File Changes for kent

v312_preview to v312_preview2 (2015-02-02 to 2015-02-09) v312

• src/hg/cirm/cdw/cdwFakeManifestFromSubmit/cdwFakeManifestFromSubmit.c
  • lines changed 2, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 1, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c
  • lines changed 1, context: html, text, full: html, text
    Fixed edwSamPairedEndStats/cdwSamPairedEndStats mixup.
    
• src/hg/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c
  • lines changed 1, context: html, text, full: html, text
    Fixed cdwSamRepeatAnalysis/edwSamRepeatAnalysis mixup.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 9, context: html, text, full: html, text
    Filling in cdwSubmit.fileCount field in database.
    
  • lines changed 32, context: html, text, full: html, text
    Adding validations for vcf and pdf files.
    
• src/hg/cirm/cdw/cdwQuery/cdwQuery.c
  • lines changed 158, context: html, text, full: html, text
    SQL-like query for files matching tags seems to work.
    
• src/hg/cirm/cdw/cdwQuery/makefile
  • lines changed 4, context: html, text, full: html, text
    SQL-like query for files matching tags seems to work.
    
• src/hg/cirm/cdw/cdwRunDaemon/cdwRunDaemon.c
  • lines changed 20, context: html, text, full: html, text
    Sanitizing stderr a bit before putting it into database with SQL.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 17, context: html, text, full: html, text
    A small step in adapting to submissions being on local file system.
    
  • lines changed 245, context: html, text, full: html, text
    It compiles but still is very much in development, not working.
    
  • lines changed 379, context: html, text, full: html, text
    Getting a bit closer to working.
    
  • lines changed 48, context: html, text, full: html, text
    Actually storing manifest and metadata files.
    
  • lines changed 4, context: html, text, full: html, text
    Filling in cdwSubmit.fileCount field in database.
    
  • lines changed 22, context: html, text, full: html, text
    Saving userId in cdwFile table.
    
  • lines changed 48, context: html, text, full: html, text
    Adding option to get md5 sums from a precomputed file. Also will take md5 sum from database if it is there and file name, size, and update time match. Adding support for .pdf and .vcf files.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 3, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 5, context: html, text, full: html, text
    Adding userId to file record and swapping submitFileId for manifestFileId and metaFileId in submit record.
    
  • lines changed 2, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 3, context: html, text, full: html, text
    Adding a PDF file recognizer/minimal validator.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 1, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 3, context: html, text, full: html, text
    Adding userId to file record and swapping submitFileId for manifestFileId and metaFileId in submit record.
    
  • lines changed 1, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 7, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 66, context: html, text, full: html, text
    Adding userId to file record and swapping submitFileId for manifestFileId and metaFileId in submit record.
    
  • lines changed 45, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 3, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 6, context: html, text, full: html, text
    Adding userId to file record and swapping submitFileId for manifestFileId and metaFileId in submit record.
    
  • lines changed 1, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 6, context: html, text, full: html, text
    Changing technicalReplicate to part, since that's how it's used.
    
  • lines changed 4, context: html, text, full: html, text
    Removing validKey from cdwValidFile
    
  • lines changed 2, context: html, text, full: html, text
    Changing experiment column to meta and fixing edwBamStats name typo.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 7, context: html, text, full: html, text
    Adding a PDF file recognizer/minimal validator.
    
• src/hg/cirm/quakeLab/djangoModels/take3/models.as
  • lines changed 99, context: html, text, full: html, text
    New version of django models from quake lab.
    
• src/hg/cirm/quakeLab/djangoModels/take3/models.py
  • lines changed 148, context: html, text, full: html, text
    New version of django models from quake lab.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/makefile
  • lines changed 4, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/models.as
  • lines changed 51, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
  • lines changed 1, context: html, text, full: html, text
    Adding meta output.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/models.c
  • lines changed 594, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
  • lines changed 6, context: html, text, full: html, text
    Adding meta output.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/models.h
  • lines changed 201, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
  • lines changed 1, context: html, text, full: html, text
    Defining unknown2 as something real.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/quakeFakeMouseManifest.c
  • lines changed 149, context: html, text, full: html, text
    Looks like this will fake manifest for the mouse experiments from the quake lab pilot data.
    
  • lines changed 41, context: html, text, full: html, text
    Adding meta output.
    
  • lines changed 15, context: html, text, full: html, text
    Changing some uglyfs to verboses. Making a missing SampleSheet a logged error rather than an aborting error.
    
• src/hg/oneShot/freen/freen.c
  • lines changed 39, context: html, text, full: html, text
    Freen generates a big sample metadata file
    
• src/inc/meta.h
  • lines changed 4, context: html, text, full: html, text
    Adding maxDepth parameter to metaWriteAll.
    
  • lines changed 2, context: html, text, full: html, text
    Adding note that this line of development is moving to tagStorm.
    
• src/inc/ra.h
  • lines changed 13, context: html, text, full: html, text
    Implementing a raNextTagValWithIndent function.
    
  • lines changed 4, context: html, text, full: html, text
    Removing INLINE from raNextTagVal since it was causeing compile problems.
    
• src/inc/tagStorm.h
  • lines changed 68, context: html, text, full: html, text
    Streamlining interface and moving tagStorm code to src/lib.
    
  • lines changed 9, context: html, text, full: html, text
    Adding flattened ra output and reworking standard write a bit.
    
  • lines changed 20, context: html, text, full: html, text
    Adding routines that allow you to build up a tagStorm in memory.
    
  • lines changed 5, context: html, text, full: html, text
    Adding tagStormUniqueIndex.
    
  • lines changed 25, context: html, text, full: html, text
    Adding stuff for finding tags within a stanza.
    
  • lines changed 5, context: html, text, full: html, text
    Adding new method to add stanza that puts it at end of existing stanzas rather than at beginning.
    
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    Removing stray blank line.
    
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Streamlining interface and moving tagStorm code to src/lib.
    
• src/lib/meta.c
  • lines changed 11, context: html, text, full: html, text
    Adding maxDepth parameter to metaWriteAll.
    
  • lines changed 2, context: html, text, full: html, text
    Adding note that this line of development is moving to tagStorm.
    
• src/lib/ra.c
  • lines changed 25, context: html, text, full: html, text
    Implementing a raNextTagValWithIndent function.
    
  • lines changed 11, context: html, text, full: html, text
    Removing INLINE from raNextTagVal since it was causeing compile problems.
    
• src/lib/tagStorm.c
  • lines changed 245, context: html, text, full: html, text
    Streamlining interface and moving tagStorm code to src/lib.
    
  • lines changed 65, context: html, text, full: html, text
    Adding flattened ra output and reworking standard write a bit.
    
  • lines changed 105, context: html, text, full: html, text
    Adding tagStormWriteAsFlatTab
    
  • lines changed 1, context: html, text, full: html, text
    Removing some debugging code.
    
  • lines changed 56, context: html, text, full: html, text
    Adding routines that allow you to build up a tagStorm in memory.
    
  • lines changed 22, context: html, text, full: html, text
    Adding tagStormUniqueIndex.
    
  • lines changed 33, context: html, text, full: html, text
    Adding stuff for finding tags within a stanza.
    
  • lines changed 20, context: html, text, full: html, text
    Adding new method to add stanza that puts it at end of existing stanzas rather than at beginning.
    
• src/lib/vcf.c
  • lines changed 53, context: html, text, full: html, text
    Making it so that there can be warning messages as well as errors for VCF files. Changing message 'missing ##fileformat= header line? Assuming 4.1.' to a warning and indeed making it assume 4.1. Also having a missing #CHROM POS type header also just a warning.
    
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding tagStorm dir to compile targets.
    
• src/meta/metaFlatten/metaFlatten.c
  • lines changed 1, context: html, text, full: html, text
    Adding maxDepth parameter to metaWriteAll. Adding depth command line option to metaReformat which uses this.
    
• src/meta/metaHoist/metaHoist.c
  • lines changed 1, context: html, text, full: html, text
    Adding maxDepth parameter to metaWriteAll. Adding depth command line option to metaReformat which uses this.
    
• src/meta/metaReformat/metaReformat.c
  • lines changed 5, context: html, text, full: html, text
    Adding maxDepth parameter to metaWriteAll. Adding depth command line option to metaReformat which uses this.
    
• src/oneShot/testTagStorm/makefile
  • lines changed 3, context: html, text, full: html, text
    New variant of meta tags starting to work.
    
  • lines changed 3, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
• src/oneShot/testTagStorm/testTagStorm.c
  • lines changed 262, context: html, text, full: html, text
    New variant of meta tags starting to work.
    
  • lines changed 209, context: html, text, full: html, text
    Streamlining interface and moving tagStorm code to src/lib.
    
  • lines changed 23, context: html, text, full: html, text
    Adding flattened ra output and reworking standard write a bit.
    
  • lines changed 7, context: html, text, full: html, text
    Adding tagStormWriteAsFlatTab
    
  • lines changed 81, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
• src/tagStorm/makefile
  • lines changed 18, context: html, text, full: html, text
    Adopting metaHoist to tagStorm.
    
• src/tagStorm/tagStormFromTab/makefile
  • lines changed 3, context: html, text, full: html, text
    A few parts working, but the whole is not.
    
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
  • lines changed 283, context: html, text, full: html, text
    A few parts working, but the whole is not.
    
  • lines changed 60, context: html, text, full: html, text
    Refactoring, and creating a yet unused function.
    
  • lines changed 23, context: html, text, full: html, text
    Refactoring so it fills in metadata stanza from parting fields info rather than table.
    
  • lines changed 31, context: html, text, full: html, text
    Doing the recursive bits. It still needs to do leaf output.
    
  • lines changed 11, context: html, text, full: html, text
    Adding leaves.
    
• src/tagStorm/tagStormHoist/makefile
  • lines changed 3, context: html, text, full: html, text
    Adopting metaHoist to tagStorm.
    
• src/tagStorm/tagStormHoist/tagStormHoist.c
  • lines changed 143, context: html, text, full: html, text
    Adopting metaHoist to tagStorm.
    
  • lines changed 1, context: html, text, full: html, text
    Renaming tagStormAddTag to tagStormUpdate tag.
    
• src/tagStorm/tagStormInfo/makefile
  • lines changed 3, context: html, text, full: html, text
    Utility to look for info about a tag storm seems to work.
    
• src/tagStorm/tagStormInfo/tagStormInfo.c
  • lines changed 101, context: html, text, full: html, text
    Utility to look for info about a tag storm seems to work.
    
  • lines changed 8, context: html, text, full: html, text
    Making the names output default rather than an option.
    
• src/tagStorm/tagStormInfo/test.in
  • lines changed 146, context: html, text, full: html, text
    Utility to look for info about a tag storm seems to work.
    
• src/tagStorm/tagStormJoinTab/expected.tags
  • lines changed 942, context: html, text, full: html, text
    Tag storm to tab-sep joiner seems to work.
    
• src/tagStorm/tagStormJoinTab/makefile
  • lines changed 3, context: html, text, full: html, text
    Tag storm to tab-sep joiner seems to work.
    
• src/tagStorm/tagStormJoinTab/tagStormJoinTab.c
  • lines changed 79, context: html, text, full: html, text
    Tag storm to tab-sep joiner seems to work.
    
• src/tagStorm/tagStormJoinTab/test.tab
  • lines changed 155, context: html, text, full: html, text
    Tag storm to tab-sep joiner seems to work.
    
• src/tagStorm/tagStormJoinTab/test.tags
  • lines changed 122, context: html, text, full: html, text
    Tag storm to tab-sep joiner seems to work.
    
• src/tagStorm/tagStormQuery/makefile
  • lines changed 3, context: html, text, full: html, text
    Tag storm file sql-like query utility seems to work.
    
• src/tagStorm/tagStormQuery/tagStormQuery.c
  • lines changed 98, context: html, text, full: html, text
    Tag storm file sql-like query utility seems to work.
    
• src/tagStorm/tagStormQuery/test.tags
  • lines changed 122, context: html, text, full: html, text
    Tag storm file sql-like query utility seems to work.
    
• src/tagStorm/tagStormReformat/expected.files
  • lines changed 25, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
• src/tagStorm/tagStormReformat/expected.ra
  • lines changed 494, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
• src/tagStorm/tagStormReformat/expected.tab
  • lines changed 35, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
• src/tagStorm/tagStormReformat/makefile
  • lines changed 14, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
• src/tagStorm/tagStormReformat/tagStormReformat.c
  • lines changed 81, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
  • lines changed 18, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
  • lines changed 1, context: html, text, full: html, text
    Adding flatten option to usage message.
    
• src/tagStorm/tagStormReformat/test.in
  • lines changed 146, context: html, text, full: html, text
    Moving tagStorm test scaffold to regular directory and polishing into a reformat utility.
    
• src/utils/paraMd5/makefile
  • lines changed 3, context: html, text, full: html, text
    Utility for multithreaded md5 calculation seems to work.
    
• src/utils/paraMd5/paraMd5.c
  • lines changed 74, context: html, text, full: html, text
    Utility for multithreaded md5 calculation seems to work.
    
  • lines changed 3, context: html, text, full: html, text
    Improving name of subroutine.