2. Added code to create new rawAlignment, processedAlignment, coverageTracks, and logs dirs when new analysis report dir is created.
3. Added code to remove split fastq bisulfite files after alignments have completed
4. Added a new field (column) for fastq file name in the Sample class to parse from the fresh data report
5. Fixed bug where output format wasn't specified as .sam for genomic sequences
6. Changed code to explicitly call filenames
7. Added code to Sample class to parse additional field for sequencing adapter from fresh data report
8. Added fields for SequenceLane, Read1Adapter, Read2Adapter, File(path)
9. Added code to catch "None" for Read1Adapter and Read2Adapter
10. Changed permissions of newly-created tomato/job/ folders to 777
11. Fixed broken path to fastqc app run prior to alignment
12. Fixed a soft-linking error to be more explicit with file matching
13. Made the code more readable by using StringBuilder to construct the cmd.txt file
14. Fixed a few potential errors with constructing the cmd.txt file
15. Added logging
