Commits for kent
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v288_preview to v288_preview2 (2013-08-07 to 2013-08-13) v288
- Seems to work.
- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 412, context: html, text, full: html, text
- src/utils/fastqStatsAndSubsample/makefile - lines changed 3, context: html, text, full: html, text
- Made it so linefile on gzipped files doesn't abort with an error message if you close it before reading it all.
- Making it write out '@' line again.
- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 11, context: html, text, full: html, text
- Adding smallOk option.
- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 31, context: html, text, full: html, text
- Seems to work. Has run on about 1/3 of ENCODE2.
- src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c - lines changed 177, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/makefile - lines changed 4, context: html, text, full: html, text
- Adding new edwMakeContaminationQa program to build.
- src/hg/encode3/encodeDataWarehouse/makefile - lines changed 1, context: html, text, full: html, text
- Making it so it only does work if it hasn't done it already.
- src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c - lines changed 66, context: html, text, full: html, text
- Seems to work. Sadly it does change line length.
- src/utils/faUniqify/faUniqify.c - lines changed 60, context: html, text, full: html, text
- src/utils/faUniqify/makefile - lines changed 3, context: html, text, full: html, text
- Main ra parsing function is generate and passes visual inspection. Haven't tried compiling it yet though.
- src/utils/raToStructGen/makefile - lines changed 3, context: html, text, full: html, text
- src/utils/raToStructGen/raToStructGen.c - lines changed 261, context: html, text, full: html, text
- Output now compiles.
- src/utils/raToStructGen/raToStructGen.c - lines changed 4, context: html, text, full: html, text
- Added basesInSample output.
- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 93, context: html, text, full: html, text
- Little fixer seems to work.
- src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/edwFixBasesInSample.c - lines changed 62, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/makefile - lines changed 4, context: html, text, full: html, text
- Improving comment.
- Removing weak attempt at fix that Mark properly fixed.
- Making raToStruct.c module compile.
- Making it generate a new function.
- src/utils/raToStructGen/raToStructGen.c - lines changed 41, context: html, text, full: html, text
- Making it work ok with /dev/null as fastq output. Fixing an integer overflow bug.
- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 32, context: html, text, full: html, text
- Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
- src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 159, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 45, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 561, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 49, context: html, text, full: html, text
- Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
- src/hg/encode3/encodeDataWarehouse/lib/edwFastqFileFromRa.c - lines changed 305, context: html, text, full: html, text
- Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
- src/hg/encode3/encodeDataWarehouse/inc/edwFastqFileFromRa.h - lines changed 15, context: html, text, full: html, text
- Adding support routines for edwFastqFiles.
- src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 12, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 58, context: html, text, full: html, text
- Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
- src/hg/encode3/encodeDataWarehouse/lib/makefile - lines changed 1, context: html, text, full: html, text
- Moving code generated .h file _before_ the compile!
- src/hg/encode3/encodeDataWarehouse/lib/redoSchema - lines changed 2, context: html, text, full: html, text
- Moving it back from hive to scratch while hive is being delicate. Adding e. coli contamination target.
- src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 6, context: html, text, full: html, text
- Allowing mm10 as a ucscDb.
- src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 3, context: html, text, full: html, text
- Making it call external fastqStatsAndSubsample program. Allowing 'unknown' format files to get license plate.
- src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 151, context: html, text, full: html, text
- Adding keepTemp command line option. Getting sample from already downsampled file in edwFastqFile table.
- src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c - lines changed 21, context: html, text, full: html, text
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