feat: add seqinfo to gi if pairs format is 4dn

js2264 · Oct 4, 2023 · 3232261 · 3232261
1 parent 3807f49
commit 3232261
Showing 1 changed file with 15 additions and 0 deletions.
diff --git a/R/parse-pairs.R b/R/parse-pairs.R
@@ -208,6 +208,21 @@
 
     # -- Add pairdist
     gi$distance <- InteractionSet::pairdist(gi) 
+
+    # -- Add seqinfo
+    if (.fmt == '4dn') {
+        chrs <- fileComments |> 
+            grep('#chromsize: ', x = _, value = TRUE) |>
+            gsub("#chromsize: ", "", x = _)
+        si <- gsub(".* ", "", chrs)
+        names(si) <- gsub(" .*", "", chrs)
+        GenomeInfoDb::seqlevels(gi) <- names(si)
+        GenomeInfoDb::seqinfo(gi) <- GenomeInfoDb::Seqinfo(
+            names(si), 
+            as.numeric(si)
+        )
+    }
+
     return(gi)
 }