ENH count.ngl

Key Changes:

    Added filter() step with samflag(secondary=False) which is the NGless equivalent of -F 256

    The filtered alignments are then passed to count()

    Maintained your existing integer conversion and output

Author: celiosantosjr

macrel/data/scripts/count.ngl

@@ -1,10 +1,16 @@
 ngless "1.0"
 
-input = samfile(ARGV[1], name='MACREL')
-counts = count(input,
+# First filter to keep only primary alignments
+filtered = filter(input, keep_if=[
+    samflag(secondary=False)  # -F 256 equivalent
+])
+
+# Then count on the filtered alignments
+counts = count(filtered,
     features=["seqname"],
     include_minus1=False,
-    counts = as_integer(round(counts))
     normalization={raw})
 
+# Ensure integer counts
+counts = as_integer(round(counts))
 write(counts, ofile=ARGV[2])