estimateReadFiltering

[dpryan79]

It'd be nice to at least have a script to output the following:

• Duplicates
• singletons
• total reads (include unmapped)
• mapped reads
• blacklisted reads

[dpryan79]

This can be a random gist for now.

[dpryan79]

The script will in the end track the following:

• Duplicates (marked externally, e.g., by picard)
• Duplicates due to --ignoreDuplicates
• Singletons
• wrong strand (due to --filterRNAstrand)
• too low mapq
• excluded SAM flag (due to --samFlagExclude)
• included SAM flag (due to --samFlagInclude)
• reads in blacklisted regions
• mapped reads
• Total reads (including unmapped)

[dpryan79]

The current script is here

[dpryan79]

• Get the formatting to work in the --help output at the top (the list is broken).

[dpryan79]

This is now implemented in the develop branch.