Update README

README

@@ -33,7 +33,7 @@ git pull origin master
 - Python 3
 - BioPython for Python3
 
-For build_xls_results script, these python3 modules are required:
+For build_results script, these python3 modules are required:
     - yalm
     - pybedtools
     - pysam
@@ -54,8 +54,11 @@ Required parameters:
 
 Optional parameters:
 - coverage: mean coverage of the reads for each individual (default: 15)
+- force-polymorphism: Force polymorphism for each SV
+- read-len: Generate reads having a length of LEN (default: 100)
+- insert-len-mean: Generate inserts (fragments) having an average length of LEN (default: 300)
+- insert-len-sd: Set the standard deviation of the insert (fragment) length (%) (default: 30)
 - output-directory: directory where outputs will be written (see below) (default: <current>/res)
-- tmp-directory: temporary directory (default: <current>/tmp)
 
 
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@@ -73,6 +76,7 @@ If endLength is not specified, it defaults to the value of startLength (i.e. one
 If increment is not specified, it defaults to 1.
 
 1 line by SV type, like above.
+You can add several lines for a same SV type, to use several concentrations of SV sizes.
 
 IMPORTANT: only deletion is implemented yet.
 
@@ -95,9 +99,9 @@ In the output directory there are:
 As pirs works only on Intel CPUs, this software is only compatible with Intel. Tested and failed on AMD CPUs.
 
 
-############################
-# Generate XLS result file #
-############################
+#########################
+# Generate result files #
+#########################
 
 Until you launched the jflow pipelines, you can compare results calculated with original ones to evaluate the pipeline
 and the tools used inside.
@@ -114,6 +118,9 @@ Recommanded parameters:
   -f FILTERED_VCF, --filtered-vcf FILTERED_VCF
                         VCF file containing the filtered results: VCF file inside the "Filter" component of the CNV detection workflow
 
+  -g GENOTYPES, --genotypes GENOTYPES
+                        VCF file containing genotypes (default: None)
+
 Optionnal parameters:
 
 Some options to define how the SV founds must be close to the original ones to be considered the same ones:
@@ -126,7 +133,16 @@ Some options to define how the SV founds must be close to the original ones to b
 
 Output EXCEL file:
   -o OUTPUT, --output OUTPUT
-                        output Excel file (default: results.xslx)
+                        output prefix (default: results)
+
+Other parameters:
+  --no-xls              Do not build Excel file (default: False)
+  --haploid             The organism is haploid (default: False)
+
+
+# Outputs
+
+XLS files with tables to compare detected results to True ones. Tables are also available into TSV files.
 
 
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