Commits for hiram

v352_preview2 to v352_base (2017-07-10 to 2017-07-17) v352

ed0bf66804ab170c0eab944e32bf970257a9a609 Tue Jul 11 09:59:33 2017 -0700

• add crispr track generation procedure refs #19514
  • src/hg/makeDb/doc/criGri1.txt - lines changed 27, context: html, text, full: html, text

b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700

• adding truncate option and tests to verify everything works refs #19514
  • src/utils/bedClip/bedClip.c - lines changed 34, context: html, text, full: html, text
  • src/utils/bedClip/tests/badEnd.result - lines changed 5, context: html, text, full: html, text
  • src/utils/bedClip/tests/badEndExample.bed.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/utils/bedClip/tests/badName.result - lines changed 7, context: html, text, full: html, text
  • src/utils/bedClip/tests/badNameExample.bed.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/utils/bedClip/tests/badStart.result - lines changed 10, context: html, text, full: html, text
  • src/utils/bedClip/tests/badStartExample.bed.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/utils/bedClip/tests/ce6.chrom.sizes - lines changed 7, context: html, text, full: html, text
  • src/utils/bedClip/tests/clip.result - lines changed 10, context: html, text, full: html, text
  • src/utils/bedClip/tests/clipExample.bed.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/utils/bedClip/tests/makefile - lines changed 22, context: html, text, full: html, text
  • src/utils/bedClip/tests/truncate.result - lines changed 12, context: html, text, full: html, text
  • src/utils/bedClip/tests/twoFields.result - lines changed 5, context: html, text, full: html, text
  • src/utils/bedClip/tests/twoFieldsExample.bed.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

b2bdbec05767ec56a8a070a546959c3da514b354 Tue Jul 11 14:45:02 2017 -0700

• use bedClip binary from PATH refs #19514
  • src/utils/bedClip/tests/makefile - lines changed 1, context: html, text, full: html, text

4a9f5caa2ea145d8ef8d86b6d4abb9a5d70bc345 Tue Jul 11 14:54:48 2017 -0700

• adding score calculation and second PAM sequence refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 108, context: html, text, full: html, text

e37af94374417fa6f35f3b8a9a9629226905610a Tue Jul 11 15:31:54 2017 -0700

• would like to have vmPeak value to decide on memory usage refs #18969
  • src/inc/obscure.h - lines changed 3, context: html, text, full: html, text
  • src/lib/obscure.c - lines changed 30, context: html, text, full: html, text

a6402cd35ac18b36a7d4ee1a6e41df145a519e98 Tue Jul 11 16:03:50 2017 -0700

• prepare to thread this process refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 62, context: html, text, full: html, text

12e32063d966167f47e6236fc70d88e9900246cb Wed Jul 12 10:21:22 2017 -0700

• add cpg islands build procedures refs #19777
  • src/hg/makeDb/doc/oryCun2.txt - lines changed 26, context: html, text, full: html, text

feb770798e0b4ad51ec5b7fc1a82fd1363a66ba1 Wed Jul 12 11:51:53 2017 -0700

• adding threading and eliminate strand char storage, now does not work correctly refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 310, context: html, text, full: html, text

d75dbdc035385f4122259f47091fc09c06ad16c2 Thu Jul 13 11:29:41 2017 -0700

• appears to work OK with threads refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 94, context: html, text, full: html, text

b8456c1e9a533efa1cce9556dd2fd717f83bc7f4 Thu Jul 13 17:13:36 2017 -0700

• get the bed output file open immediately in case there is trouble and do not thread unless explicitly requested refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 26, context: html, text, full: html, text

2b666729ac4d08d038c80a8a6ab7dc8278d30dce Thu Jul 13 17:19:00 2017 -0700

• allow shoulder argument and correct bedClip -truncate and using fasterCrispro.py refs #19514
  • src/hg/utils/automation/doCrispr.pl - lines changed 5, context: html, text, full: html, text

0f25fca4ed573b955b6a34b8df5c3dcb92331058 Thu Jul 13 18:30:47 2017 -0700

• correct typo refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 1, context: html, text, full: html, text

cea77f8093025f6b5c5784b14dc0fd9cbd30f8b3 Fri Jul 14 13:45:36 2017 -0700

• minor fixup in a comment that ends up in the generated scripts refs #19514
  • src/hg/utils/automation/doCrispr.pl - lines changed 1, context: html, text, full: html, text

131be66e554e489d599a2e54988a45f1985e194e Mon Jul 17 08:27:54 2017 -0700

• correct selection of guides vs. ranges to avoid duplicates when ranges are split refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 36, context: html, text, full: html, text

18bfbc2dcae0de9347b04ae04dce6dfce3427c77 Mon Jul 17 10:02:36 2017 -0700

• v352 final build refs #19715
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

5f3ca34a0412ffc6b3e172eb1ca77a72fd5e0e0f Mon Jul 17 10:04:24 2017 -0700

• New version number v352
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text