Merge per-sample counts with full outer join

VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

ervx

@@ -23,7 +23,7 @@ import argparse  # potential python3 3rd party package, added in python/3.5
 
 # Pipeline Metadata and globals 
 __author__   = 'Skyler Kuhn'
-__version__  = 'v0.1.1'
+__version__  = 'v0.1.2'
 __email__    = '[email protected]'
 __home__     =  os.path.dirname(os.path.abspath(__file__))
 _name        = os.path.basename(sys.argv[0])

workflow/scripts/telescope_count_merge.R

@@ -39,8 +39,11 @@ print("LIST:")
 print(l)
 print("List Length:")
 print(length(l))
-counts_merged <- Reduce(function (...) { merge(..., all = FALSE, by = "transcript") },   # Inner join
-                        l)
+# Merge per-sample counts using a full 
+# outer join and set missing values to 0
+counts_merged <- Reduce(function (...) { merge(..., all = TRUE, by = "transcript") }, l)
+counts_merged[is.na(counts_merged)] <- 0
+
 if (is.null(family_anno_table)){
   write.csv(counts_merged, paste0(out_dir,"/counts.csv"), row.names=FALSE)
   } else {