--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pybedtools/settings.py	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,104 @@
+_bedtools_path = ""
+_R_path = ""
+
+tempfile_prefix = "pybedtools."
+tempfile_suffix = ".tmp"
+
+# Checking for BEDTools will happen when creating the first BedTool; other
+# checks happen at first use (BAM object creation; tabix-ing a BedTool)
+_bedtools_installed = False
+_R_installed = False
+_v_2_15_plus = False
+_v_2_27_plus = False
+bedtools_version = []
+
+KEEP_TEMPFILES = False
+_DEBUG = True
+
+# Check calls against these names to only allow calls to known BEDTools
+# programs (basic security)
+#
+_prog_names = {
+    # Genome arithmetic
+    "intersectBed": "intersect",
+    "windowBed": "window",
+    "closestBed": "closest",
+    "coverageBed": "coverage",
+    "mapBed": "map",
+    "genomeCoverageBed": "genomecov",
+    "mergeBed": "merge",
+    "clusterBed": "cluster",
+    "complementBed": "complement",
+    "subtractBed": "subtract",
+    "slopBed": "slop",
+    "shiftBed": "shift",
+    "flankBed": "flank",
+    "sortBed": "sort",
+    "randomBed": "random",
+    "shuffleBed": "shuffle",
+    "annotateBed": "annotate",
+    "spacing": "spacing",
+    # multi-way
+    "multiIntersectBed": "multiinter",
+    "unionBedGraphs": "unionbedg",
+    # PE
+    "pairToBed": "pairtobed",
+    "pairToPair": "pairtopair",
+    # format conversion
+    "bamToBed": "bamtobed",
+    "bedToBam": "bedtobam",
+    "bedpeToBam": "bedpetobam",
+    "bed12ToBed6": "bed12tobed6",
+    "bamToFastq": "bamtofastq",
+    # fasta
+    "fastaFromBed": "getfasta",
+    "maskFastaFromBed": "maskfasta",
+    "nucBed": "nuc",
+    # bam-centric
+    "multiBamCov": "multicov",
+    "tagBam": "tag",
+    # stats
+    "jaccard": "jaccard",
+    "reldist": "reldist",
+    # misc
+    "getOverlap": "overlap",
+    "bedToIgv": "igv",
+    "linksBed": "links",
+    "windowMaker": "makewindows",
+    "groupBy": "groupby",
+    "expandCols": "expand",
+    "sample": "sample",
+    "fisher": "fisher",
+    "split": "split",
+}
+
+_old_names = list(_prog_names.keys())
+_new_names = list(_prog_names.values())
+
+_column_names = {
+    "bed": [
+        "chrom",
+        "start",
+        "end",
+        "name",
+        "score",
+        "strand",
+        "thickStart",
+        "thickEnd",
+        "itemRgb",
+        "blockCount",
+        "blockSizes",
+        "blockStarts",
+    ],
+    "gff": [
+        "seqname",
+        "source",
+        "feature",
+        "start",
+        "end",
+        "score",
+        "strand",
+        "frame",
+        "attributes",
+    ],
+}