All File Changes

v281_preview to v281_preview2 (2013-03-12 to 2013-03-19) v281

• src/hg/encode/makefile
  • lines changed 2, context: html, text, full: html, text
    adding support for hg/encode3/ to makefile system
• src/hg/encode/validateFiles/README
  • lines changed 18, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/expected/bam1.out
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/expected/bed12ok.out
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/expected/bigWig1.out
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/expected/bigWigTruncated.out
  • lines changed 2, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/expected/tagAlign1.out
  • lines changed 6, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/expected/tagAlign2.out
  • lines changed 6, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/bam1.bam
  • lines changed 0, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/bed12.as.note
  • lines changed 2, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/bed12bad.txt
  • lines changed 69, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/bed12ok.txt
  • lines changed 10, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/bed6bad.txt
  • lines changed 15, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/bigWig1.bw
  • lines changed 0, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/bigWigTruncated.bw
  • lines changed 0, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/gnfAtlas2.bed15
  • lines changed 10, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/hg18_chromInfo.txt
  • lines changed 49, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/hg19_chromInfo.txt
  • lines changed 93, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/hugechrom1.txt
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/tagAlign1.txt
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/input/tagAlign2.txt
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/makefile
  • lines changed 34, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodFemaleHg18.gappedPeak
  • lines changed 13, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodFemaleHg19.bed10
  • lines changed 34, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodFemaleHg19.bed11
  • lines changed 35, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodFemaleHg19.bed12
  • lines changed 35, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodFemaleHg19.narrowPeak
  • lines changed 40, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodHg18.fasta
  • lines changed 50, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodHg19.csfasta
  • lines changed 49, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodHg19.csqual
  • lines changed 49, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodHg19.fastq
  • lines changed 100, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg18.bedGraph
  • lines changed 29, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg18.pairedTagAlign
  • lines changed 63, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg18.tagAlign
  • lines changed 150, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed3
  • lines changed 89, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed4
  • lines changed 91, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed5
  • lines changed 89, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed6
  • lines changed 90, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed7
  • lines changed 141882, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed8
  • lines changed 141883, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed9
  • lines changed 141884, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.bedRrbs
  • lines changed 141883, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak
  • lines changed 94, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak.gz
  • lines changed 0, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMaleHg19.short.bedRrbs
  • lines changed 2000, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodMalehg19.bedRnaElements
  • lines changed 624500, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodNoGenderHg19.bed15
  • lines changed 40, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/tests/goodNoGenderHg19.bedLogR
  • lines changed 69, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 1829, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode/validateFiles/validateFilesUsage
  • lines changed 59, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/importEncode2/encode2ExpDumpFlat/encode2ExpDumpFlat.c
  • lines changed 170, context: html, text, full: html, text
    Writing utility to query an encode2 relationalized database to make a flattened version of experiment file, easier for human reading.
• src/hg/encode3/importEncode2/encode2ExpDumpFlat/makefile
  • lines changed 18, context: html, text, full: html, text
    Writing utility to query an encode2 relationalized database to make a flattened version of experiment file, easier for human reading.
• src/hg/encode3/importEncode2/encodeExpToCvDb/encodeExpToCvDb.c
  • lines changed 506, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/encode3/importEncode2/encodeExpToCvDb/experiment.sql
  • lines changed 36, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/encode3/importEncode2/encodeExpToCvDb/go
  • lines changed 5, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/encode3/importEncode2/encodeExpToCvDb/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
  • lines changed 2, context: html, text, full: html, text
    Adjusting paths in makefile after move of directory.
• src/hg/encode3/importEncode2/encodeExpToCvDb/result.sql
  • lines changed 13, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/encode3/importEncode2/encodeExpToCvDb/series.sql
  • lines changed 8, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/encode3/importEncode2/testCvToSql/README
  • lines changed 2, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/encode3/importEncode2/testCvToSql/makefile
  • lines changed 18, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/encode3/importEncode2/testCvToSql/splitAntibody.ra
  • lines changed 7, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/encode3/importEncode2/testCvToSql/splitAntibody.sql
  • lines changed 34, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/encode3/importEncode2/testCvToSql/splitAntibodyModel.py
  • lines changed 49, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/encode3/importEncode2/testCvToSql/testCvToSql.c
  • lines changed 967, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/encode3/importEncode2/testCvToSql/tryIt
  • lines changed 37, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/encode3/makefile
  • lines changed 44, context: html, text, full: html, text
    adding support for hg/encode3/ to makefile system
• src/hg/encode3/validateFiles/README
  • lines changed 18, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/expected/bam1.out
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/expected/bed12ok.out
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/expected/bigWig1.out
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/expected/bigWigTruncated.out
  • lines changed 2, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/expected/tagAlign1.out
  • lines changed 6, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/expected/tagAlign2.out
  • lines changed 6, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/bam1.bam
  • lines changed 0, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/bed12.as.note
  • lines changed 2, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/bed12bad.txt
  • lines changed 69, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/bed12ok.txt
  • lines changed 10, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/bed6bad.txt
  • lines changed 15, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/bigWig1.bw
  • lines changed 0, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/bigWigTruncated.bw
  • lines changed 0, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/gnfAtlas2.bed15
  • lines changed 10, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/hg18_chromInfo.txt
  • lines changed 49, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/hg19_chromInfo.txt
  • lines changed 93, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/hugechrom1.txt
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/tagAlign1.txt
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/input/tagAlign2.txt
  • lines changed 1, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/makefile
  • lines changed 34, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodFemaleHg18.gappedPeak
  • lines changed 13, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodFemaleHg19.bed10
  • lines changed 34, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodFemaleHg19.bed11
  • lines changed 35, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodFemaleHg19.bed12
  • lines changed 35, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodFemaleHg19.narrowPeak
  • lines changed 40, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodHg18.fasta
  • lines changed 50, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodHg19.csfasta
  • lines changed 49, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodHg19.csqual
  • lines changed 49, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodHg19.fastq
  • lines changed 100, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg18.bedGraph
  • lines changed 29, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg18.pairedTagAlign
  • lines changed 63, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg18.tagAlign
  • lines changed 150, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed3
  • lines changed 89, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed4
  • lines changed 91, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed5
  • lines changed 89, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed6
  • lines changed 90, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed7
  • lines changed 141882, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed8
  • lines changed 141883, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed9
  • lines changed 141884, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bedRrbs
  • lines changed 141883, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.broadPeak
  • lines changed 94, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.broadPeak.gz
  • lines changed 0, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.short.bedRrbs
  • lines changed 2000, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodMalehg19.bedRnaElements
  • lines changed 624500, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodNoGenderHg19.bed15
  • lines changed 40, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/tests/goodNoGenderHg19.bedLogR
  • lines changed 69, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
• src/hg/encode3/validateFiles/validateFiles.c
  • lines changed 1829, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
  • lines changed 9, context: html, text, full: html, text
    Since we are trying to abort on the first error, no need for the -showBadAlign option since it should always show it.
  • lines changed 7, context: html, text, full: html, text
    type=bam is better for consistency than type=BAM
  • lines changed 2, context: html, text, full: html, text
    useful comment added
• src/hg/encode3/validateFiles/validateFilesUsage
  • lines changed 59, context: html, text, full: html, text
    Moved validateFiles from hg/encode/ to hg/encode3/ for further use in the new ENCODE3 system. Git will retain all history since the git mv command was used.
  • lines changed 59, context: html, text, full: html, text
    This temp file is no longer needed and is out of date anyway!
• src/hg/encode3/validateManifest/NOTES
  • lines changed 340, context: html, text, full: html, text
    Initial checking for validateManifest. This is very early development-stage still.
• src/hg/encode3/validateManifest/makefile
  • lines changed 19, context: html, text, full: html, text
    Initial checking for validateManifest. This is very early development-stage still.
  • lines changed 4, context: html, text, full: html, text
    First crude attempt at defining and running validateFiles commandlines from validateManifest.
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 420, context: html, text, full: html, text
    Initial checking for validateManifest. This is very early development-stage still.
  • lines changed 212, context: html, text, full: html, text
    First crude attempt at defining and running validateFiles commandlines from validateManifest.
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    Fixing bug reported via MLQ: When repeatedly adding/modifying customtracks and saving sessions without any cartResets or session loads,
    the same ctfile was used in both saved sessions and the user's active
    cart, so modifications after saving a session were leaking back to
    saved sessions. Fix: copy custom tracks not only when loading a
    saved session, but also immediately after saving a session, so that
    the user's active cart no longer has the same ctfile (and customTrash
    database tables, etc) as the saved session.
    fixes #10396, refs #10323
    
• src/hg/htdocs/ENCODE/contacts.html
  • lines changed 15, context: html, text, full: html, text
    Updating ENCODE/contacts.html to point to Stanford for upcoming ENCODE questions, ref #9288
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    added missing denisova announcement. refs #10368
  • lines changed 1, context: html, text, full: html, text
    removed extra '-' in denisova announcement. refs #10368
• src/hg/inc/cart.h
  • lines changed 4, context: html, text, full: html, text
    Fixing bug reported via MLQ: When repeatedly adding/modifying customtracks and saving sessions without any cartResets or session loads,
    the same ctfile was used in both saved sessions and the user's active
    cart, so modifications after saving a session were leaking back to
    saved sessions. Fix: copy custom tracks not only when loading a
    saved session, but also immediately after saving a session, so that
    the user's active cart no longer has the same ctfile (and customTrash
    database tables, etc) as the saved session.
    fixes #10396, refs #10323
    
• src/hg/lib/cart.c
  • lines changed 14, context: html, text, full: html, text
    Fixing bug reported via MLQ: When repeatedly adding/modifying customtracks and saving sessions without any cartResets or session loads,
    the same ctfile was used in both saved sessions and the user's active
    cart, so modifications after saving a session were leaking back to
    saved sessions. Fix: copy custom tracks not only when loading a
    saved session, but also immediately after saving a session, so that
    the user's active cart no longer has the same ctfile (and customTrash
    database tables, etc) as the saved session.
    fixes #10396, refs #10323
    
  • lines changed 28, context: html, text, full: html, text
    if loading a session, don't copy the custom tracks till after the assembly hubs have been loaded since the cart variable for the custom tracks as the database name in it. ref #10396
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    Trivial addition of support for HGVS position range nomenclature,which has "_" between start and end (instead of "-"). refs #10392
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added panPan1.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    add panPan1.lift = no for panPan1
  • lines changed 1, context: html, text, full: html, text
    adding panPan1.genbank.mrna.native.pslCDnaFilter
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added panPan1.
• src/hg/makeDb/genbank/src/dbload/gbMDParse.c
  • lines changed 6, context: html, text, full: html, text
    ignore join() operators in misc_differences field in genbank records
• src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
  • lines changed 1, context: html, text, full: html, text
    fix compiler warning about safef
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Adjusted the minCheck threshold for .jaxAlleleInfo.name and .jaxAllele.name from 0.9 to 0.89 which fixed two mm9 joinerCheck errors
  • lines changed 1, context: html, text, full: html, text
    Adjusted the minCheck threshold of hg19.wgEncodeGencodeAttrsV11.transcriptId from 0.30 to 0.29 which fixed an hg19 joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted the minCheck threshold of hg19.wgEncodeGencodeAttrsV12.transcriptId from 0.30 to 0.29 which fixed an hg19 joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted the minCheck threshold of hg19.wgEncodeGencodeAttrsV14.transcriptId from 0.185827 to 0.18 which fixed an hg19 joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted the minCheck threshold of .gad.name from 0.95 to 0.94 which fixed an hg19 joinerCheck error
• src/hg/makeDb/trackDb/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/human/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/human/hg13/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/human/hg15/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/mouse/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/mouse/mm4/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/zebrafish/danRer1/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/zebrafish/danRer1/bacEndSingles.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/zebrafish/danRer2/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/zebrafish/danRer2/bacEndSingles.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndSingles.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndSingles.html
  • lines changed 2, context: html, text, full: html, text
    Added missing semicolon after quote html code, fixed broken link
• src/hg/makefile
  • lines changed 2, context: html, text, full: html, text
    adding support for hg/encode3/ to makefile system
• src/hg/oneShot/encodeExpToCvDb/encodeExpToCvDb.c
  • lines changed 9, context: html, text, full: html, text
    Untangling antibody/control conflation a bit.
  • lines changed 506, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/oneShot/encodeExpToCvDb/experiment.sql
  • lines changed 36, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/oneShot/encodeExpToCvDb/go
  • lines changed 5, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/oneShot/encodeExpToCvDb/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/oneShot/encodeExpToCvDb/result.sql
  • lines changed 13, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/oneShot/encodeExpToCvDb/series.sql
  • lines changed 8, context: html, text, full: html, text
    Starting to move around encode2->encode3 code to a more logical place.
• src/hg/oneShot/testCvToSql/README
  • lines changed 2, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/oneShot/testCvToSql/splitAntibody.ra
  • lines changed 7, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/oneShot/testCvToSql/splitAntibody.sql
  • lines changed 34, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/oneShot/testCvToSql/splitAntibodyModel.py
  • lines changed 49, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/oneShot/testCvToSql/testCvToSql.c
  • lines changed 1, context: html, text, full: html, text
    There's a new targetClass field.
  • lines changed 967, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/oneShot/testCvToSql/tryIt
  • lines changed 37, context: html, text, full: html, text
    Moving more of encode2->3 migration code out of oneShot.
• src/hg/utils/phyloTrees/80way.commonNames.nh
  • lines changed 80, context: html, text, full: html, text
    moving toward 100 definitions refs #10272
• src/hg/utils/phyloTrees/80way.nh
  • lines changed 80, context: html, text, full: html, text
    moving toward 100 definitions refs #10272
• src/hg/utils/phyloTrees/90way.commonNames.nh
  • lines changed 90, context: html, text, full: html, text
    at 90 species refs #10272
• src/hg/utils/phyloTrees/90way.nh
  • lines changed 90, context: html, text, full: html, text
    at 90 species refs #10272
• src/hg/utils/phyloTrees/96way.commonNames.nh
  • lines changed 96, context: html, text, full: html, text
    up to date with known available assemblies refs #10272
• src/hg/utils/phyloTrees/96way.nh
  • lines changed 96, context: html, text, full: html, text
    up to date with known available assemblies refs #10272
• src/hg/utils/phyloTrees/96way.scientificNames.nh
  • lines changed 96, context: html, text, full: html, text
    adding scientific name tree refs #10272
• src/hg/utils/phyloTrees/asciiTree.pl
  • lines changed 47, context: html, text, full: html, text
    moving toward 100 definitions refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 114, context: html, text, full: html, text
    moving toward 100 definitions refs #10272
  • lines changed 20, context: html, text, full: html, text
    at 90 species refs #10272
  • lines changed 7, context: html, text, full: html, text
    adding scientific name tree refs #10272
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 15, context: html, text, full: html, text
    moving toward 100 definitions refs #10272
  • lines changed 27, context: html, text, full: html, text
    adding scientific name tree refs #10272
• src/hg/utils/phyloTrees/primates.txt
  • lines changed 3, context: html, text, full: html, text
    adding scientific name tree refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 72, context: html, text, full: html, text
    adding scientific name tree refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 23, context: html, text, full: html, text
    moving toward 100 definitions refs #10272
  • lines changed 11, context: html, text, full: html, text
    adding scientific name tree refs #10272
• src/inc/bbiFile.h
  • lines changed 8, context: html, text, full: html, text
    Fixing a bug where sometimes zoom summaries would not be written out by bedGraphToBigWig. I'm seeing a lot of code that can be shared between bedGraphToBigWig and bedToBigBed. Refactored to share some now, will do more shortly.
  • lines changed 32, context: html, text, full: html, text
    Making bedToBigBed and bedGraphToBigWig share more code. Cure is only half as bad as disease (trading sharing 64 lines for having a function with 16 parameters.)
• src/lib/bbiWrite.c
  • lines changed 29, context: html, text, full: html, text
    Fixing a bug where sometimes zoom summaries would not be written out by bedGraphToBigWig. I'm seeing a lot of code that can be shared between bedGraphToBigWig and bedToBigBed. Refactored to share some now, will do more shortly.
  • lines changed 87, context: html, text, full: html, text
    Making bedToBigBed and bedGraphToBigWig share more code. Cure is only half as bad as disease (trading sharing 64 lines for having a function with 16 parameters.)
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 31, context: html, text, full: html, text
    Fixing a bug where sometimes zoom summaries would not be written out by bedGraphToBigWig. I'm seeing a lot of code that can be shared between bedGraphToBigWig and bedToBigBed. Refactored to share some now, will do more shortly.
  • lines changed 69, context: html, text, full: html, text
    Making bedToBigBed and bedGraphToBigWig share more code. Cure is only half as bad as disease (trading sharing 64 lines for having a function with 16 parameters.)
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 40, context: html, text, full: html, text
    Fixing a bug where sometimes zoom summaries would not be written out by bedGraphToBigWig. I'm seeing a lot of code that can be shared between bedGraphToBigWig and bedToBigBed. Refactored to share some now, will do more shortly.
  • lines changed 71, context: html, text, full: html, text
    Making bedToBigBed and bedGraphToBigWig share more code. Cure is only half as bad as disease (trading sharing 64 lines for having a function with 16 parameters.)
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v281 preview2

• lines changed: 2401084
• files changed: 199