Commits for hiram

v352_preview to v352_preview2 (2017-07-03 to 2017-07-10) v352

06c77dae09aa4152ecd65ae128f222bba6e0695a Mon Jul 3 10:43:42 2017 -0700

• remove Matt email add Chris Lee and Jairo refs #19715
  • src/utils/qa/weeklybld/doNewBranch.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doNewReview.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doNewReview2.csh - lines changed 1, context: html, text, full: html, text

47a2243d25c47d9cf3ebba86d65a42075afed829 Mon Jul 3 13:32:14 2017 -0700

• remove donnak email and fix chmalee to ucsc.edu refs #19715
  • src/utils/qa/weeklybld/doNewBranch.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doNewReview.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doNewReview2.csh - lines changed 1, context: html, text, full: html, text

47205c92c3cffc5a7db8835b772e32b8717bd253 Wed Jul 5 10:31:25 2017 -0700

• now counting bits with intrinsics builtin popcnt instruction and better representation of the base bit values refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 146, context: html, text, full: html, text

ee4f9523a021f9ea6c4ba9c0695975024936a03f Wed Jul 5 10:32:00 2017 -0700

• need CFLAGS with -mpopcnt to use intrinsic builtin function refs #18969
  • src/utils/crisprKmers/makefile - lines changed 1, context: html, text, full: html, text

4068e4c5ce3d0b375d570f651539b0709adba981 Wed Jul 5 15:58:19 2017 -0700

• beginning to use a ranges specification to limit the comparisons refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 300, context: html, text, full: html, text

e20e93ca2a36c232d2fe3b2d918d03674f89d5d4 Fri Jul 7 08:56:14 2017 -0700

• the linked lists are too slow, maybe try arrays refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 234, context: html, text, full: html, text

f8b37f0a0b7ac9bbd5529692fa61b921a6a2b67f Fri Jul 7 23:57:27 2017 -0700

• check in before removing all the garbage, appears to be working with arrays much faster refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 344, context: html, text, full: html, text

458277a2bb9ff317669cd0e19e1cd1c1b29e2bff Sat Jul 8 00:41:33 2017 -0700

• removed all the garbage, see if it still works refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 341, context: html, text, full: html, text

47a02857acb0e52455455f577dbe801d9b2b0a66 Sat Jul 8 23:04:40 2017 -0700

• now recording off-target data and discovered that (a > 1) is dramatically different from (a >> 1) with no warning of course, refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 75, context: html, text, full: html, text

95a4ab24a874500faece4f5e71815b950697afb3 Mon Jul 10 00:16:59 2017 -0700

• adding some fake color to the bed output to test runtime on some larger ranges refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 82, context: html, text, full: html, text

a9ba05c24c4d3ed2806bb6be67c2295ed3531b64 Mon Jul 10 10:02:34 2017 -0700

• v352 preview2 refs #19715
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text