summary statistics

[evezeyl]

• we could reuse scripts from Lex: to output:

• distribution of insert size. There we would need to remap the reads after pilon (maybe need to correct label but I think there is an option in bwa mem ). so while we are here we could:

• maybe aslo make this gap size file (need to add brachets in print () of the script to work and its ok)
  could be nice to extract

• wrongly oriented PE read (good to have an idea)

• and output the .bam and index -> so can look at everything in IGV

• and maybe a line to know how many reads have been corrected by spades (particularly if we reuse those).

And - all the output in one file with the versions used in your commit (can glue that from my git - as I checked all on the bifrost conda env)