Commits for galt

v290_base to v291_preview (2013-09-30 to 2013-10-07) v291

• Revert "net.c: Adding read and write timeouts to the tcp open. One site was connecting but then failing to send a response and hanging indefinitely."
  This reverts commit b1daa872c111d286d607213ce0ba97d74133b9dd.
  
  Although the relatively short 10 second read/write timeout works for bigDataUrl connections,
  it does not work for robots accessing html sites that can take a long time to return a response.
  This approach was too simple. It is being reverted.
  
  • src/lib/net.c - lines changed 15, context: html, text, full: html, text
• minor improvement to preserve the timestamp when copying the executable to hgwbeta
  • src/hg/qaPushQ/makefile - lines changed 1, context: html, text, full: html, text
• making the cmpReal operator actually check for valid allowed operators, and not just being not "ignored"
  • src/hg/hgTables/filterFields.c - lines changed 1, context: html, text, full: html, text
• Adding a useful real-world example of BLAT on the negative strand.
  • src/hg/htdocs/FAQ/FAQformat.html - lines changed 27, context: html, text, full: html, text
• oops: fixing off-by-one error on target coordinates.
  • src/hg/htdocs/FAQ/FAQformat.html - lines changed 39, context: html, text, full: html, text
• trying to find reasonable limits for warning for protein and translated dnax; improving warn message; fixes #5798
  • src/hg/hgBlat/hgBlat.c - lines changed 16, context: html, text, full: html, text