kmcp
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TODO: save the search result into a serializing binary file for fast downstream parsing
The current tab-delimited search result format is redundant and inefficient for parsing in kmcp profile
. So we can use a compact binary format to save the temporary result.
-
kmcp search
: a flag-b/--binary-outpu
would be added to choose the output format optionally. - A new command
kmcp view
should be added to convert the binary to plain text format. -
kmcp merge
needs to be compatible with both plain and binary formats. -
kmcp profile
needs to be compatible with both plain and binary formats.
#query | qLen | qKmers | FPR | hits | target | chunkIdx | chunks | tLen | kSize | mKmers | qCov | tCov | jacc | queryIdx |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
read_1 | 150 | 130 | 7.4626e-15 | 1 | GCF_000007805.1 | 2 | 10 | 6397126 | 21 | 130 | 1.0000 | 0.0002 | 0.0002 | 0 |
read_2 | 150 | 130 | 7.4626e-15 | 1 | GCF_000007805.1 | 8 | 10 | 6397126 | 21 | 130 | 1.0000 | 0.0002 | 0.0002 | 1 |
read_3 | 150 | 130 | 7.4626e-15 | 1 | GCF_000003835.1 | 8 | 10 | 12115052 | 21 | 130 | 1.0000 | 0.0001 | 0.0001 | 2 |
read_4 | 150 | 130 | 7.4626e-15 | 1 | GCF_000003835.1 | 3 | 10 | 12115052 | 21 | 130 | 1.0000 | 0.0001 | 0.0001 | 3 |