reads.csv pass/fail bugs and clarifications

[MikeAxtell]

As of 4b8b45b the reads.csv output file has some bugs and discrepancies with the documentation in the README.

• The README states that reads.csv "Also includes a Pass/Fail result. A 'Pass' indicates the miRNA meets the read floor and has a precision greater than 75% in that library. A 'Fail' indcates one of these criteria are not met." However, it also appears cases where 0 miRNA and/or miRNA-star reads are also called 'Fail' in reads.csv. Calling a 'Fail' if there are 0 reads for either/both the miRNA/miRNA* is the correct behavior. However, this should be documented in the README, which currently does not state that criterion.
• The addition of a 'flags' column to reads.csv would greatly enhance user understanding why certain cases fail.
• Here is an example snippet from a reads.csv file, showing analysis for a single locus 'Cluster_1308' in three FASTQ files: you can see that it has a 'Pass' in the third case. BUT, there are fewer than 10 total reads in that case. According to the README, it should be a 'Fail' in that third line due to less than 10 total reads. In the overall 'miRScore_results.csv' output file, this locus is given a 'Fail'. Which seems correct because all three libraries failed. Just that the reads.csv is not correctly reporting the 'result'.

[Aez35]

Fixed as of 657feba.

[MikeAxtell]

The README still needs to be updated to accurately describe all of the possible conditions that can cause a 'Fail' in a reads.csv line. Right now the README does not mention lack of mature miRNA and/or star reads as a possible failure cause.

[MikeAxtell]

Also, what about the addition of a 'flags' column to reads.csv?

[Aez35]

Fixed as of commit fefe4a6

Thank you