #9363
• src/hg/lib/web.c
  • lines changed 4, context: html, text, full: html, text
    tweaks to UI, added help link to official-euro redirect message
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 43, context: html, text, full: html, text
    Add back missing dataset (HAIB GM12878 Egr-1). refs #10042. ENCODE Uniform TFBS track
  • lines changed 1, context: html, text, full: html, text
    Tweak long label for added dataset. refs #10042. ENCODE Uniform TFBS track.
  • lines changed 1, context: html, text, full: html, text
    Adding notes file required for ENCODE QA. refs #10042. ENCODE Uniform TFBS
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeAwgTfbsUniform.release1.notes
  • lines changed 1428, context: html, text, full: html, text
    Adding notes file required for ENCODE QA. refs #10042. ENCODE Uniform TFBS
• src/hg/makeDb/doc/hg19.txt
  • lines changed 68, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
  • lines changed 2, context: html, text, full: html, text
    Correcting the /hive path for dbNSFP2.0
• src/hg/makeDb/doc/nomLeu3.txt
  • lines changed 11, context: html, text, full: html, text
    Updating genbank date stamp, adding blat server. refs #9812
  • lines changed 9, context: html, text, full: html, text
    update dbDb.description during QA to make it like the others, refs #9812
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    adding nomLeu3 refs #9812
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    adding nomLeu3 refs #9812
  • lines changed 1, context: html, text, full: html, text
    not read for nomLeu3 yet
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Lowered minCheck threshold of entry in refSeqId identifier section from 0.35 to 0.32 which fixed an hg19 joinerCheck error
  • lines changed 22, context: html, text, full: html, text
    Removed old ucscRetro tables from rules and updated the rules to check version 5 for hg19. Updated rules to use macros.
  • lines changed 1, context: html, text, full: html, text
    Changed hg19.kg5ToKg6.newId to kgDb.kg5ToKg6.newId so it would include mm10 as well (redmine #10442)
  • lines changed 2, context: html, text, full: html, text
    Removed droWil1 and mm6 from the database definitions as these assemblies aren't even on dev anymore; they are not mentioned anywhere else in all.joiner
  • lines changed 2, context: html, text, full: html, text
    Reduced the minCheck threshold from 0.97 to 0.96 for two entries which fixed an ornAna1 joinerCheck error (redmine #9407)
  • lines changed 1, context: html, text, full: html, text
    Added rn5 to the ensGeneDb list (redmine #9407)
• src/hg/makeDb/trackDb/human/gwasCatalog.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link on track page refs #10098
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding metadata to makefile. #10042: ENCODE Uniform TFBS
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgTfbsUniform.ra
  • lines changed 695, context: html, text, full: html, text
    Add download file md5sums to track metadata. refs #10042
  • lines changed 18, context: html, text, full: html, text
    Add missing HAIB GM12878 Egr-1 to metadata. It had no Rep1 so was dropped. refs #10042 ENCODE Uniform TFBS
  • lines changed 221, context: html, text, full: html, text
    Add HAIB GM12878 EGR1 dataset. refs #10042 . ENCODE Uniform TFBS track
  • lines changed 5, context: html, text, full: html, text
    Add composite to metadata. refs #10042. ENCODE Uniform TFBS track
  • lines changed 6, context: html, text, full: html, text
    Add composite to metadata. refs #10042. ENCODE Uniform TFBS track
  • lines changed 6, context: html, text, full: html, text
    One more try at adding composite to metadata. refs #10042. ENCODE Uniform TFBS track.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging Analysis Working Group Uniform TFBS on beta (release 1) refs #10042
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAwgTfbsUniform.ra
  • lines changed 12935, context: html, text, full: html, text
    Staging Analysis Working Group Uniform TFBS on beta (release 1) refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html
  • lines changed 92, context: html, text, full: html, text
    Revisions to track description from Anshul. refs #10042. ENCODE Uniform TFBS track
  • lines changed 11, context: html, text, full: html, text
    Formatting track description. refs #10042. ENCODE Uniform TFBS track.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra
  • lines changed 7, context: html, text, full: html, text
    Add HAIB GM12878 EGR1 dataset. refs #10042 . ENCODE Uniform TFBS track
  • lines changed 1, context: html, text, full: html, text
    Tweak long label for added dataset. refs #10042. ENCODE Uniform TFBS track.
  • lines changed 538, context: html, text, full: html, text
    Fix up tier designations on cell types. Other settings tweaks. refs #10042. ENCODE Uniform TFBS track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
  • lines changed 5, context: html, text, full: html, text
    Warn users off ENCODE HudsonAlpha Methyl450 track due to data problems (ML #10231). It will be replaced by a hub. #10447
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 1, context: html, text, full: html, text
    Warn users off ENCODE HudsonAlpha Methyl450 track due to data problems (ML #10231). It will be replaced by a hub. #10447
• src/hg/makeDb/trackDb/pig/susScr2/numtSeq2012.html
  • lines changed 80, context: html, text, full: html, text
    Renamed file to match usual track/table conventions. refs #8533
  • lines changed 3, context: html, text, full: html, text
    Added PMID/PMCID refs #8533
• src/hg/makeDb/trackDb/pig/susScr2/numtSeqSusScr2.html
  • lines changed 80, context: html, text, full: html, text
    Redoing removal of old version of this file.
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Making C version of genePredToBed so as to have somewhat better error reporting.
• src/hg/oneShot/freen/freen.c
  • lines changed 62, context: html, text, full: html, text
    Using C to generate an ugly SQL query.
  • lines changed 58, context: html, text, full: html, text
    Testing some metaDb fetching functions that were really slow. Turns out metaDb needed an optimize tables.
• src/hg/oneShot/freen/makefile
  • lines changed 5, context: html, text, full: html, text
    Testing makefile capabilities, you can include wildcards for file names, cool.
• src/hg/utils/dbNsfpToBed.pl
  • lines changed 379, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/utils/gffToBed/gffToBed.c
  • lines changed 83, context: html, text, full: html, text
    Making a rather general gffToBed program.
  • lines changed 2, context: html, text, full: html, text
    Removing boilerplate about command line options.
  • lines changed 3, context: html, text, full: html, text
    Putting in a null check to avoid a crash.
  • lines changed 1, context: html, text, full: html, text
    Adding a sanity assert after a problematic library function.
• src/hg/utils/gffToBed/makefile
  • lines changed 18, context: html, text, full: html, text
    Making a rather general gffToBed program.
• src/hg/utils/gffToBed/test.gff
  • lines changed 61300, context: html, text, full: html, text
    Making a rather general gffToBed program.
• src/hg/utils/gffToBed/testGtf.gff
  • lines changed 133, context: html, text, full: html, text
    Making a rather general gffToBed program.
• src/hg/utils/makefile
  • lines changed 3, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
  • lines changed 1, context: html, text, full: html, text
    Adding gffToBed to build
• src/hg/utils/mergeSortedBed3Plus.pl
  • lines changed 64, context: html, text, full: html, text
    Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
    http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
    dbNSFP2.0 contains precomputed predictions from a variety of tools of the
    effects of all possible missense variants on protein-coding Gencode rel 9
    (Ens 64) transcripts. For example, it contains scores and predictions
    from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
    LRT), as well as GERP scores at CDS positions and associated domain
    information from InterPro and IDs from UniProt. Each subset is
    extracted into a bigBed or bigWig file so that users of the Variant
    Annotation Integrator will be able to apply one or more of these
    prediction methods to their variants.
    refs #6152
    
• src/hg/utils/phyloTrees/96way.commonNames.nh
  • lines changed 9, context: html, text, full: html, text
    made capitalization consistent throughout
  • lines changed 1, context: html, text, full: html, text
    one more capitalization tweak refs #10272
  • lines changed 6, context: html, text, full: html, text
    adding green sea turtle cheMyd1 and formalize the construction of the common and scientific name files from the Nway.nh file via the makefile targets refs #10272
• src/hg/utils/phyloTrees/96way.nh
  • lines changed 5, context: html, text, full: html, text
    adjusting lengths to get mm10 and rn5 back to where they belong
• src/hg/utils/phyloTrees/96way.scientificNames.nh
  • lines changed 5, context: html, text, full: html, text
    adding green sea turtle cheMyd1 and formalize the construction of the common and scientific name files from the Nway.nh file via the makefile targets refs #10272
• src/hg/utils/phyloTrees/97way.commonNames.nh
  • lines changed 97, context: html, text, full: html, text
    adding green sea turtle cheMyd1 and formalize the construction of the common and scientific name files from the Nway.nh file via the makefile targets refs #10272
• src/hg/utils/phyloTrees/97way.nh
  • lines changed 97, context: html, text, full: html, text
    adding green sea turtle cheMyd1 refs #10444, #10272
• src/hg/utils/phyloTrees/97way.scientificNames.nh
  • lines changed 97, context: html, text, full: html, text
    adding green sea turtle cheMyd1 and formalize the construction of the common and scientific name files from the Nway.nh file via the makefile targets refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 12, context: html, text, full: html, text
    made capitalization consistent throughout
  • lines changed 2, context: html, text, full: html, text
    added a substituion to get hyphen into star-nosed. don't know how to test, though refs #10272
  • lines changed 1, context: html, text, full: html, text
    one more capitalization tweak refs #10272
  • lines changed 1, context: html, text, full: html, text
    adding green sea turtle cheMyd1 and formalize the construction of the common and scientific name files from the Nway.nh file via the makefile targets refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 15, context: html, text, full: html, text
    adding green sea turtle cheMyd1 and formalize the construction of the common and scientific name files from the Nway.nh file via the makefile targets refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding green sea turtle cheMyd1 and formalize the construction of the common and scientific name files from the Nway.nh file via the makefile targets refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 3, context: html, text, full: html, text
    adding green sea turtle cheMyd1 #10272
• src/inc/basicBed.h
  • lines changed 10, context: html, text, full: html, text
    Renaming bedOutputN_Opt into bedOutFlexible and making it a public function.
• src/inc/gff.h
  • lines changed 1, context: html, text, full: html, text
    Making gff reader routines work on a wider variety of gffs including those that reuse same gene names on different chromosomes. THis comes up in pseudo-autosomal parts of X and Y in ensembl gene sets.
• src/inc/portable.h
  • lines changed 2, context: html, text, full: html, text
    fix a problem that Hiram found where twoBitIsFile was errAborting if you gave it a directory name which is how netToAxt was calling it.
• src/index/ixIxx/ixIxx.c
  • lines changed 1, context: html, text, full: html, text
    Added blank line to improve readability.
• src/lib/basicBed.c
  • lines changed 22, context: html, text, full: html, text
    Renaming bedOutputN_Opt into bedOutFlexible and making it a public function.
• src/lib/gff.c
  • lines changed 57, context: html, text, full: html, text
    Making a rather general gffToBed program.
  • lines changed 73, context: html, text, full: html, text
    Making gff reader routines work on a wider variety of gffs including those that reuse same gene names on different chromosomes. THis comes up in pseudo-autosomal parts of X and Y in ensembl gene sets.
  • lines changed 1, context: html, text, full: html, text
    Turning a warning down a notch.
• src/lib/osunix.c
  • lines changed 12, context: html, text, full: html, text
    fix a problem that Hiram found where twoBitIsFile was errAborting if you gave it a directory name which is how netToAxt was calling it.
• src/lib/twoBit.c
  • lines changed 4, context: html, text, full: html, text
    fix a problem that Hiram found where twoBitIsFile was errAborting if you gave it a directory name which is how netToAxt was calling it.
• src/utils/qa/getTableStatus.csh
  • lines changed 4, context: html, text, full: html, text
    made it possible to use euronode in addition to genome-euro
• src/utils/qa/updateTimes.csh
  • lines changed 33, context: html, text, full: html, text
    added genome-euro to updateTimes.csh. added verbose mode that prints machine names instead of a dot
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v281 final build
• src/utils/qa/whoMadeIt.csh
  • lines changed 3, context: html, text, full: html, text
    added Fan Hsu to list of names to combine (with fanhsu) so only listed once as total

• lines changed: 87906
• files changed: 226