7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

diff --git src/htslib/test/test_view.pl src/htslib/test/test_view.pl
deleted file mode 100755
index 2df34830c20..00000000000
--- src/htslib/test/test_view.pl
+++ /dev/null
@@ -1,93 +0,0 @@
-#! /usr/bin/env perl
-#
-#    Copyright (C) 2013 Genome Research Ltd.
-#
-#    Author: James Bonfield <jkb@sanger.ac.uk>
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-# DEALINGS IN THE SOFTWARE.
-use strict;
-use warnings;
-
-my $err_count = 0;
-my $suc_count = 0;
-
-sub test {
-    my ($cmd) = @_;
-    print "  $cmd\n";
-    if (system("$cmd || exit 1") != 0) {
-        print "FAIL $!\n";
-        $err_count++;
-    } else {
-        $suc_count++;
-    }
-}
-
-foreach my $sam (glob("*#*.sam")) {
-    my ($base, $ref) = ($sam =~ /((.*)#.*)\.sam/);
-    $ref .= ".fa";
-
-    my $bam  = "$base.tmp.bam";
-    my $cram = "$base.tmp.cram";
-
-    print "\n=== Testing $sam, ref $ref ===\n";
-
-    # SAM -> BAM -> SAM
-    test "./test_view -S -b $sam > $bam";
-    test "./test_view $bam > $bam.sam_";
-    test "./compare_sam.pl $sam $bam.sam_";
-
-    # SAM -> CRAM -> SAM
-    test "./test_view -t $ref -S -C $sam > $cram";
-    test "./test_view -D $cram > $cram.sam_";
-    test "./compare_sam.pl -nomd $sam $cram.sam_";
-
-    # BAM -> CRAM -> BAM -> SAM
-    $cram = "$bam.cram";
-    test "./test_view -t $ref -C $bam > $cram";
-    test "./test_view -b -D $cram > $cram.bam";
-    test "./test_view $cram.bam > $cram.bam.sam_";
-    test "./compare_sam.pl -nomd $sam $cram.bam.sam_";
-
-    # SAM -> CRAM3 -> SAM
-    $cram = "$base.tmp.cram";
-    test "./test_view -t $ref -S -C -o VERSION=3.0 $sam > $cram";
-    test "./test_view -D $cram > $cram.sam_";
-    test "./compare_sam.pl -nomd $sam $cram.sam_";
-
-    # BAM -> CRAM3 -> BAM -> SAM
-    $cram = "$bam.cram";
-    test "./test_view -t $ref -C -o VERSION=3.0 $bam > $cram";
-    test "./test_view -b -D $cram > $cram.bam";
-    test "./test_view $cram.bam > $cram.bam.sam_";
-    test "./compare_sam.pl -nomd $sam $cram.bam.sam_";
-
-    # CRAM3 -> CRAM2
-    $cram = "$base.tmp.cram";
-    test "./test_view -t $ref -C -o VERSION=2.1 $cram > $cram.cram";
-
-    # CRAM2 -> CRAM3
-    test "./test_view -t $ref -C -o VERSION=3.0 $cram.cram > $cram";
-    test "./test_view $cram > $cram.sam_";
-    test "./compare_sam.pl -nomd $sam $cram.sam_";
-}
-
-print "\nSuccesses $suc_count\n";
-print "\nFailures  $err_count\n";
-
-exit ($err_count > 0);