do notuse system /tmp, user ~/tmp
Merge pull request #28 from janders3-nmdp/user_specific_tmpdir

do notuse system /tmp, user ~/tmp
adding Travis CI configuration with no-op build script
adding Travis CI badge to readme
Update process_fastq.bash
Merge pull request #31 from warrenlr/patch-1

Update process_fastq.bash
Merge pull request #33 from mheuer-nmdp/travis-configuration

Adding Travis CI configuration with no-op build script
Merge pull request #35 from mheuer-nmdp/travis-badge

Adding Travis CI badge to readme
now splitter will find fastq files in subdirs at preliminary check
Merge pull request #38 from janders3-nmdp/less_dumb_fastq_check

now splitter will find fastq files in subdirs at preliminary check - fix #37
Redirect mpileup (reads) output to file
Merge pull request #40 from ckennedy-nmdp/process-labcorp-data

Redirect mpileup (reads) output to file
documentation/warning updates
Merge pull request #48 from janders3-nmdp/lowram_warning

documentation/warning updates
some in-progress enhancements to splitter to handle osx, redhat, and soon, to deal with single-core machines and single-sample runs
Fix issue #41 -- reverse complement minus strand HLA genes so they can be properly interpreted. Warning: this is a hack and should be replaced with properly configured tool where filtered regions include the strand (a la GFF or HML)
Merge pull request #55 from ckennedy-nmdp/fix-bug-41

Fix issue #41 -- reverse complement minus strand HLA genes so they can b...
Fix bug #56, which is caused by improper formatting of regions files for filtering -- in this case spaces instead of tabs between index and coordinate fields produced an ArrayOutOfBoundsException. Sometimes formatting issues arise when copying files around. I put an error message into the code (Mark will have to reformat the regions files in /mnt/common/)
Take Michael's suggestion and use '\s+' to split -- simpler, better
Merge pull request #57 from ckennedy-nmdp/bug56

Fix bug #56, which is caused by improper formatting of regions files for...