Commits for ceisenhart

v300_base to v301_preview (2014-05-19 to 2014-05-26) v301

• fixed problem in command line argument check, updated usage output
  • src/hg/bedIntersect/bedIntersect.c - lines changed 5, context: html, text, full: html, text
• initial commit for mott trimming
  • src/utils/fastqMottTrim/fastqMottTrim.c - lines changed 196, context: html, text, full: html, text
  • src/utils/fastqMottTrim/makefile - lines changed 3, context: html, text, full: html, text
• updated comments changed a < to <=
  • src/utils/fastqMottTrim/fastqMottTrim.c - lines changed 56, context: html, text, full: html, text
• converts a bam file to a fastq filesome illumina header data is lost
  
  • src/utils/bamToFastq/bamToFastq.c - lines changed 128, context: html, text, full: html, text
• Modified comments, camel cased variables
  • src/utils/fastqMottTrim/fastqMottTrim.c - lines changed 37, context: html, text, full: html, text
• Modified comments, camel cased variables
  • src/utils/bamToFastq/bamToFastq.c - lines changed 9, context: html, text, full: html, text
• Synching with latest changes Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent