File: update-kalign-invocation.patch

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Description: update kalign invocation arguments.
Author: Étienne Mollier <emollier@debian.org>
Bug-Debian: https://bugs.debian.org/1129866
Forwarded: no
Last-Update: 2026-03-09
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- bioperl-run.orig/lib/Bio/Tools/Run/Alignment/Kalign.pm
+++ bioperl-run/lib/Bio/Tools/Run/Alignment/Kalign.pm
@@ -464,7 +464,7 @@
 	undef $tfh;
 	$self->outfile_name($outfile);
     }
-    $param_string .= " -out ".$self->outfile_name;
+    $param_string .= " -i - -o ".$self->outfile_name;
     
     if ($self->quiet() || $self->verbose < 0) {
 	my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';