Commits for kent

v291_base to v292_preview (2013-10-21 to 2013-10-28) v292

• Making blat top out at 75k instead of 25k reads.
  • src/hg/hgBlat/hgBlat.c - lines changed 1, context: html, text, full: html, text
• Making it keep chromosome 1, and be much less likely to pick a non-aligning read for the sample.
  • src/hg/encode3/encPipe/sampleBam/sampleBam.c - lines changed 7, context: html, text, full: html, text
• Updating production executable location.
  • src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/makk - lines changed 1, context: html, text, full: html, text
• Updating production executable location.
  • src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/makk - lines changed 1, context: html, text, full: html, text
• Removing special treatment of replicate named 'both'
  • src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c - lines changed 1, context: html, text, full: html, text
• Updating production executable location.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/makk - lines changed 1, context: html, text, full: html, text
• Removing special treatment of replicate named 'both'
  • src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c - lines changed 3, context: html, text, full: html, text
• Adding lineFileNextRealWithSize.
  • src/inc/linefile.h - lines changed 4, context: html, text, full: html, text
  • src/lib/linefile.c - lines changed 10, context: html, text, full: html, text
• Making this tolerate new lines in fastq files between stanzas.
  • src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 3, context: html, text, full: html, text