Commits for kent
switch to files view, user index
v281_preview2 to v281_base (2013-03-19 to 2013-03-25) v281
- Renaming testCvToSql to encodeCvToDb
- src/hg/encode3/importEncode2/encodeCvToDb/README - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeCvToDb/encodeCvToDb.c - lines changed 967, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeCvToDb/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeCvToDb/splitAntibody.ra - lines changed 7, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeCvToDb/splitAntibody.sql - lines changed 34, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeCvToDb/splitAntibodyModel.py - lines changed 49, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeCvToDb/tryIt - lines changed 37, context: html, text, full: html, text
- src/hg/encode3/importEncode2/testCvToSql/README - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/importEncode2/testCvToSql/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/encode3/importEncode2/testCvToSql/splitAntibody.ra - lines changed 7, context: html, text, full: html, text
- src/hg/encode3/importEncode2/testCvToSql/splitAntibody.sql - lines changed 34, context: html, text, full: html, text
- src/hg/encode3/importEncode2/testCvToSql/splitAntibodyModel.py - lines changed 49, context: html, text, full: html, text
- src/hg/encode3/importEncode2/testCvToSql/testCvToSql.c - lines changed 967, context: html, text, full: html, text
- src/hg/encode3/importEncode2/testCvToSql/tryIt - lines changed 37, context: html, text, full: html, text
- Describing encode2Meta database and how to build it some.
- src/hg/encode3/importEncode2/README - lines changed 17, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2Meta.as - lines changed 434, 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/encode2ExpDumpFlat/encode2ExpDumpFlat.c - lines changed 81, context: html, text, full: html, text
- Updating makefile to cope with move of source code.
- src/hg/encode3/importEncode2/encodeCvToDb/makefile - lines changed 3, context: html, text, full: html, text
- Updating a bit to cope with ENCODE changes in last year.
- src/hg/encode3/importEncode2/encodeCvToDb/splitAntibody.ra - lines changed 1, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeCvToDb/splitAntibodyModel.py - lines changed 4, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeCvToDb/tryIt - lines changed 10, 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/encodeExpToCvDb.c - lines changed 35, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeExpToCvDb/experiment.sql - lines changed 2, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encodeExpToCvDb/go - lines changed 4, context: html, text, full: html, text
- Added blank line to improve readability.
- src/index/ixIxx/ixIxx.c - lines changed 1, context: html, text, full: html, text
- Using C to generate an ugly SQL query.
- src/hg/oneShot/freen/freen.c - lines changed 62, context: html, text, full: html, text
- Initial cut at program to make manifest file from Encode2 data.
- src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c - lines changed 225, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2Manifest/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.
- src/hg/encode3/importEncode2/encode2CopyManifest/encode2CopyManifest.c - lines changed 281, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2CopyManifest/makefile - lines changed 18, context: html, text, full: html, text
- Making extended case and coloring options dialog check boxes and radio buttons sticky. fixes #10325
- Making it convert narrowPeak into a particular bigBed.
- src/hg/encode3/importEncode2/encode2CopyManifest/encode2CopyManifest.c - lines changed 103, 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/encode2CopyManifest.c - lines changed 310, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2CopyManifest/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/encode2FlattenFastqSubdirs.c - lines changed 111, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 310, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MakeEncode3/makefile - lines changed 18, context: html, text, full: html, text
- Avoiding making renames to self in simple case with no subdirs.
- src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/encode2FlattenFastqSubdirs.c - lines changed 4, 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 - lines changed 434, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2Meta.as.txt - lines changed 434, context: html, text, full: html, text
- Making C version of genePredToBed so as to have somewhat better error reporting.
- src/hg/genePredToBed/expected.bed - lines changed 100, context: html, text, full: html, text
- src/hg/genePredToBed/genePredToBed.c - lines changed 69, context: html, text, full: html, text
- src/hg/genePredToBed/makefile - lines changed 22, context: html, text, full: html, text
- 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.
- Making a rather general gffToBed program.
- src/hg/utils/gffToBed/gffToBed.c - lines changed 83, context: html, text, full: html, text
- src/hg/utils/gffToBed/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/utils/gffToBed/test.gff - lines changed 61300, context: html, text, full: html, text
- src/hg/utils/gffToBed/testGtf.gff - lines changed 133, 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.
- Adding more specific file types, especially to convert to big bed.
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 204, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MakeEncode3/makefile - lines changed 3, context: html, text, full: html, text
- Removing boilerplate about command line options.
- src/hg/utils/gffToBed/gffToBed.c - lines changed 2, context: html, text, full: html, text
- Making program to help smooth out some of those ugly cufflinks gffs.
- src/hg/encode3/importEncode2/encode2GffDoctor/encode2GffDoctor.c - lines changed 99, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2GffDoctor/makefile - lines changed 18, context: html, text, full: html, text
- If fileName doesn't end in .fastq, actually look at file before giving up.
- src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/encode2FlattenFastqSubdirs.c - lines changed 25, context: html, text, full: html, text
- Turning a warning down a notch.
- Changing peak field to int, so it can take the -1 missing data value.
- src/hg/lib/encode/narrowPeak.as - lines changed 1, context: html, text, full: html, text
- Testing makefile capabilities, you can include wildcards for file names, cool.
- src/hg/oneShot/freen/makefile - lines changed 5, context: html, text, full: html, text
- Improving comment.
- src/hg/hgTracks/multiWig.c - lines changed 1, context: html, text, full: html, text
- Fixing a few more tweaked encode2 gffs.
- src/hg/encode3/importEncode2/encode2GffDoctor/encode2GffDoctor.c - lines changed 36, context: html, text, full: html, text
- Adding md5sum column. Polishing a few other fields\n
- src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c - lines changed 17, 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/encodeExpToCvDb.c - lines changed 6, 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.
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 73, context: html, text, full: html, text
- Utility to compare md5 sums lists generated by two methods.
- src/hg/encode3/importEncode2/encode2CmpMd5/encode2CmpMd5.c - lines changed 124, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2CmpMd5/go - lines changed 1, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2CmpMd5/makefile - lines changed 18, context: html, text, full: html, text
- Starting to write program to fix problems in ENCODE2 beds.
- src/hg/encode3/importEncode2/encode2BedDoctor/encode2BedDoctor.c - lines changed 78, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2BedDoctor/expected.bed - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/encode3/importEncode2/encode2BedDoctor/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2BedDoctor/test.bed - lines changed 10, context: html, text, full: html, text
- Making doctor strip track and browser lines.
- src/hg/encode3/importEncode2/encode2BedDoctor/encode2BedDoctor.c - lines changed 42, context: html, text, full: html, text
- Adding to test case.
- src/hg/encode3/importEncode2/encode2BedDoctor/test.bed - lines changed 1, context: html, text, full: html, text
- Fixed indentation.
- src/hg/lib/encode/openChromCombinedPeaks.as - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- Turning floating point scores into integers.
- src/hg/encode3/importEncode2/encode2BedDoctor/encode2BedDoctor.c - lines changed 6, context: html, text, full: html, text
- Abbreviating more long things that might end up in bed->name field.
- src/hg/encode3/importEncode2/encode2GffDoctor/encode2GffDoctor.c - lines changed 18, 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.
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 73, context: html, text, full: html, text
- Fixes to get bigBed to accept this .as file.
- src/hg/lib/encode/openChromCombinedPeaks.as - lines changed 2, context: html, text, full: html, text
- Putting in a null check to avoid a crash.
- src/hg/utils/gffToBed/gffToBed.c - lines changed 3, context: html, text, full: html, text
- Renaming bedOutputN_Opt into bedOutFlexible and making it a public function.
- Adding new encode2 doctor - for bed files with a .as file.
- src/hg/encode3/importEncode2/encode2BedPlusDoctor/encode2BedPlusDoctor.c - lines changed 113, context: html, text, full: html, text
- 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.
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 9, context: html, text, full: html, text
- Fixing up a few more encode2 beds - this one with '.' in the thickStart/thickEnd fields.
- src/hg/encode3/importEncode2/encode2BedDoctor/encode2BedDoctor.c - lines changed 12, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 2, context: html, text, full: html, text
- Removing some rouge transcript type lines in gff doctor.
- src/hg/encode3/importEncode2/encode2GffDoctor/encode2GffDoctor.c - lines changed 4, 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.
- Adding a sanity assert after a problematic library function.
- src/hg/utils/gffToBed/gffToBed.c - lines changed 1, context: html, text, full: html, text
- Adding test case to source tree and make system.
- src/hg/encode3/importEncode2/encode2BedDoctor/expected.bed - lines changed 10, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2BedDoctor/makefile - lines changed 5, context: html, text, full: html, text
- Adding makefile to call make in all subdirectories that need it.
- src/hg/encode3/importEncode2/makefile - lines changed 38, context: html, text, full: html, text
- Adding placeholder for shortFrags.as.
- src/hg/lib/encode/shortFrags.as - lines changed 31, context: html, text, full: html, text
- Catching abort inside isFastq when file is gzipped.
- src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/encode2FlattenFastqSubdirs.c - lines changed 8, context: html, text, full: html, text
- Starting to make manifest.new output. A bunch of little fixes for strange input.
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 108, context: html, text, full: html, text
- Improving manifest.new output.
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 11, context: html, text, full: html, text
- Making a place for shared code among encode3 programs.
- src/hg/inc/encode3/encode3Valid.h - lines changed 10, context: html, text, full: html, text
- src/hg/lib/encode3/encode3Valid.c - lines changed 27, context: html, text, full: html, text
- Adding gffToBed to build
- 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/encode/shortFrags.as - lines changed 5, context: html, text, full: html, text
- Moving calcValidKey function to library.
- src/hg/encode3/validateManifest/validateManifest.c - lines changed 22, context: html, text, full: html, text
- Fixed a place where doctor was actually munging things up.
- src/hg/encode3/importEncode2/encode2BedDoctor/encode2BedDoctor.c - lines changed 3, context: html, text, full: html, text
- Fixing integer overflows.
- src/hg/encode3/importEncode2/encode2BedPlusDoctor/encode2BedPlusDoctor.c - lines changed 12, 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/encode2GffDoctor.c - lines changed 11, context: html, text, full: html, text
- Coping with new outputType and size fields.
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 13, context: html, text, full: html, text
- Adding size and output_type fields.
- src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c - lines changed 32, context: html, text, full: html, text
- Adding module for shared encode3 validation routines.
- Moving encode2Manifest to a library.
- src/hg/inc/encode3/encode2Manifest.h - lines changed 35, context: html, text, full: html, text
- src/hg/lib/encode3/encode2Manifest.c - lines changed 60, context: html, text, full: html, text
- Starting to work on program work expanded fastq tarballs back into manifest
- src/hg/encode3/importEncode2/encode2FastqSubdirsInManifest/encode2FastqSubdirsInManifest.c - lines changed 61, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2FastqSubdirsInManifest/makefile - lines changed 18, 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/encode2FastqSubdirsInManifest.c - lines changed 12, 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/encode2Md5UpdateManifest.c - lines changed 88, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2Md5UpdateManifest/go - lines changed 1, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2Md5UpdateManifest/makefile - lines changed 19, context: html, text, full: html, text
- Moving manifestInfo to library as encode2Manifest.
- src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 76, context: html, text, full: html, text
- Dealing with addition of several new fields to manifest.
- src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c - lines changed 14, 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/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2BedPlusDoctor/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/makefile - lines changed 19, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2GffDoctor/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MakeEncode3/makefile - lines changed 3, context: html, text, full: html, text
- An interesting first cut.
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 428, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2Meta/makefile - lines changed 18, context: html, text, full: html, text
- Suppressing output of some fields.
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 26, context: html, text, full: html, text
- Removing some unused code. Making it load mdbs for all databases up front.
- src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c - lines changed 49, context: html, text, full: html, text
- Separating file from other metadata output. Slimming down what is written a bit.
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 121, 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/freen.c - lines changed 58, context: html, text, full: html, text
- Commenting each suppressed tag. Sorting and polishing output.
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 26, context: html, text, full: html, text
- making close enough hoisting attempts on a few more fields. Cutting out sort of meaningless highest level tag
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 12, context: html, text, full: html, text
- fixing bug where composite meta objects got entered twice into tree.
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 29, context: html, text, full: html, text
- Adding hg19/ or mm9/ to file names.
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 3, 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/encode2Meta.c - lines changed 22, context: html, text, full: html, text
switch to files view, user index