File Changes for ceisenhart

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

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