Commits for ceisenhart

v336_base to v337_preview (2016-07-25 to 2016-08-01) v337

4abb3bf5c776ba0b89e6f83fe212952085b829fa Thu Jul 28 12:23:24 2016 -0700

• Adding in library file changes and makefile changes for cdwFlowCharts
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 12, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/makefile - lines changed 1, context: html, text, full: html, text

0dd9fe6d748b1908de30e74ed8b63a04db54e3f2 Thu Jul 28 15:16:14 2016 -0700

• adding in a trim step to the pairedEndQa validation step, refs #17334
  
  • src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c - lines changed 18, context: html, text, full: html, text

b58525c691493b60efa96dc132d2e8cc0b242010 Thu Jul 28 15:26:44 2016 -0700

• Replacing the cutadapt call with Jim's new C program cdwFastqPolyFilter, refs #17334
  
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 28, context: html, text, full: html, text

829a8225ba4cd3d54afb68c55763cfa6ac1a914c Thu Jul 28 15:27:24 2016 -0700

• Adding in a polyA trim step before running BWA, refs 7334
  
  • src/hg/cirm/cdw/cdwMakeContaminationQa/cdwMakeContaminationQa.c - lines changed 17, context: html, text, full: html, text

56e53f8d956070beb48dcf83ea3735a09062682c Fri Jul 29 13:19:59 2016 -0700

• Adding in a wrangler column to the cdwSubmit table to keep track of who submits what
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 3, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.as - lines changed 1, context: html, text, full: html, text

5800a214862f57bfbf06d92ce613f3558423d2e3 Fri Jul 29 13:32:53 2016 -0700

• Adding a print out of the wrangler value to the program
  
  • src/hg/cirm/cdw/cdwCheckDataset/cdwCheckDataset.c - lines changed 2, context: html, text, full: html, text