File Changes for galt

v266_preview2 to v266_base (2012-04-17 to 2012-04-24) v266

• src/hg/encode/validateFiles/expected/tagAlign1.out
  • lines changed 1, context: html, text, full: html, text
    fixing bug in BAM validator, needed if (errs > ), added the old Error Count 0 back to the end of succesful runs, at least for nonBED, fixed make test to actually do something
• src/hg/encode/validateFiles/expected/tagAlign2.out
  • lines changed 1, context: html, text, full: html, text
    fixing bug in BAM validator, needed if (errs > ), added the old Error Count 0 back to the end of succesful runs, at least for nonBED, fixed make test to actually do something
• src/hg/encode/validateFiles/input/bed12.as
  • lines changed 17, context: html, text, full: html, text
    no nags
• src/hg/encode/validateFiles/input/bed12.as.note
  • lines changed 2, context: html, text, full: html, text
    no nags
• src/hg/encode/validateFiles/makefile
  • lines changed 12, context: html, text, full: html, text
    fixing bug in BAM validator, needed if (errs > ), added the old Error Count 0 back to the end of succesful runs, at least for nonBED, fixed make test to actually do something
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 2, context: html, text, full: html, text
    fixing bug in BAM validator, needed if (errs > ), added the old Error Count 0 back to the end of succesful runs, at least for nonBED, fixed make test to actually do something
  • lines changed 8, context: html, text, full: html, text
    improving the help msg for vf b2bb hglb
  • lines changed 53, context: html, text, full: html, text
    fixed long lines per jims review; also removed odd condition on start/end coords
  • lines changed 2, context: html, text, full: html, text
    fix comment location
• src/hg/lib/customFactory.c
  • lines changed 2, context: html, text, full: html, text
    simple optimization suggested by jim
• src/hg/lib/fullBed.as
  • lines changed 1, context: html, text, full: html, text
    keeping .as score as uint for many reasons. stuck with int for bed struct still in support of old CTs
• src/hg/lib/fullBed.sql
  • lines changed 1, context: html, text, full: html, text
    keeping .as score as uint for many reasons. stuck with int for bed struct still in support of old CTs
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 7, context: html, text, full: html, text
    improving the help msg for vf b2bb hglb
• src/inc/basicBed.h
  • lines changed 1, context: html, text, full: html, text
    keeping .as score as uint for many reasons. stuck with int for bed struct still in support of old CTs
• src/inc/linefile.h
  • lines changed 6, context: html, text, full: html, text
    remove -lm dependency on linefile; also enables others to use callback methods to support other types
• src/lib/basicBed.c
  • lines changed 1, context: html, text, full: html, text
    keeping .as score as uint for many reasons. stuck with int for bed struct still in support of old CTs
• src/lib/lineFileOnBigBed.c
  • lines changed 110, context: html, text, full: html, text
    remove -lm dependency on linefile; also enables others to use callback methods to support other types
  • lines changed 1, context: html, text, full: html, text
    a little cleanup is nice
• src/lib/linefile.c
  • lines changed 79, context: html, text, full: html, text
    remove -lm dependency on linefile; also enables others to use callback methods to support other types
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    remove -lm dependency on linefile; also enables others to use callback methods to support other types
• src/utils/asCompare/asCompare.c
  • lines changed 1, context: html, text, full: html, text
    fixing header
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 6, context: html, text, full: html, text
    improving the help msg for vf b2bb hglb
• src/utils/git-reports/git-reports.c
  • lines changed 2, context: html, text, full: html, text
    fixing problem between htmlEncoding and wanting to preserve newlines in comments