change 1
Merge pull request #1 from schryer/master

Changed file iterator to remove bug.
merged
Merge branch 'master' of https://github.com/markusli/five-prime-counter
Choose input file, writes output as a .csv file.
Update test2.py
Added a script to trim the reads and align them to a reference genome using BWA MEM algorith
Added a script to trim the reads and align them to a reference genome
Merge branch 'master' of https://github.com/markusli/five-prime-counter
Switched output to an uncompressed file as BWA aligner doesn't handle packaged files.
added algorithm to find 3' ends of aligned reads in a .sam file and compare it against the full reference genome. Checks whether the next nucleotide could be 'A' or not
fixed 'sketchy' read finder and added two output files into which the reads are sorted according to whether they are 'sketchy' or not.
Merge branch 'master' of https://github.com/Markusli/five-prime-counter
Changed test2.py to plot to file.