Added ngsLD as submodule

mfumagalli · May 8, 2018 · 17cd6d3 · 17cd6d3
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diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,8 @@
 
+1.0.2 / 08-05-2018
+==================
+  * Added ngsLD as a sub-repository
+
 1.0.1 / 20-05-2016
 ==================
   * Added ngsF-HMM as a sub-repository

diff --git a/Makefile b/Makefile
@@ -2,7 +2,7 @@
 export HTSSRC=../htslib/
 
 EXT = htslib angsd
-TOOLS = ngsSim ngsPopGen ngsUtils ngsDist ngsF ngsF-HMM
+TOOLS = ngsSim ngsPopGen ngsUtils ngsDist ngsLD ngsF ngsF-HMM
 
 all: $(EXT) $(TOOLS)
 

diff --git a/README.md b/README.md
@@ -44,6 +44,8 @@ Packages
 
 * [ngsF-HMM](https://github.com/fgvieira/ngsF-HMM) is a program developed and written by F.G. Vieira to estimate per-individual inbreeding tracts using a two-state Hidden Markov Model ([Vieira et al. 2016](http://bioinformatics.oxfordjournals.org/content/32/14/2096)). It uses a probabilistic framework that takes the uncertainty of genotype's assignation into account; making it specially suited for low-quality or low-coverage datasets. It is not officially part of ngsTools so it must be installed separately.
 
+* [ngsLD](https://github.com/fgvieira/ngsLD) is a program that calculates pairwise Linkage Disequilibrium (LD) under a probabilistic framework ([Fox et al., 2018](http://onlinelibrary.wiley.com/doi/10.1111/bij.12511/abstract)).
+
 
 Installation
 --------------------------------------------------

diff --git a/ngsLD b/ngsLD
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@@ Expand Up / @@ -44,6 +44,8 @@ Packages @@
     * [ngsF-HMM](https://github.com/fgvieira/ngsF-HMM) is a program developed and written by F.G. Vieira to estimate per-individual inbreeding tracts using a two-state Hidden Markov Model ([Vieira et al. 2016](http://bioinformatics.oxfordjournals.org/content/32/14/2096)). It uses a probabilistic framework that takes the uncertainty of genotype's assignation into account; making it specially suited for low-quality or low-coverage datasets. It is not officially part of ngsTools so it must be installed separately.
+    * [ngsLD](https://github.com/fgvieira/ngsLD) is a program that calculates pairwise Linkage Disequilibrium (LD) under a probabilistic framework ([Fox et al., 2018](http://onlinelibrary.wiley.com/doi/10.1111/bij.12511/abstract)).
     Installation
     --------------------------------------------------
@@ Expand Down @@