Takes an anvi'o linkmers report, generates an oligotyping output.
A linkmers-txt artifact describes each of your short reads that mapped to specific target nucleotide positions in a reference contig. This program counts the total occurance of each combination in those target positions within each of your samples.
For example, if your linkmers-txt focused on two target positions, and you ran the following:
anvi-oligotype-linkmers -i linkmers-txt
The output (which by default is called
oligotype-counts-001.txt) might look like the following:
key AG CA CG GA GG TA TG sample_001 0 320 12 2 0 3 579 sample_002 0 142 2 0 2 10 353 sample_003 3 404 1 1 0 2 610 sample_004 0 209 6 0 1 0 240
Note that combinations with zero reads in every sample are not included.
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__resources__ tag in this file to see an example.