support samtools >= 1.10

bio-tradis (1.4.5+dfsg-2) UNRELEASED; urgency=medium

  * Team upload.

  * debian/patches/samtools1.10: remove version parsing code that can't handle

    samtools version 1.10

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 25 Dec 2019 13:28:31 +0100

bio-tradis (1.4.5+dfsg-1) unstable; urgency=medium

  * Team upload.

Author: Michael R. Crusoe <michael.crusoe@gmail.com>

Description: skip broken samtools version parsing code that can't handle version 1.10+

--- bio-tradis.orig/lib/Bio/Tradis/Samtools.pm

+++ bio-tradis/lib/Bio/Tradis/Samtools.pm

@@ -20,40 +20,6 @@

 has 'exec'         => ( is => 'ro', isa => 'Str', default => 'samtools' );

 has 'threads'      => ( is => 'ro', isa => 'Int', default => 1 );

-has 'exec_version' => ( is => 'ro', isa => 'Str', lazy    => 1, builder => '_build_exec_version' );

-

-sub _build_exec_version {

-    my ($self) = @_;

-		

-    my $fp = $self->find_exe($self->exec);

-		if(!$fp)

-		{

-			 exit("ERROR: Can't find required ".$self->exec." in your \$PATH");

-  	}

-		my $cmd_version = $self->exec." 2>&1 | grep Version";

-		my ($version_string) = qx($cmd_version);

-		

-		if(defined($version_string))

-		{

-			#Version: 0.1.19-44428cd

-			#Version: 1.2 (using htslib 1.2)

-			# we dont use 3rd number in version so just look for 0.1, 1.2

-			if($version_string =~ /Version:[\t\s]+(\d+)\.(\d+)/)

-			{

-				return $1.'.'.$2;

-			}

-			else

-			{

-				print STDERR "ERROR: Couldn't identify samtools version";

-			}

-		}

-		else

-		{

-			print STDERR "ERROR: Couldn't identify samtools version";

-		}

-		# reasonable fallback

-    return '0.1';

-}

 sub find_exe {

     my ( $self, $bin ) = @_;

@@ -64,29 +30,12 @@

     return;

 }

-sub _is_version_less_than_1 {

-    my ($self) = @_;

-    if($self->exec_version < 1.0)

-		{

-			return 1;

-		}

-		else

-		{

-			return 0;

-		}

-}

 sub run_sort {

     my ( $self, $input_file, $output_file ) = @_;

     my $cmd;

-    if ( $self->_is_version_less_than_1 ) {

-			  $output_file =~ s/\.bam//i;

-        $cmd = join( ' ', ( $self->exec, 'sort', $input_file, $output_file) );

-    }

-    else {

-        $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp',  '-o', $output_file, $input_file ) );

-    }

+    $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp',  '-o', $output_file, $input_file ) );

     system($cmd);

 }

samtools1.10

#!/usr/bin/make -f

# DH_VERBOSE := 1

DH_VERBOSE := 1

export LC_ALL=C.UTF-8

TEST_FILES = $(shell find t -name "*.t")