angie: changes by file

branch to review (2009-12-14 to 2010-01-04) v222

• src/hg/hgTracks/bamTrack.c
  • 1.20 lines changed: 19, context: html, text, full: html, text
    For pairSearchRange, don't do two bamFetch's -- very inefficient. Just expand the search range up front.
• src/hg/makeDb/doc/danRer5.txt
  • 1.19 lines changed: 7, context: html, text, full: html, text
    LiftOver to danRer6
• src/inc/common.h
  • 1.164 lines changed: 31, context: html, text, full: html, text
    Added must{Open,Read,Write,Close}Fd and mustLseek to common.c, for operations on file descriptors. Some were already in lib/tests/pipelineTester.c - replaced those.
• src/lib/common.c
  • 1.141 lines changed: 94, context: html, text, full: html, text
    Added must{Open,Read,Write,Close}Fd and mustLseek to common.c, for operations on file descriptors. Some were already in lib/tests/pipelineTester.c - replaced those.
• src/lib/net.c
  • 1.78 lines changed: 3, context: html, text, full: html, text
    Fixed comparison edge condition (not a huge problem, it just set tv_{sec,usec} to {0,1000000} not {1,0}) and more importantly, added a missing EOF check that was allowing unexpected EOF from FTP to result in inf. loop.
• src/lib/udc.c
  • 1.31 lines changed: 145, context: html, text, full: html, text
    Changed all FILE * vars and operations (fopen etc) to integer file descriptors and 'man 2' operations (open etc), for unbuffered I/O which should make it harder for the bitmap file to get out of sync with the sparseData file when there are multiple udcFile*'s accessing the same part of a URL and those files. Unfortunately this doesn't completely prevent udcTest failures (try seed=1261180550), just reduces frequency a bit. Also added a speed optimization: to avoid heavy reconnect penalty when we need to skip a few udc blocks because they have already been cached, just read and discard those blocks' data.
• src/lib/tests/pipelineTester.c
  • 1.5 lines changed: 23, context: html, text, full: html, text
    Added must{Open,Read,Write,Close}Fd and mustLseek to common.c, for operations on file descriptors. Some were already in lib/tests/pipelineTester.c - replaced those.
• src/lib/tests/udcTest.c
  • 1.2 lines changed: 209, context: html, text, full: html, text
    Added options -fork (true concurrent access: actually gets no errors unlike the same-process/interleaved-access test!), -seed (try 1261180550 for big failure on empty cache files without -fork), and -protocol (default ftp, can do http instead, boring/no errors).