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[DOC] Add a raptor layout tutorial #201

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[DOC] Add a search assignment for the hibf.
Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
Irallia committed Dec 12, 2022
commit c538eb1983d2e9f85106ad321a121e5c60dc20d3
19 changes: 16 additions & 3 deletions doc/tutorial/04_search/index.md
Original file line number Diff line number Diff line change
@@ -351,18 +351,31 @@ If no minimizers are used, our thresholding ensures that the (H)IBF gives no fal
there are few false negatives, because the minimizer compression is not lossless.

\assignment{Assignment 4: Search with hibf.}
We want to use the `hibf.index` from the index tutorial assignment again and use ...
We want to use the `hibf.index` from the index tutorial assignment again. <!-- and use X as X-parameter. -->

Lets search now with ..., with creating a `search6.output`.
Lets search now for the `1024/reads/mini.fastq` querries with creating a `search6.output`.
\endassignment

\solution
You should have run
```bash
raptor search --index hibf.index --query query.fasta --output search6.output
raptor search --hibf --index hibf.index --query 1024/reads/mini.fastq --output search6.output
```
Your `search6.output` should look like:
```text
#0 1024/bins/bin_0712.fasta
#1 1024/bins/bin_0406.fasta
...
#1021 1024/bins/bin_0533.fasta
#1022 1024/bins/bin_0624.fasta
#QUERY_NAME USER_BINS
0
1
...
1047555
1047556
```
\note
You can also calculate the second hibf index B and you will see that they will give slightly different results
(`diff search6.output search7.output`).
\endsolution