Commits for galt

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

• Initial checking for validateManifest. This is very early development-stage still.
  • src/hg/encode3/validateManifest/NOTES - lines changed 340, context: html, text, full: html, text
  • src/hg/encode3/validateManifest/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/encode3/validateManifest/validateManifest.c - lines changed 420, 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/README - lines changed 18, context: html, text, full: html, text
  • src/hg/encode/validateFiles/expected/bam1.out - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/validateFiles/expected/bed12ok.out - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/validateFiles/expected/bigWig1.out - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/validateFiles/expected/bigWigTruncated.out - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/validateFiles/expected/tagAlign1.out - lines changed 6, context: html, text, full: html, text
  • src/hg/encode/validateFiles/expected/tagAlign2.out - lines changed 6, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/bam1.bam - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode/validateFiles/input/bed12.as.note - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/bed12bad.txt - lines changed 69, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/bed12ok.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/bed6bad.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/bigWig1.bw - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode/validateFiles/input/bigWigTruncated.bw - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode/validateFiles/input/gnfAtlas2.bed15 - lines changed 10, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/hg18_chromInfo.txt - lines changed 49, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/hg19_chromInfo.txt - lines changed 93, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/hugechrom1.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/tagAlign1.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/validateFiles/input/tagAlign2.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/validateFiles/makefile - lines changed 34, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodFemaleHg18.gappedPeak - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodFemaleHg19.bed10 - lines changed 34, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodFemaleHg19.bed11 - lines changed 35, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodFemaleHg19.bed12 - lines changed 35, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodFemaleHg19.narrowPeak - lines changed 40, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodHg18.fasta - lines changed 50, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodHg19.csfasta - lines changed 49, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodHg19.csqual - lines changed 49, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodHg19.fastq - lines changed 100, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg18.bedGraph - lines changed 29, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg18.pairedTagAlign - lines changed 63, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg18.tagAlign - lines changed 150, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed3 - lines changed 89, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed4 - lines changed 91, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed5 - lines changed 89, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed6 - lines changed 90, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed7 - lines changed 141882, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed8 - lines changed 141883, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed9 - lines changed 141884, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bedRrbs - lines changed 141883, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak - lines changed 94, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode/validateFiles/tests/goodMaleHg19.short.bedRrbs - lines changed 2000, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMalehg19.bedRnaElements - lines changed 624500, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodNoGenderHg19.bed15 - lines changed 40, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodNoGenderHg19.bedLogR - lines changed 69, context: html, text, full: html, text
  • src/hg/encode/validateFiles/validateFiles.c - lines changed 1829, context: html, text, full: html, text
  • src/hg/encode/validateFiles/validateFilesUsage - lines changed 59, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/README - lines changed 18, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/expected/bam1.out - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/expected/bed12ok.out - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/expected/bigWig1.out - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/expected/bigWigTruncated.out - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/expected/tagAlign1.out - lines changed 6, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/expected/tagAlign2.out - lines changed 6, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/bam1.bam - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode3/validateFiles/input/bed12.as.note - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/bed12bad.txt - lines changed 69, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/bed12ok.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/bed6bad.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/bigWig1.bw - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode3/validateFiles/input/bigWigTruncated.bw - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode3/validateFiles/input/gnfAtlas2.bed15 - lines changed 10, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/hg18_chromInfo.txt - lines changed 49, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/hg19_chromInfo.txt - lines changed 93, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/hugechrom1.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/tagAlign1.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/input/tagAlign2.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/makefile - lines changed 34, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodFemaleHg18.gappedPeak - lines changed 13, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodFemaleHg19.bed10 - lines changed 34, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodFemaleHg19.bed11 - lines changed 35, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodFemaleHg19.bed12 - lines changed 35, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodFemaleHg19.narrowPeak - lines changed 40, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodHg18.fasta - lines changed 50, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodHg19.csfasta - lines changed 49, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodHg19.csqual - lines changed 49, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodHg19.fastq - lines changed 100, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg18.bedGraph - lines changed 29, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg18.pairedTagAlign - lines changed 63, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg18.tagAlign - lines changed 150, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.bed3 - lines changed 89, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.bed4 - lines changed 91, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.bed5 - lines changed 89, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.bed6 - lines changed 90, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.bed7 - lines changed 141882, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.bed8 - lines changed 141883, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.bed9 - lines changed 141884, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.bedRrbs - lines changed 141883, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.broadPeak - lines changed 94, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.broadPeak.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode3/validateFiles/tests/goodMaleHg19.short.bedRrbs - lines changed 2000, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodMalehg19.bedRnaElements - lines changed 624500, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodNoGenderHg19.bed15 - lines changed 40, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/tests/goodNoGenderHg19.bedLogR - lines changed 69, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/validateFiles.c - lines changed 1829, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/validateFilesUsage - 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/validateFiles/validateFilesUsage - lines changed 59, context: html, text, full: html, text
• adding support for hg/encode3/ to makefile system
  • src/hg/encode/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/makefile - lines changed 44, context: html, text, full: html, text
  • src/hg/makefile - lines changed 2, 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.
  • src/hg/encode3/validateFiles/validateFiles.c - lines changed 9, context: html, text, full: html, text
• type=bam is better for consistency than type=BAM
  • src/hg/encode3/validateFiles/validateFiles.c - lines changed 7, context: html, text, full: html, text
• useful comment added
  • src/hg/encode3/validateFiles/validateFiles.c - lines changed 2, context: html, text, full: html, text
• First crude attempt at defining and running validateFiles commandlines from validateManifest.
  • src/hg/encode3/validateManifest/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/validateManifest/validateManifest.c - lines changed 212, context: html, text, full: html, text