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fix doc and examples
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tlemane committed Oct 19, 2023
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4 changes: 2 additions & 2 deletions docs/kmindex/docs/construction.md
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Expand Up @@ -97,8 +97,8 @@ In presence/absence mode, the index only contains the presence/absence pattern o

The [kmindex](https://github.com/tlemane/kmindex) repository offers an `examples` directory where these commands can be tested.
```bash
kmindex build --fof fof1.txt --run-dir D1_index --index ./G --register-as D1 --hard-min --kmer-size 25 --bloom-size 1000000 # (1)!
kmindex build --fof fof2.txt --run-dir D2_index --index ./G --register-as D2 --hard-min --kmer-size 25 --bloom-size 1000000 # (2)!
kmindex build --fof fof1.txt --run-dir D1_index --index ./G --register-as D1 --hard-min 1 --kmer-size 25 --bloom-size 1000000 # (1)!
kmindex build --fof fof2.txt --run-dir D2_index --index ./G --register-as D2 --hard-min 1 --kmer-size 25 --bloom-size 1000000 # (2)!
```

1. Creates a directory `G` containing the index for the `D1` dataset
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4 changes: 2 additions & 2 deletions examples/data/1_build.sh
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#!/bin/bash

kmtricks pipeline --file fof1.txt --run-dir D1 --hard-min 1 --kmer-size 25 --mode hash:bf:bin
kmtricks pipeline --file fof2.txt --run-dir D2 --hard-min 1 --kmer-size 25 --mode hash:bf:bin
kmindex build --fof fof1.txt --run-dir ./D1 --index ./G --register-as D1 --hard-min 1 --kmer-size 25 --bloom-size 1000000
kmindex build --fof fof2.txt --run-dir ./D2 --index ./G --register-as D2 --hard-min 1 --kmer-size 25 --bloom-size 1000000
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4 changes: 0 additions & 4 deletions examples/data/2_register.sh

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