diff --git a/docs/kmindex/docs/construction.md b/docs/kmindex/docs/construction.md index e2f205d..c47e733 100644 --- a/docs/kmindex/docs/construction.md +++ b/docs/kmindex/docs/construction.md @@ -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 diff --git a/examples/data/1_build.sh b/examples/data/1_build.sh index 2a8253b..f1fa66c 100755 --- a/examples/data/1_build.sh +++ b/examples/data/1_build.sh @@ -1,4 +1,4 @@ #!/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 diff --git a/examples/data/3_query.sh b/examples/data/2_query.sh similarity index 100% rename from examples/data/3_query.sh rename to examples/data/2_query.sh diff --git a/examples/data/2_register.sh b/examples/data/2_register.sh deleted file mode 100755 index d853193..0000000 --- a/examples/data/2_register.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -kmindex register --name D1 --global-index G --index ./D1 -kmindex register --name D2 --global-index G --index ./D2 diff --git a/examples/data/4_run_server.sh b/examples/data/3_run_server.sh similarity index 100% rename from examples/data/4_run_server.sh rename to examples/data/3_run_server.sh diff --git a/examples/data/5_get_request.sh b/examples/data/4_get_request.sh similarity index 100% rename from examples/data/5_get_request.sh rename to examples/data/4_get_request.sh diff --git a/examples/data/6_post_request.sh b/examples/data/5_post_request.sh similarity index 100% rename from examples/data/6_post_request.sh rename to examples/data/5_post_request.sh