Support for threading and additional read simulation parameters

example.config

@@ -1,19 +1,17 @@
 #REQUIRED PARAMETERS
-treefile_path = example/example.tre #Must be newick or Nexus format, and include branch lengths
+treefile_path =  example/example.tre
 number_of_variable_sites = 20
-base_genome_name = gi #Should be the label of a tip in your tree
-base_genome_path = example/mini_ref.fasta
+base_genome_name = gi
+base_genome_path =  example/mini_ref.fasta
 output_dir = example_out
-
-
-#parameters of evolutionary model (comma seperated), in order ac, ag, at, cg, ct, gc (gc = 1)
+# parameters of evolutionary model (comma seperated), in order ac, ag, at, cg, ct, gc (gc = 1)
 rate_matrix = 1,1,1,1,1,1
 
-#parameters for read simulation
-coverage = 20 #either an integer or a file name of a comma delimited file with tip names and coverage
 
-#OPTIONAL PARAMETERS
+
+# OPTIONAL PARAMETERS
 prefix = sim_ #optional prefix prepended to sequence names, default is using orginal sequence names
+threads = 10
 
 #Optional evolutionary model parameters
 gamma_shape = 5 #dafault is no rate variation across sites
@@ -23,10 +21,46 @@ mutation_clustering = ON
 percent_clustered = 0.25 #The percentage of variable sites whose distance to another site is drawn from the clustering distribution
 exponential_mean = 125 #Minimum allowed value = 2
 
-#ART Optional parameters (for more fine grained control ART can be run seperately on the mutated genomes found in outdir/fasta_files)
-error_model1 = example/ErrprofR1.txt  # If you haven't generated have one of your own using ART, you can use one supplied by ART.
-error_model2 = example/ErrprofR2.txt  # Un-comment these lines (delete the first #) to set a non-default error profile
-read_length = 150 #maximum value with example error profile is 150, use a default or generate adifferent error profile for longer reads.
+## ART Optional parameters (for more fine grained control ART can be run seperately on the mutated genomes found in outdir/fasta_files)
+#error_model1 = example/ErrprofR1.txt  # If you haven't generated have one of your own using ART, you can use one supplied by ART.
+#error_model2 = example/ErrprofR2.txt  # Un-comment these lines (delete the first #) to set a non-default error profile
+
+## Read length, can be one value or list of comma separated values up to 250bp
+## Read length may be truncated if selected read platform doesn't support it
+read_length = 150,250
+
+## Insert fragment length.  Can be uniform [fragment_size] 
+## or randomly distributed between [frag_low, frag_high]
 fragment_size = 380
+# frag_low = 600 # Start of random frag length range
+# frag_high = 1000 # End of random frag length range
+# frag_step = 7 # Step size for binning frag length
+
+## Insert fragment length standard deviation.  Can be uniform [stdev_frag_size] 
+## or randomly distributed between [stdev_frag_low, stdev_frag_high]
 stdev_frag_size = 120
+# stdev_frag_low = 10 # Start of random frag length stdev range
+# stdev_frag_high = 100 # End of random frag length stdev range
+# stdev_frag_step = 3 # Step size for binning frag length stdev
+
+## Average genomic real coverage.  Can be uniform [coverage] across dataset
+## or randomly distributed between [coverage_low, coverage_high]
+coverage = 20
+# coverage_low = 20 # Start of random coverage range
+# coverage_high = 87 # End of random coverage range
+# coverage_step = 1 # Step size for binning random coverage
+
+## Average QS2 bias to introduce.  Can be 0 (no value provided) across dataset
+# or randomly distributed between [qs2_low, qs2_high]
+# qs2_low = -3 # Start of QS2 bias range
+# qs2_high = 0 # End of QS2 bias range
+# qs2_step = 1 # Step size for binning QS2 bias
 
+# Platform read error profile used to generate reads
+readProfile = MSv3 # Read platform
+## Supports the following (between read length)
+## Defaults to MiSeq v3 to allow reads up to 250bp
+## GA1 - GenomeAnalyzer I (1-44bp), GA2 - GenomeAnalyzer II (1-75bp)
+## HS10 - HiSeq 1000 (1-100bp), HS20 - HiSeq 2000 1-100bp), HS25 - HiSeq 2500 (1-150bp)
+## HSXn - HiSeqX PCR free (1-150bp), HSXt - HiSeqX TruSeq (1-150bp),  MinS - MiniSeq TruSeq (1-50bp)
+## MSv1 - MiSeq v1 (1-250bp), MSv3 - MiSeq v3 (1-250bp), NS50 - NextSeq500 v2 (1-75bp)