Addresses two bugs. 1) Created 2 fastq files from the combined reads instead of only 1. 2) There was a potentially nasty bug with the seqio.concat_files function where in some instances if the input and output file were the same it would keep writing until the disk was full
Easy script to convert sai file to sorted/indexed bam file
More documentation about how to run the executables
Fixed a bunch of bugs and such with testing. All tests pass now too :)
Ignore stuff
Merging dev for release
Fixing stuff. Why was build in the repo?
Added more useful returns for index_ref
Had to change how BWAIndex deals with its hackish way around the output file for times when it is run in a multiprocessor environment as the output file would be identical for all processes and be deleted by one process and the rest would raise an OSError exception because they tried to delete an already deleted file
Merging in Github dev branch