56aff44eacee07bc3679dd18fe70ad621f6142d5
hiram
  Mon Sep 1 23:45:50 2025 -0700
allow stdin as argument to asciiTree and updated perl issues for binaryTree

diff --git src/hg/utils/phyloTrees/binaryTree.pl src/hg/utils/phyloTrees/binaryTree.pl
index ae6a11c7ea3..346587ba353 100755
--- src/hg/utils/phyloTrees/binaryTree.pl
+++ src/hg/utils/phyloTrees/binaryTree.pl
@@ -61,31 +61,32 @@
 #	This 'string' becomes the internal node 'name' of this branch, and
 #	the distance is recorded.  The 'parent' of this branch becomes
 #	the 'current' node.
 # 4 effectively ignoring the commas.  They are supposed to mean the next
 #	element goes into the left, but we are keeping track of this
 #	with the nextLeft boolean.  The polytomys are a series of elements
 #	more than two, with commas at the ends of the element names
 #
 # Tree print: recursive function:
 # 1. if right pointer exists output (  and print right tree then
 #        if left pointer, output )nodeName:length, and print left tree
 # 2. no pointers, this is a leaf, print name:length when parent right
 #	pointer got here, else print ,name:length when left pointer got here
 
 use strict;
-use warnings;
+use warnings FATAL => 'all';
+no warnings 'recursion';
 use Getopt::Long;
 
 ##############################################################################
 sub usage() {
   printf STDERR "usage: binaryTree.pl [options] file.phy
 options:
   -noInternal - do not output internal node names
   -defaultDistance=0.1 - use this distance when not given in input
   -allDistances=0.1 - use this distance for everything, default use input
   -lineOutput - output one line per leaf output, indented per depth
   -quoteNames - add 'quotes' on node names, default not quoted
   -nameTranslate=<file> - two column file, translate names from input file,
 	first column is name in input file, second column is output name
 	tab separation columns
   -bothNames - during nameTranslate, use both names in output: name1/name2