added support for 4.1, lilrb fix and expansion enabled

README.md

@@ -1,7 +1,5 @@
 # fs-tool 
 
-# NOTE: under development and might have some breaking changes, please wait for downwload until 2020-06-01 
-
 [![Release][ico-version]][link-version]
 [![Build Status][ico-travis]][link-travis]
 [![Software License][ico-license]](LICENSE.md)
@@ -13,8 +11,6 @@ The kir ligand motifs can be updated using the tool.
 
 Detailed instructions and descriptions are available in the [Documentation][link-docs] (documentation will be available soon).
 
-
-
 ## Install
 
 ### Binary
@@ -58,7 +54,7 @@ $ ./fs-tool -h
 
 ```
 
-fstool 0.2.3
+fstool 0.2.5
 Calculates fraction of shared bound motifs between HLA alleles while incorporating KIR ligand and LILRB binding
 information.
 
@@ -110,7 +106,7 @@ The `target/release/fs-tool` is for examples after building the tool from source
 To run comparison on positions `1,3,7`, and to name the output measure `Example` while updating data from EBI:
 
 ``` bash
-$ ./target/release/fs-tool -b tests/netmhcpan/netmhcpan_wBA.txt  --prefix "example_cohort_Gag_180_209" -o example_result
+$ ./target/release/fs-tool -b tests/input/binding_predictions/netmhcpan_wBA.txt  --prefix "example_cohort_Gag_180_209" -o example_result
 ```
 
 
@@ -121,7 +117,7 @@ to drop the default measures `TCR` and `KIR` the flag `--drop-default-measures`
 To perform calculations, using the default measures, for `A02:01` and `C08:02` the following command can be ran:
 
 ``` bash
-$ ./target/release/fs-tool   -b tests/netmhcpan/netmhcpan_wBA.txt  --prefix "example_cohort_Gag_180_209" -o example_result -i A03:01 C08:02 -c tests/example_cohort.csv
+$ ./target/release/fs-tool   -b tests/input/binding_predictions/netmhcpan_wBA.txt  --prefix "example_cohort_Gag_180_209" -o example_result -i A03:01 C08:02 -c tests/input/cohorts/example_cohort.csv
 ```
 
 ### Output