Updates the docs

Author: StuntsPT

docs/future.md

@@ -2,5 +2,5 @@
 Here is a list of the features that are currently planned to implement in *Structure_threader*.
 
 * ~~Add a "setup.py" installation process~~
-* Add unit tests
+* ~~Add unit tests~~
 * ~~Allow the fastStructure wrapper to use the ".bed" format too.~~

docs/index.md

@@ -2,14 +2,15 @@
 
 ## Description
 
-A program to parallelize and automate the runs of [Structure](http://web.stanford.edu/group/pritchardlab/structure.html), [fastStructure](https://rajanil.github.io/fastStructure/) and [MavericK](http://www.bobverity.com/home/maverick/what-is-maverick/) software.
+A program to parallelize and automate the runs of [Structure](http://web.stanford.edu/group/pritchardlab/structure.html), [fastStructure](https://rajanil.github.io/fastStructure/), [MavericK](http://www.bobverity.com/home/maverick/what-is-maverick/) and [ALStructure](https://github.com/StoreyLab/alstructure) software.
 
 
 ## Requirements
 
 Python 3. The main program only uses modules from the standard library.
 In order to draw the plots, matplotlib >= 1.4 is required.
 To run "fastChooseK.py" (fastStructure wrapper only), numpy is also required.
+In order to use "ALStructure", you need to have [R](https://www.r-project.org/) installed too.
 
 
 ## Where to get it

docs/test_data.md

@@ -27,6 +27,20 @@ The used commands were:
     tar cvfJ BigTestData.str.tar.xz BigTestData.str
 
 
+## BigTestData.bed.tar.xz
+This file is a *PLINK* formatted `.bed`, `.bim` and `.fam` set of files. They were obtained in the exact same way as `BigTestData.str.tar.xz`, except for the conversion using *PGDSPIDER*, which was not used. Instead, the filtered VCF file was reduced to 501 individuals and 1000 SNPs with the following command:
+
+    head -n 1253 Chr22.recode.vcf |cut -f 1-510 > Testdata.vcf
+
+This file was then converted to the *PLINK* format and compressed with the following commands:
+
+    plink1.9 --vcf Testdata.vcf
+    mv plink.bed BigTestData.bed
+    mv plink.fam BigTestData.fam
+    mv plink.bim BigTestData.bim
+    tar cvfJ BigTestData.bed.tar.xz BigTestData.bed BigTestData.fam BigTestData.bim
+
+
 ## extraparams and mainparams
 The *STRUCTURE* parameter files that were used in the benchmarking process.
 
@@ -48,5 +62,6 @@ The used commands were:
 ## parameter.txt
     The *MavericK* parameter file that is used in the unit tests.
 
+
 ## mav_benchmark_parameters
     The file with the *MAvericK* benchmark parameters.

docs/usage.md

@@ -21,16 +21,17 @@ Using the `run` mode, the program currently takes the following arguments:
     * *STRUCTURE* location (if you want to run *STRUCTURE*; -st)
     * *fastStructure* location (if you want to run *fastStructure*; -fs)
     * *MavericK* location (if you want to run *MavericK*; -mv)
+    * *ALStructure_wrapper.R* location (if you want to run *ALStructure*; -als)
 * Number of K - you have to pass one and only one of the following arguments:
     * K (To test all values of "K" from 1 to "K"; -K)
     * Klist (To test all values of "K" in the provided list; -Klist)
-* Replicates (ignored for *fastStructure* and *MavericK*; -R)
+* Replicates (ignored for *fastStructure*, *MavericK* and *ALStructure*; -R)
 * Number of threads to use (-t)
 * Q-matrix plotting options:
   * Disable plot drawing (--no_plots)
   * Force plotting the given values together (--override_bestk)
   * Draw the plots only in grayscale (-bw)
-* Other options                
+* Other options
     * Enable logging - useful when problems arise (--log)
     * Do not run the BestK tests (--no-tests)
     * Add extra arguments to pass to the wrapped program (--extra_opts) [Example: prior=logistic seed=123]