README.md in bio-gemma-wrapper-0.99.2 vs README.md in bio-gemma-wrapper-0.99.3

@@ -6,15 +6,16 @@
 Nat. Genet., 2016)](cfw.gif)
 
 ## Introduction
 
 Gemma-wrapper allows running GEMMA with LOCO, GEMMA with caching,
-GEMMA in parallel (now the default), and GEMMA on PBS. Gemma-wrapper
-is used to run GEMMA as part of the https://genenetwork.org/
-environment.
+GEMMA in parallel (now the default with LOCO), and GEMMA on
+PBS. Gemma-wrapper is used to run GEMMA as part of the
+https://genenetwork.org/ environment.
 
-Note that gemma-wrapper is projected to be integrated into gemma2/lib.
+Note that a version of gemma-wrapper is projected to be integrated
+into gemma itself.
 
 GEMMA is a software toolkit for fast application of linear mixed
 models (LMMs) and related models to genome-wide association studies
 (GWAS) and other large-scale data sets.
 
@@ -27,10 +28,18 @@
 gemma-wrapper requires a recent version of GEMMA and essentially
 does a pass-through of all standard GEMMA invocation switches. On
 return gemma-wrapper can return a JSON object (--json) which is
 useful for web-services.
 
+## Performance
+
+LOCO runs in parallel by default which is at least a 5x performance
+improvement on a machine with enough cores. GEMMA without LOCO,
+however, does not run in parallel by default.  Performance
+improvements with the parallel implementation for LOCO and non-LOCO
+can be viewed [here](./test/performance/releases.gmi).
+
 ## Installation
 
 Prerequisites are
 
 * A recent version of [GEMMA](https://github.com/genetics-statistics/GEMMA)
@@ -51,19 +60,23 @@
 
 ```
 Usage: gemma-wrapper [options] -- [gemma-options]
         --permutate n                Permutate # times by shuffling phenotypes
         --permute-phenotypes filen   Phenotypes to be shuffled in permutations
-        --loco [x,y,1,2,3...]        Run full LOCO
+        --loco                       Run full leave-one-chromosome-out (LOCO)
+        --chromosomes [1,2,3]        Run specific chromosomes
         --input filen                JSON input variables (used for LOCO)
         --cache-dir path             Use a cache directory
         --json                       Create output file in JSON format
-        --force                      Force computation
-        --slurm [options]            Submit to slurm PBS
+        --force                      Force computation (override cache)
+        --parallel                   Run jobs in parallel
+        --no-parallel                Do not run jobs in parallel
+        --slurm[=opts]               Use slurm PBS for submitting jobs
         --q, --quiet                 Run quietly
     -v, --verbose                    Run verbosely
-        --debug                      Show debug messages and keep intermediate output
+    -d, --debug                      Show debug messages and keep intermediate output
+        --dry-run                    Show commands, but don't execute
         --                           Anything after gets passed to GEMMA
 
     -h, --help                       display this help and exit
 ```
 
@@ -97,10 +110,11 @@
 the data files are found):
 
     gemma-wrapper -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
+        -a test/data/input/BXD_snps.txt \
         -gk \
         -debug
 
 Run it twice to see
 
@@ -114,10 +128,11 @@
 You can also get JSON output on STDOUT by providing the --json switch
 
     gemma-wrapper --json -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
+        -a test/data/input/BXD_snps.txt \
         -gk \
         -debug > K.json
 
 K.json is something that can be parsed with a calling program, and is
 also below as input for the GWA step. Example:
@@ -131,21 +146,22 @@
 default. If you want something else provide a --cache-dir, e.g.
 
     gemma-wrapper --cache-dir ~/.gemma-cache -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
+        -a test/data/input/BXD_snps.txt \
         -gk \
         -debug
 
 will store K in ~/.gemma-cache.
 
 ### GWA
 
 Run the LMM using the K's captured earlier in K.json using the --input
 switch
 
-    gemma-wrapper --json --loco --input K.json -- \
+    gemma-wrapper --json --input K.json -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
         -c test/data/input/BXD_covariates2.txt \
         -a test/data/input/BXD_snps.txt \
         -lmm 2 -maf 0.1 \
@@ -161,10 +177,10 @@
 using the -loco switch (for supported formats check
 https://github.com/genetics-statistics/GEMMA/issues/46). To loop all
 chromosomes first create all K's with
 
     gemma-wrapper --json \
-        --loco 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X -- \
+        --loco -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
         -a test/data/input/BXD_snps.txt \
         -gk \
         -debug > K.json