Merge pull request #77 from databio/ref_validator_refactoring

Ref validator refactoring

bedboss/_version.py

@@ -1 +1 @@
-__version__ = "0.4.0"
+__version__ = "0.5.0"

bedboss/bedbuncher/tools/bedsetStat.R

@@ -67,7 +67,7 @@ if (is.null(opt$json)) {
 #'
 #' Calculates how many regionsets (bedfiles) overlap at least said percentage 
 #' of regions included in the universe. The universe is considered a union of 
-#' all regionsets (bedfiles) in the colection of 
+#' all regionsets (bedfiles) in the collection of 
 #' regionsets (bedset, or set of bedfiles)
 #'
 #' @param queryList GRangesList object with regionsets to be considered

bedboss/bedmaker/utils.py

@@ -22,7 +22,7 @@ def get_chrom_sizes(genome: str, rfg_config: Union[str, Path]) -> str:
     """
 
     _LOGGER.info("Determining path to chrom.sizes asset via Refgenie.")
-    # initalizing refginie config file
+    # initializing refginie config file
     rgc = get_rgc(rfg_config=rfg_config)
 
     try:

bedboss/bedstat/tools/regionstat.R

@@ -314,7 +314,7 @@ doItAall <- function(query, fileId, genome, cellMatrix) {
     ) 
   }
 
-  # QThist plot
+  # QThis plot
   if (exists("bedmeta")){
     if ("mean_region_width" %in% names(bedmeta)){
       run_plot = FALSE

bedboss/cli.py

@@ -552,7 +552,7 @@ def convert_universe(
 def check_requirements():
     from bedboss.bedboss import requirements_check
 
-    print("Checking piplines requirements...")
+    print("Checking pipelines requirements...")
     requirements_check()
 
 

bedboss/refgenome_validator/__init__.py

@@ -1,4 +1,2 @@
 from bedboss.refgenome_validator.genome_model import GenomeModel
-from bedboss.refgenome_validator.refgenomevalidator import RefValidator
-
-# __all__ = ["GenomeModel"]
+from bedboss.refgenome_validator.main import ReferenceValidator