After discussing with @demis001 we think it will be best to reformat the make_summary output such that the unassembled reads section is put beneath the contigs section and the numReads is aligned with both.
These changes would allow for investigators to easily sort/filter via the command line and in excel
- ctg# field would be removed
- Unassembled reads would still be grouped by the
--group-by column
- The project/sample name column for each line would then be concatenated with the contig name
- For unassembled reads the same would occur, however, each line would get it's own identifier number(aka, the first unassembled line would be ur1, the second would be ur2)
- All other columns would be removed from the report and could be gathered by the user or another script very easily such as
grep '.' projectdir/results/*/*.count
After discussing with @demis001 we think it will be best to reformat the make_summary output such that the unassembled reads section is put beneath the contigs section and the numReads is aligned with both.
These changes would allow for investigators to easily sort/filter via the command line and in excel
--group-bycolumngrep '.' projectdir/results/*/*.count