Cluster

bin/2.1_clustering/cdhit_wrapper.R

@@ -199,6 +199,11 @@ cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed"
     data.table::fwrite(x = cluster_table, file = summary, append = TRUE, sep = "\t", col.names = TRUE)
   }
 
+
+  # cast start and end column to integer64 to prevent scientific notation e.g. 1e+10
+  # start and end are assumed to be at position 2 and 3
+  result[, c(2, 3) := lapply(.SD, bit64::as.integer64), .SDcols = c(2, 3)]
+
   data.table::fwrite(x = result, file = output, sep = "\t", col.names = keep_col_names)
 }
 

bin/2.1_clustering/reduce_sequence.R

@@ -231,6 +231,10 @@ reduce_sequence <- function(input, kmer = 10, motif = 10, output = "reduced.bed"
     names(merged) <- col_names
   }
 
+  # cast start and end column to integer64 to prevent scientific notation e.g. 1e+10
+  # start and end are assumed to be at position 2 and 3
+  merged[, c(2, 3) := lapply(.SD, bit64::as.integer64), .SDcols = c(2, 3)]
+
   data.table::fwrite(merged, file = output, sep = "\t", col.names = keep_col_names)
 }
 

masterenv.yml

@@ -21,3 +21,4 @@ dependencies:
   - matplotlib
   - seaborn
   - crossmap
+  - r-bit64