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This repository was archived by the owner on Mar 29, 2022. It is now read-only.
combining -ctga with -names does not work. The output keeps showing taxID instead of the taxon name
-ctga prints both 5' and 3' in the same line with no differentiation. One has to count the columns to find out when the 3' G>A starts. If -p is 5 is ok, but I was testing with -p 15 and it is clumsy. Maybe split in two different lines? Make two columns? Something else?
maybe we can have more options for filtering the print output? I was actually every time piping metadamage print into some "awk '{if ($2>1000 && $12>0.20) print}'" whenever I used it. For example, it would be nice to be able to filter the output by a) number of alignments, b) C>T frequency and c) G>A frequency. And actually my awk solution is no good because it only prints the "matching line", it would be great if metadamage actually included the next relevant lines. For example, if I am filtering for C>T frequency > 0.20, to include also the frequencies of position 2,3,4 etc so we can access the damage pattern.
Issues with metadamage print output right now:
combining -ctga with -names does not work. The output keeps showing taxID instead of the taxon name
-ctga prints both 5' and 3' in the same line with no differentiation. One has to count the columns to find out when the 3' G>A starts. If -p is 5 is ok, but I was testing with -p 15 and it is clumsy. Maybe split in two different lines? Make two columns? Something else?
maybe we can have more options for filtering the print output? I was actually every time piping metadamage print into some "awk '{if ($2>1000 && $12>0.20) print}'" whenever I used it. For example, it would be nice to be able to filter the output by a) number of alignments, b) C>T frequency and c) G>A frequency. And actually my awk solution is no good because it only prints the "matching line", it would be great if metadamage actually included the next relevant lines. For example, if I am filtering for C>T frequency > 0.20, to include also the frequencies of position 2,3,4 etc so we can access the damage pattern.