File Changes for kent

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/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
• 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/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/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/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/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 1, context: html, text, full: html, text
    Adding gffToBed to build
• 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/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.