Commits for kent

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

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