Commits for ceisenhart

v301_base to v302_preview (2014-06-09 to 2014-06-16) v302

• Created the basic framework for bamSplitByChrom, which will take in a bam file and return a bam file for each chromosome present in the initial file
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 102, context: html, text, full: html, text
• Program seems to be running as expceted, has not been tested yet.
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 49, context: html, text, full: html, text
• Removed test functions and white space, camel cased variables and added comments.
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 20, context: html, text, full: html, text
• Fixed an I/O bug
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 16, context: html, text, full: html, text
• Merges multiple bam files into a single bam file, for testing bamSplitByChrom
  • src/utils/bamMerge/bamMerge.c - lines changed 76, context: html, text, full: html, text
• Not working for chromosomes with underscores in their name. Working for others.
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 3, context: html, text, full: html, text
• Not working for unique chromosomes
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 31, context: html, text, full: html, text
• getting new fastq librariesMerge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
  
• Updated to with new library file'fq', fixed indenting and comment missplacement
  
  • src/utils/fastqMottTrim/fastqMottTrim.c - lines changed 100, context: html, text, full: html, text
• changed structure to increase efficiency, added 'unmapped.bam' to output
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 62, context: html, text, full: html, text
• Removed a function that was librarified, updated comments and stylistic errors
  • src/utils/bamMerge/bamMerge.c - lines changed 12, context: html, text, full: html, text
• Removed functions that were already in the library,replaced the functions with their counterparts in the library
  
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 19, context: html, text, full: html, text
• Changed comments and librarified functions
  • src/utils/bamToFastq/bamToFastq.c - lines changed 61, context: html, text, full: html, text
• Added comments and fixed stylistic errors
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 11, context: html, text, full: html, text
• Removed memory leak, fixed some stylistic errors
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 29, context: html, text, full: html, text
  • src/utils/bamToFastq/bamToFastq.c - lines changed 11, context: html, text, full: html, text
• stylistic changes
  • src/inc/fq.h - lines changed 7, context: html, text, full: html, text
  • src/lib/fq.c - lines changed 8, context: html, text, full: html, text
  • src/utils/fastqMottTrim/fastqMottTrim.c - lines changed 8, context: html, text, full: html, text
• stylistic changes
  • src/utils/bamToFastq/bamToFastq.c - lines changed 2, context: html, text, full: html, text
• stylistic changes, testing new option '-unmapped'
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 20, context: html, text, full: html, text
• changed bamSplitByChrom so that the outputs are put into a user specified directory
  • src/utils/bamSplitByChrom/bamSplitByChrom.c - lines changed 43, context: html, text, full: html, text
• testing AUTO SQL
  • src/hg/oneShot/freen/freen.c - lines changed 40, context: html, text, full: html, text
• Fixing merge conflicts
  • src/hg/oneShot/freen/freen.c - lines changed 24, context: html, text, full: html, text