add trimming to LepAnchor

conda_setup.yml

@@ -1,5 +1,6 @@
 name: lepwrap
 channels:
+  - conda-forge/label/main
   - bioconda
   - conda-forge
   - defaults
@@ -148,7 +149,7 @@ dependencies:
   - multidict=5.1.0=py39h3811e60_1
   - nbformat=5.1.3=pyhd8ed1ab_0
   - ncurses=6.2=h58526e2_4
-  - networkx=2.3=py_0
+  - networkx=2.5=py_0
   - numpy=1.20.3=py39hdbf815f_0
   - oauth2client=4.1.3=py_0
   - oauthlib=3.0.1=py_0
@@ -206,6 +207,7 @@ dependencies:
   - r-cli=2.5.0=r40hc72bb7e_0
   - r-clipr=0.7.1=r40h142f84f_0
   - r-colorspace=2.0_1=r40hcfec24a_0
+  - r-cowplot=1.1.1=r40hc72bb7e_0
   - r-cpp11=0.2.7=r40hc72bb7e_0
   - r-crayon=1.4.1=r40hc72bb7e_0
   - r-curl=4.3.1=r40hcfec24a_0
@@ -223,9 +225,11 @@ dependencies:
   - r-farver=2.1.0=r40h03ef668_0
   - r-forcats=0.5.1=r40hc72bb7e_0
   - r-fs=1.5.0=r40h0357c0b_0
+  - r-fuzzyjoin=0.1.6=r40_0
   - r-gargle=1.1.0=r40hc72bb7e_0
   - r-gdtools=0.2.2=r40h36050f4_1
   - r-generics=0.1.0=r40hc72bb7e_0
+  - r-geosphere=1.5_10=r40hcfec24a_2
   - r-ggplot2=3.3.3=r40hc72bb7e_0
   - r-glue=1.4.2=r40hcfec24a_0
   - r-googledrive=1.0.1=r40h6115d3f_1
@@ -281,6 +285,8 @@ dependencies:
   - r-rvest=1.0.0=r40hc72bb7e_0
   - r-scales=1.1.1=r40h6115d3f_0
   - r-selectr=0.4_2=r40h6115d3f_1
+  - r-sp=1.4_5=r40hcfec24a_0
+  - r-stringdist=0.9.6.3=r40hcfec24a_0
   - r-stringi=1.6.2=r40hcabe038_0
   - r-stringr=1.4.0=r40h6115d3f_2
   - r-svglite=2.0.0=r40h03ef668_0
@@ -354,4 +360,4 @@ dependencies:
   - yarl=1.6.3=py39h3811e60_1
   - zipp=3.4.1=pyhd8ed1ab_0
   - zlib=1.2.11=h516909a_1010
-  - zstd=1.5.0=ha95c52a_0
+  - zstd=1.5.0=ha95c52a_0

config.yaml

@@ -60,7 +60,7 @@ exp_lg: 24
 iterations: 100
 
 # Set threads_per to the number of threads you would like to use per linkage group for ordering
-threads_per: 5
+threads_per: 2
 
 # Choose your distance method by commenting the line you dont want
 dist_method: "useKosambi=1"
@@ -76,22 +76,22 @@ phase_iterations: 2
 # Edge trimming will examine the first and last X% of markers in a linkage group
 # and remove clusters that are N centimorgans away from the next marker
 # you can "skip" trimming by making edge_length really low (e.g. 1)
-# and trim_cutoff really high (e.g. 40) 
+# and trim_cutoff really high (e.g. 50) 
 
 # Set edge_length to the percent number of markers you would like to examine from either end of the linkage group
 # Value can be an integer or decimal, i.e. 15 is the same as 0.15, which both mean "15%"
-edge_length: 15
+edge_length: 1
 
 # Set trim_cuttoff to the centiMorgan distance cutoff (10 is reasonable)
-trim_cutoff: 10 
+trim_cutoff: 40 
 
 
 
 ####################
 #### Lep-Anchor ####
 ####################
 # change this to true if you also want to run Lep-Anchor
-run_lepanchor: false
+run_lepanchor: true
 
 # the path to the genome assembly you are trying to anchor
 # ideally it *is not* gzipped and ends in .fa, but there are built-in workarounds if it is. 
@@ -114,3 +114,19 @@ proximity_file: "/dev/null"
 OS_info: "Ubuntu"
 #OS_info: "CentOS5"
 #OS_info: "CentOS6"
+
+
+#-----------------#
+#  Edge Trimming  #
+#-----------------#
+# Edge trimming will examine the first and last X% of markers in a linkage group
+# and remove clusters that are N% centimorgans (of the total cM span) away from 
+# the next marker. You can "skip" trimming by making edge_length really low (e.g. 1)
+# and trim_cutoff really high (e.g. 50) 
+
+# Set edge_length to the percent number of markers you would like to examine from either end of the linkage group
+# Value can be an integer or decimal, i.e. 15 is the same as 0.15, which both mean "15%"
+LA_edge_length: 20
+
+# Set trim_cuttoff to the centiMorgan distance cutoff (5 is reasonable)
+LA_trim_cutoff: 3