This fixes broken tests due to msys2 changes. (#1892)

Due to changes in how msys2 perl reported the identity of the OS it was built
for, our tests were failing to adapt to the Windows style file locations.

Background:
https://www.msys2.org/news/#2025-02-14-moving-msys2-closer-to-cygwin

Msys2 PR:
msys2/MSYS2-packages#5177

Author: whitwham

test/test-bcf-sr.pl

@@ -71,7 +71,7 @@ sub parse_params
         error("Unknown parameter \"$arg\". Run -h for help.\n");
     }
     $$opts{tmp} = exists($$opts{keep_files}) ? $$opts{keep_files} : tempdir(CLEANUP=>1);
-    if ($^O =~ /^msys/) {
+    if ($^O =~ /^(cygwin|msys)/) {
         $$opts{tmp} = cygpath($$opts{tmp});
     }
     if ( $$opts{keep_files} ) { cmd("mkdir -p $$opts{keep_files}"); }

test/test.pl

@@ -104,7 +104,7 @@ sub cygpath {
 sub safe_tempdir
 {
     my $dir = tempdir(CLEANUP=>1);
-    if ($^O =~ /^msys/) {
+    if ($^O =~ /^(cygwin|msys)/) {
         $dir = cygpath($dir);
     }
     return $dir;
@@ -129,7 +129,7 @@ sub parse_params
     $$opts{path} = $FindBin::RealBin;
     $$opts{bin}  = $FindBin::RealBin;
     $$opts{bin}  =~ s{/test/?$}{};
-    if ($^O =~ /^msys/) {
+    if ($^O =~ /^(cygwin|msys)/) {
         $$opts{path} = cygpath($$opts{path});
         $$opts{bin}  = cygpath($$opts{bin});
     }
@@ -1085,7 +1085,7 @@ sub test_index
     # Tabix and custom index names
     _cmd("$$opts{bin}/tabix -fp vcf $$opts{tmp}/index.vcf.gz");
     my $wtmp = $$opts{tmp};
-    if ($^O =~ /^msys/) {
+    if ($^O =~ /^(cygwin|msys)/) {
         $wtmp =~ s/\//\\\\/g;
     }
     test_cmd($opts,out=>'tabix.out',cmd=>"$$opts{bin}/tabix $wtmp/index.vcf.gz##idx##$wtmp/index.vcf.gz.tbi 1:10000060-10000060");