[galaxy-dev] [hg] galaxy 3153: Merge with 24f195c617da80ae71dd8281b7517973301...

11 Dec 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/14214b45db3f
changeset: 3153:14214b45db3f
user:      rc
date:      Mon Dec 07 14:45:47 2009 -0500
description:
Merge with 24f195c617da80ae71dd8281b75179733016bcb6

diffstat:

 buildbot_setup.sh                                |   16 +-
 lib/galaxy/datatypes/binary.py                   |   49 ++-
 lib/galaxy/datatypes/sequence.py                 |   36 +--
 lib/galaxy/datatypes/test/1.bam                  |      
 lib/galaxy/tools/__init__.py                     |   47 +---
 lib/galaxy/tools/parameters/basic.py             |   71 +++--
 lib/galaxy/tools/parameters/input_translation.py |  106 ++++++++
 lib/galaxy/tools/parameters/sanitize.py          |  167 +++++++++++++
 lib/galaxy/tools/util/maf_utilities.py           |   11 +-
 lib/galaxy/util/__init__.py                      |   66 +-----
 lib/galaxy/web/controllers/async.py              |    2 +-
 lib/galaxy/web/controllers/root.py               |    2 +-
 lib/galaxy/web/controllers/tool_runner.py        |    9 +-
 test-data/1.bam                                  |      
 test-data/2.sam                                  |   10 +
 test-data/2.tabular                              |   20 +-
 test-data/3.sam                                  |   10 +
 test-data/chrM.fa                                |  335 ---------------------------
 test-data/chr_m.fasta                            |  335 +++++++++++++++++++++++++++
 test-data/joiner_out3.bed                        |   32 +-
 test-data/sam_to_bam_in1.sam                     |   10 -
 test-data/sam_to_bam_in2.sam                     |   10 -
 test-data/sam_to_bam_out1.bam                    |      
 test-data/sam_to_bam_out2.bam                    |      
 tools/data_source/biomart.xml                    |   17 +-
 tools/data_source/biomart_test.xml               |   17 +-
 tools/data_source/data_source.py                 |    2 +
 tools/data_source/epigraph_import.xml            |    3 +-
 tools/data_source/epigraph_import_test.xml       |    3 +-
 tools/data_source/eupathdb.xml                   |   19 +-
 tools/data_source/flymine.xml                    |    3 +-
 tools/data_source/flymine_test.xml               |    3 +-
 tools/data_source/gramene_mart.xml               |   17 +-
 tools/data_source/modmine.xml                    |    3 +-
 tools/data_source/ratmine.xml                    |    3 +-
 tools/data_source/ucsc_tablebrowser.xml          |   19 +-
 tools/data_source/ucsc_tablebrowser_archaea.xml  |   23 +-
 tools/data_source/ucsc_tablebrowser_test.xml     |   23 +-
 tools/data_source/upload.py                      |   57 +++-
 tools/data_source/wormbase.xml                   |   17 +-
 tools/data_source/wormbase_test.xml              |   17 +-
 tools/emboss_5/emboss_fuzznuc.xml                |   12 +-
 tools/filters/grep.py                            |   41 ++-
 tools/filters/grep.xml                           |   13 +-
 tools/filters/joiner.xml                         |    2 +-
 tools/plotting/xy_plot.xml                       |    7 +-
 tools/samtools/sam_to_bam.py                     |  134 ++++++----
 tools/samtools/sam_to_bam.xml                    |   43 +--
 tools/sr_mapping/bowtie_wrapper.xml              |    4 +-
 tools/sr_mapping/lastz_wrapper.xml               |   31 +-
 50 files changed, 1084 insertions(+), 793 deletions(-)

diffs (2808 lines):

diff -r b01c8245ef74 -r 14214b45db3f buildbot_setup.sh

--- a/buildbot_setup.sh	Mon Dec 07 14:45:09 2009 -0500
+++ b/buildbot_setup.sh	Mon Dec 07 14:45:47 2009 -0500
@@ -2,13 +2,22 @@
 
 cd `dirname $0`
 
+: ${HOSTTYPE:=`uname -m`}
+
+# link to HYPHY is arch-dependent
+case "$OSTYPE" in
+    linux-gnu)
+        kernel=`uname -r | cut -f1,2 -d.`
+        HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy"
+        ;;
+esac
+
 LINKS="
 /depot/data2/galaxy/alignseq.loc
 /depot/data2/galaxy/binned_scores.loc
 /depot/data2/galaxy/blastdb.loc
 /depot/data2/galaxy/bowtie_indices.loc
 /depot/data2/galaxy/encode_datasets.loc
-/home/universe/linux-i686/HYPHY
 /depot/data2/galaxy/lastz_seqs.loc
 /depot/data2/galaxy/liftOver.loc
 /depot/data2/galaxy/maf_index.loc
@@ -44,6 +53,11 @@
     ln -sf $link tool-data
 done
 
+if [ -d "$HYPHY" ]; then
+    echo "Linking $HYPHY"
+    ln -sf $HYPHY tool-data/HYPHY
+fi
+
 for sample in $SAMPLES; do
     file=`echo $sample | sed -e 's/\.sample$//'`
     echo "Copying $sample to $file"
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/datatypes/binary.py	Mon Dec 07 14:45:47 2009 -0500
@@ -7,7 +7,7 @@
 from galaxy.datatypes import metadata
 from galaxy.datatypes.sniff import *
 from urllib import urlencode, quote_plus
-import zipfile
+import zipfile, gzip
 import os, subprocess, tempfile
 
 log = logging.getLogger(__name__)
@@ -54,32 +54,35 @@
 
     def init_meta( self, dataset, copy_from=None ):
         Binary.init_meta( self, dataset, copy_from=copy_from )
-        """
-        GVK 12/2/09: just noticed this - not good and doesn't work, so commenting out for now.
-        def set_meta( self, dataset, overwrite = True, **kwd ):
-            # Sets index for BAM file.
-            index_file = dataset.metadata.bam_index
-            if not index_file:
-                index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset )
+    def set_meta( self, dataset, overwrite = True, **kwd ):
+        """ Sets index for BAM file. """
+        # These metadata values are not accessible by users, always overwrite
+        index_file = dataset.metadata.bam_index
+        if not index_file:
+            index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset )
+        try:
+            # Using a symlink from ~/database/files/dataset_XX.dat, create a temporary file
+            # to store the indexex generated from samtools, something like ~/tmp/dataset_XX.dat.bai
             tmp_dir = tempfile.gettempdir()
-            tmpf1 = tempfile.NamedTemporaryFile( dir=tmp_dir )
-            tmpf1bai = '%s.bai' % tmpf1.name
-            try:
-                os.system( 'cd %s' % tmp_dir )
-                os.system( 'cp %s %s' % ( dataset.file_name, tmpf1.name ) )
-                os.system( 'samtools index %s' % tmpf1.name )
-                os.system( 'cp %s %s' % ( tmpf1bai, index_file.file_name ) )
-            except Exception, ex:
-                sys.stderr.write( 'There was a problem creating the index for the BAM file\n%s\n' + str( ex ) )
-            tmpf1.close()
-            if os.path.exists( tmpf1bai ):
-                os.remove( tmpf1bai )
-            dataset.metadata.bam_index = index_file
-        """
+            tmp_file_path = os.path.join( tmp_dir, os.path.basename( dataset.file_name ) )
+            # Here tmp_file_path looks something like /tmp/dataset_XX.dat
+            os.symlink( dataset.file_name, tmp_file_path )
+            command = 'samtools index %s' % tmp_file_path
+            proc = subprocess.Popen( args=command, shell=True )
+            proc.wait()
+        except:
+            err_msg = 'Error creating index file (%s) for BAM file (%s)' % ( str( tmp_file_path ), str( dataset.file_name ) )
+            log.exception( err_msg )
+            sys.stderr.write( err_msg )
+        # Move the temporary index file ~/tmp/dataset_XX.dat.bai to be ~/database/files/_metadata_files/dataset_XX.dat
+        shutil.move( '%s.bai' % ( tmp_file_path ), index_file.file_name )
+        os.unlink( tmp_file_path )
+        dataset.metadata.bam_index = index_file
     def sniff( self, filename ):
+        # BAM is compressed in the BGZF format, and must not be uncompressed in Galaxy.
         # The first 4 bytes of any bam file is 'BAM\1', and the file is binary. 
         try:
-            header = open( filename ).read(4)
+            header = gzip.open( filename ).read(4)
             if binascii.b2a_hex( header ) == binascii.hexlify( 'BAM\1' ):
                 return True
             return False
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/datatypes/sequence.py	Mon Dec 07 14:45:47 2009 -0500
@@ -309,35 +309,21 @@
             return #this is not a MAF file
         dataset.metadata.species = species
         dataset.metadata.blocks = blocks
-        #only overwrite the contents if our newly determined chromosomes don't match stored
+        
+        #write species chromosomes to a file
         chrom_file = dataset.metadata.species_chromosomes
-        compare_chroms = {}
-        if chrom_file:
-            try:
-                for line in open( chrom_file.file_name ):
-                    fields = line.split( "\t" )
-                    if fields:
-                        spec = fields.pop( 0 )
-                        if spec:
-                            compare_chroms[spec] = fields
-            except:
-                pass
-        #write out species chromosomes again only if values are different
-        if not species_chromosomes or compare_chroms != species_chromosomes:
-            tmp_file = tempfile.TemporaryFile( 'w+b' )
-            for spec, chroms in species_chromosomes.items():
-                tmp_file.write( "%s\t%s\n" % ( spec, "\t".join( chroms ) ) )
-            
-            if not chrom_file:
-                chrom_file = dataset.metadata.spec['species_chromosomes'].param.new_file( dataset = dataset )
-            tmp_file.seek( 0 )
-            open( chrom_file.file_name, 'wb' ).write( tmp_file.read() )
-            dataset.metadata.species_chromosomes = chrom_file
-            tmp_file.close()
+        if not chrom_file:
+            chrom_file = dataset.metadata.spec['species_chromosomes'].param.new_file( dataset = dataset )
+        chrom_out = open( chrom_file.file_name, 'wb' )
+        for spec, chroms in species_chromosomes.items():
+            chrom_out.write( "%s\t%s\n" % ( spec, "\t".join( chroms ) ) )
+        chrom_out.close()
+        dataset.metadata.species_chromosomes = chrom_file
+        
         index_file = dataset.metadata.maf_index
         if not index_file:
             index_file = dataset.metadata.spec['maf_index'].param.new_file( dataset = dataset )
-        indexes.write( open( index_file.file_name, 'w' ) )
+        indexes.write( open( index_file.file_name, 'wb' ) )
         dataset.metadata.maf_index = index_file
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/datatypes/test/1.bam
Binary file lib/galaxy/datatypes/test/1.bam has changed
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/tools/__init__.py	Mon Dec 07 14:45:47 2009 -0500
@@ -17,6 +17,7 @@
 from parameters import *
 from parameters.grouping import *
 from parameters.validation import LateValidationError
+from parameters.input_translation import ToolInputTranslator
 from galaxy.util.expressions import ExpressionContext
 from galaxy.tools.test import ToolTestBuilder
 from galaxy.tools.actions import DefaultToolAction
@@ -299,48 +300,10 @@
         self.tool_type = root.get( "tool_type", None )
         #Force history to fully refresh after job execution for this tool. Useful i.e. when an indeterminate number of outputs are created by a tool.
         self.force_history_refresh = util.string_as_bool( root.get( 'force_history_refresh', 'False' ) )
-        # data_source tool
-        if self.tool_type == "data_source":
-            self.URL_method = root.get( "URL_method", "get" ) # get is the default
-            self.param_trans_dict = {}
-            req_param_trans = root.find( "request_param_translation" )
-            if req_param_trans is not None:
-                for req_param in req_param_trans.findall( "request_param" ):
-                    # req_param tags must look like <request_param galaxy_name="dbkey" remote_name="GENOME" missing="" />
-                    trans_list = []
-                    remote_name = req_param.get( "remote_name" )
-                    trans_list.append( req_param.get( "galaxy_name" ) )
-                    trans_list.append( req_param.get( "missing" ) )
-                    if req_param.get( "galaxy_name" ) == "data_type":
-                        # The req_param tag for data_type is special in that it can contain another tag set like
-                        # <data_type_translation>
-                        #    <format galaxy_format="tabular" remote_format="selectedFields" />
-                        # </data_type_translation>
-                        format_trans = req_param.find( "data_type_translation" )
-                        if format_trans is not None:
-                            format_trans_dict = {}
-                            for format in format_trans.findall( "format" ):
-                                remote_format = format.get( "remote_format" )
-                                galaxy_format = format.get( "galaxy_format" )                        
-                                format_trans_dict[ remote_format ] = galaxy_format
-                            trans_list.append( format_trans_dict )
-                    elif req_param.get( "galaxy_name" ) == "URL":
-                        # Some remote data sources ( e.g., Gbrowse ) send parameters back to
-                        # Galaxy in the initial response that must be added to URL prior to
-                        # Galaxy sending the secondary request to the URL.  The tag set looks
-                        # asomething like:
-                        # <add_to_url>
-                        #    <param_from_source name="d" missing="" />
-                        # </add_to_url>
-                        add_to_url = req_param.find( "add_to_url" )
-                        if add_to_url is not None:
-                            add_to_url_dict = {}
-                            for param_from_source in add_to_url.findall( "param_from_source" ):
-                                name = param_from_source.get( "name" )
-                                value = param_from_source.get( "missing" ) # only used if the source doesn't send the param name                     
-                                add_to_url_dict[ name ] = value
-                            trans_list.append( add_to_url_dict )
-                    self.param_trans_dict[ remote_name ] = trans_list
+        #load input translator, used by datasource tools to change names/values of incoming parameters
+        self.input_translator = root.find( "request_param_translation" )
+        if self.input_translator:
+            self.input_translator = ToolInputTranslator.from_element( self.input_translator )
         # Command line (template). Optional for tools that do not invoke a local program  
         command = root.find("command")
         if command is not None and command.text is not None:
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/tools/parameters/basic.py	Mon Dec 07 14:45:47 2009 -0500
@@ -7,6 +7,8 @@
 from galaxy import config, datatypes, util
 from galaxy.web import form_builder
 from galaxy.util.bunch import Bunch
+from galaxy.util import string_as_bool, sanitize_param
+from sanitize import ToolParameterSanitizer
 import validation, dynamic_options
 # For BaseURLToolParameter
 from galaxy.web import url_for
@@ -28,7 +30,9 @@
         self.type = param.get("type")
         self.label = util.xml_text(param, "label")
         self.help = util.xml_text(param, "help")
-        self.unsanitize = param.get( "unsanitize", None )
+        self.sanitizer = param.find( "sanitizer" )
+        if self.sanitizer is not None:
+            self.sanitizer = ToolParameterSanitizer.from_element( self.sanitizer )
         self.html = "no html set"
         self.repeat = param.get("repeat", None)
         self.condition = param.get( "condition", None )
@@ -122,7 +126,13 @@
         return value
         
     def to_param_dict_string( self, value, other_values={} ):
-        return str( value )
+        value = str( value )
+        if self.tool is None or self.tool.options.sanitize:
+            if self.sanitizer:
+                value = self.sanitizer.sanitize_param( value )
+            else:
+                value = sanitize_param( value )
+        return value
         
     def validate( self, value, history=None ):
         for validator in self.validators:
@@ -154,7 +164,7 @@
         self.name = elem.get( 'name' )
         self.size = elem.get( 'size' )
         self.value = elem.get( 'value' )
-        self.area = str_bool( elem.get( 'area', False ) )
+        self.area = string_as_bool( elem.get( 'area', False ) )
     def get_html_field( self, trans=None, value=None, other_values={} ):
         if self.area:
             return form_builder.TextArea( self.name, self.size, value or self.value )
@@ -262,7 +272,7 @@
         self.truevalue = elem.get( 'truevalue', 'true' )
         self.falsevalue = elem.get( 'falsevalue', 'false' )
         self.name = elem.get( 'name' )
-        self.checked = str_bool( elem.get( 'checked' ) )
+        self.checked = string_as_bool( elem.get( 'checked' ) )
     def get_html_field( self, trans=None, value=None, other_values={} ):
         checked = self.checked
         if value: 
@@ -299,7 +309,7 @@
         """
         ToolParameter.__init__( self, tool, elem )
         self.name = elem.get( 'name' )
-        self.ajax = str_bool( elem.get( 'ajax-upload' ) )
+        self.ajax = string_as_bool( elem.get( 'ajax-upload' ) )
     def get_html_field( self, trans=None, value=None, other_values={}  ):
         return form_builder.FileField( self.name, ajax = self.ajax, value = value )
     def from_html( self, value, trans=None, other_values={} ):
@@ -474,7 +484,7 @@
     """
     def __init__( self, tool, elem, context=None ):
         ToolParameter.__init__( self, tool, elem )
-        self.multiple = str_bool( elem.get( 'multiple', False ) )
+        self.multiple = string_as_bool( elem.get( 'multiple', False ) )
         self.display = elem.get( 'display', None )
         self.separator = elem.get( 'separator', ',' )
         self.legal_values = set()
@@ -492,7 +502,7 @@
             for index, option in enumerate( elem.findall( "option" ) ):
                 value = option.get( "value" )
                 self.legal_values.add( value )
-                selected = str_bool( option.get( "selected", False ) )
+                selected = string_as_bool( option.get( "selected", False ) )
                 self.static_options.append( ( option.text, value, selected ) )
         self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) )
     def get_options( self, trans, other_values ):
@@ -571,11 +581,19 @@
         if value is None:
             return "None"
         if isinstance( value, list ):
-            if not(self.repeat):
+            if not( self.repeat ):
                 assert self.multiple, "Multiple values provided but parameter is not expecting multiple values"
-            return self.separator.join( map( str, value ) )
+            value = map( str, value )
         else:
-            return str(value)
+            value = str( value )
+        if self.tool is None or self.tool.options.sanitize:
+            if self.sanitizer:
+                value = self.sanitizer.sanitize_param( value )
+            else:
+                value = sanitize_param( value )
+        if isinstance( value, list ):
+            value = self.separator.join( value )
+        return value
     def value_to_basic( self, value, app ):
         if isinstance( value, UnvalidatedValue ):
             return { "__class__": "UnvalidatedValue", "value": value.value }
@@ -741,9 +759,9 @@
     def __init__( self, tool, elem ):
         SelectToolParameter.__init__( self, tool, elem )
         self.tool = tool
-        self.numerical = str_bool( elem.get( "numerical", False ))
-        self.force_select = str_bool( elem.get( "force_select", True ))
-        self.accept_default = str_bool( elem.get( "accept_default", False ))
+        self.numerical = string_as_bool( elem.get( "numerical", False ))
+        self.force_select = string_as_bool( elem.get( "force_select", True ))
+        self.accept_default = string_as_bool( elem.get( "accept_default", False ))
         self.data_ref = elem.get( "data_ref", None )
         self.is_dynamic = True
     def get_column_list( self, trans, other_values ):
@@ -894,11 +912,11 @@
     def __init__( self, tool, elem, context=None ):
         def recurse_option_elems( cur_options, option_elems ):
             for option_elem in option_elems:
-                selected = str_bool( option_elem.get( 'selected', False ) )
+                selected = string_as_bool( option_elem.get( 'selected', False ) )
                 cur_options.append( { 'name':option_elem.get( 'name' ), 'value': option_elem.get( 'value'), 'options':[], 'selected':selected  } )
                 recurse_option_elems( cur_options[-1]['options'], option_elem.findall( 'option' ) )
         ToolParameter.__init__( self, tool, elem )
-        self.multiple = str_bool( elem.get( 'multiple', False ) )
+        self.multiple = string_as_bool( elem.get( 'multiple', False ) )
         self.display = elem.get( 'display', None )
         self.hierarchy = elem.get( 'hierarchy', 'exact' ) #exact or recurse
         self.separator = elem.get( 'separator', ',' )
@@ -1019,7 +1037,13 @@
         if len( rval ) > 1:
             if not( self.repeat ):
                 assert self.multiple, "Multiple values provided but parameter is not expecting multiple values"
-        return self.separator.join( rval )
+        rval = self.separator.join( rval )
+        if self.tool is None or self.tool.options.sanitize:
+            if self.sanitizer:
+                rval = self.sanitizer.sanitize_param( rval )
+            else:
+                rval = sanitize_param( rval )
+        return rval
     
     def get_initial_value( self, trans, context ):
         def recurse_options( initial_values, options ):
@@ -1094,7 +1118,7 @@
     def __init__( self, tool, elem ):
         ToolParameter.__init__( self, tool, elem )
         # Add metadata validator
-        if not str_bool( elem.get( 'no_validation', False ) ):
+        if not string_as_bool( elem.get( 'no_validation', False ) ):
             self.validators.append( validation.MetadataValidator() )
         # Build tuple of classes for supported data formats
         formats = []
@@ -1108,9 +1132,9 @@
             else:
                 formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ )
         self.formats = tuple( formats )
-        self.multiple = str_bool( elem.get( 'multiple', False ) )
+        self.multiple = string_as_bool( elem.get( 'multiple', False ) )
         # Optional DataToolParameters are used in tools like GMAJ and LAJ
-        self.optional = str_bool( elem.get( 'optional', False ) )
+        self.optional = string_as_bool( elem.get( 'optional', False ) )
         # TODO: Enhance dynamic options for DataToolParameters. Currently,
         #       only the special case key='build' of type='data_meta' is
         #       a valid filter
@@ -1366,13 +1390,4 @@
     runtime.
     """
     pass
-    
 
-def str_bool(in_str):
-    """
-    returns true/false of a string, since bool(str), always returns true if string is not empty
-    default action is to return false
-    """
-    if str(in_str).lower() == 'true' or str(in_str).lower() == 'yes':
-        return True
-    return False
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/tools/parameters/input_translation.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/tools/parameters/input_translation.py	Mon Dec 07 14:45:47 2009 -0500
@@ -0,0 +1,106 @@
+"""
+Tool Input Translation. 
+"""
+
+import logging
+from galaxy.util.bunch import Bunch
+
+log = logging.getLogger( __name__ )
+
+class ToolInputTranslator( object ):
+    """
+    Handles Tool input translation.
+    This is used for data source tools
+    
+    >>> from galaxy.util import Params
+    >>> from elementtree.ElementTree import XML
+    >>> translator = ToolInputTranslator.from_element( XML( 
+    ... '''
+    ... <request_param_translation>
+    ...  <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+    ...  <request_param galaxy_name="URL" remote_name="URL" missing="" >
+    ...     <append_param separator="&" first_separator="?" join="=">
+    ...         <value name="_export" missing="1" />
+    ...         <value name="GALAXY_URL" missing="0" />
+    ...     </append_param>
+    ...  </request_param>
+    ...  <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
+    ...  <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
+    ...  <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
+    ...  <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
+    ...  <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
+    ...   <value_translation>
+    ...    <value galaxy_value="tabular" remote_value="primaryTable" />
+    ...    <value galaxy_value="tabular" remote_value="selectedFields" />
+    ...    <value galaxy_value="wig" remote_value="wigData" />
+    ...    <value galaxy_value="interval" remote_value="tab" />
+    ...    <value galaxy_value="html" remote_value="hyperlinks" />
+    ...    <value galaxy_value="fasta" remote_value="sequence" />
+    ...   </value_translation>
+    ...  </request_param>
+    ... </request_param_translation>
+    ... ''' ) )
+    >>> params = Params( { 'db':'hg17', 'URL':'URL_value', 'org':'Human', 'hgta_outputType':'primaryTable'  } )
+    >>> translator.translate( params )
+    >>> print params
+    {'hgta_outputType': 'primaryTable', 'data_type': 'tabular', 'table': 'unknown table', 'URL': 'URL_value?GALAXY_URL=0&_export=1', 'org': 'Human', 'URL_method': 'post', 'db': 'hg17', 'organism': 'Human', 'dbkey': 'hg17', 'description': 'no description'}
+    """
+    @classmethod
+    def from_element( cls, elem ):
+        """Loads the proper filter by the type attribute of elem"""
+        rval = ToolInputTranslator()
+        for req_param in elem.findall( "request_param" ):
+            # req_param tags must look like <request_param galaxy_name="dbkey" remote_name="GENOME" missing="" />
+            #trans_list = []
+            remote_name = req_param.get( "remote_name" )
+            galaxy_name = req_param.get( "galaxy_name" )
+            missing = req_param.get( "missing" )
+            value_trans = {}
+            append_param = None
+            
+            value_trans_elem = req_param.find( 'value_translation' )
+            if value_trans_elem:
+                for value_elem in value_trans_elem.findall( 'value' ):
+                    remote_value = value_elem.get( "remote_value" )
+                    galaxy_value = value_elem.get( "galaxy_value" )
+                    if None not in [ remote_value, galaxy_value ]:
+                        value_trans[ remote_value ] = galaxy_value
+            
+            append_param_elem = req_param.find( "append_param" )
+            if append_param_elem:
+                separator = append_param_elem.get( 'separator', ',' ) 
+                first_separator = append_param_elem.get( 'first_separator', None )
+                join_str = append_param_elem.get( 'join', '=' )
+                append_dict = {}
+                for value_elem in append_param_elem.findall( 'value' ):
+                    value_name = value_elem.get( 'name' )
+                    value_missing = value_elem.get( 'missing' )
+                    if None not in [ value_name, value_missing ]:
+                        append_dict[ value_name ] = value_missing
+                append_param = Bunch( separator = separator, first_separator = first_separator, join_str = join_str, append_dict = append_dict )
+            
+            rval.param_trans_dict[ remote_name ] = Bunch( galaxy_name = galaxy_name, missing = missing, value_trans = value_trans, append_param = append_param  )
+        
+        return rval
+    
+    def __init__( self ):
+        self.param_trans_dict = {}
+
+    def translate( self, params ):
+        """
+        update params in-place
+        """
+        for remote_name, translator in self.param_trans_dict.iteritems():
+            galaxy_name = translator.galaxy_name #NB: if a param by name galaxy_name is provided, it is always thrown away unless galaxy_name == remote_name
+            value = params.get( remote_name, translator.missing ) #get value from input params, or use default value specified in tool config
+            if translator.value_trans and value in translator.value_trans:
+                value = translator.value_trans[ value ]
+            if translator.append_param:
+                for param_name, missing_value in translator.append_param.append_dict.iteritems():
+                    param_value = params.get( param_name, missing_value )
+                    if translator.append_param.first_separator and translator.append_param.first_separator not in value:
+                        sep = translator.append_param.first_separator
+                    else:
+                        sep = translator.append_param.separator
+                    value += '%s%s%s%s' % ( sep, param_name, translator.append_param.join_str, param_value )
+            params.update( { galaxy_name: value } )
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/tools/parameters/sanitize.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/tools/parameters/sanitize.py	Mon Dec 07 14:45:47 2009 -0500
@@ -0,0 +1,167 @@
+"""
+Tool Parameter specific sanitizing. 
+"""
+
+import logging
+import string
+import galaxy.util
+
+log = logging.getLogger( __name__ )
+
+class ToolParameterSanitizer( object ):
+    """
+    Handles tool parameter specific sanitizing.
+    
+    >>> from elementtree.ElementTree import XML
+    >>> sanitizer = ToolParameterSanitizer.from_element( XML( 
+    ... '''
+    ... <sanitizer invalid_char="">
+    ...   <valid initial="string.letters"/>
+    ... </sanitizer>
+    ... ''' ) )
+    >>> sanitizer.sanitize_param( string.printable ) == string.letters
+    True
+    >>> slash = chr( 92 )
+    >>> sanitizer = ToolParameterSanitizer.from_element( XML( 
+    ... '''
+    ... <sanitizer>
+    ...   <valid initial="none">
+    ...    <add preset="string.printable"/>
+    ...    <remove value="""/>
+    ...    <remove value="%s"/>
+    ...   </valid>
+    ...   <mapping initial="none">
+    ...     <add source=""" target="%s""/>
+    ...     <add source="%s" target="%s%s"/>
+    ...   </mapping>
+    ... </sanitizer>
+    ... ''' % ( slash, slash, slash, slash, slash ) ) )
+    >>> text = '%s"$rm&#!' % slash
+    >>> [ c for c in sanitizer.sanitize_param( text ) ] == [ slash, slash, slash, '"', '$', 'r', 'm', '&', '#', '!' ]
+    True
+    """
+    
+    VALID_PRESET = { 'default':( string.letters + string.digits +" -=_.()/+*^,:?!" ), 'none':'' }
+    MAPPING_PRESET = { 'default':galaxy.util.mapped_chars, 'none':{} }
+    DEFAULT_INVALID_CHAR = 'X'
+    
+    #class methods
+    @classmethod
+    def from_element( cls, elem ):
+        """Loads the proper filter by the type attribute of elem"""
+        #TODO: Add ability to generically specify a method to use for sanitizing input via specification in tool XML
+        rval = ToolParameterSanitizer()
+        rval._invalid_char = elem.get( 'invalid_char', cls.DEFAULT_INVALID_CHAR )
+        rval.sanitize = galaxy.util.string_as_bool( elem.get( 'sanitize', 'True' ) )
+        for valid_elem in elem.findall( 'valid' ):
+            rval._valid_chars = rval.get_valid_by_name( valid_elem.get( 'initial', 'default' ) )
+            for action_elem in valid_elem:
+                preset = rval.get_valid_by_name( action_elem.get( 'preset', 'none' ) )
+                valid_value = [ val for val in action_elem.get( 'value', [] ) ]
+                if action_elem.tag.lower() == 'add':
+                    for val in ( preset + valid_value ):
+                        if val not in rval._valid_chars:
+                            rval._valid_chars.append( val )
+                elif action_elem.tag.lower() == 'remove':
+                    for val in ( preset + valid_value ):
+                        while val in rval._valid_chars:
+                            rval._valid_chars.remove( val )
+                else:
+                    log.debug( 'Invalid action tag in valid: %s' % action_elem.tag )
+        for mapping_elem in elem.findall( 'mapping' ):
+            rval._mapped_chars = rval.get_mapping_by_name( mapping_elem.get( 'initial', 'default' ) )
+            for action_elem in mapping_elem:
+                map_source = action_elem.get( 'source', None )
+                map_target = action_elem.get( 'target', None )
+                preset = rval.get_mapping_by_name( action_elem.get( 'preset', 'none' ) )
+                if action_elem.tag.lower() == 'add':
+                    rval._mapped_chars.update( preset )
+                    if None not in [ map_source, map_target ]:
+                        rval._mapped_chars[ map_source ] = map_target
+                elif action_elem.tag.lower() == 'remove':
+                    for map_key in preset.keys():
+                        if map_key in rval._mapped_chars:
+                            del rval._mapped_chars[ map_key ]
+                    if map_source is not None and map_key in rval._mapped_chars:
+                        del rval._mapped_chars[ map_key ]
+                else:
+                    log.debug( 'Invalid action tag in mapping: %s' % action_elem.tag )        
+        return rval
+    
+    @classmethod
+    def get_valid_by_name( cls, name ):
+        rval = []
+        for split_name in name.split( ',' ):
+            split_name = split_name.strip()
+            value = []
+            if split_name.startswith( 'string.' ):
+                try:
+                    value = eval( split_name )
+                except NameError, e:
+                    log.debug( 'Invalid string preset specified: %s' % e )
+            elif split_name in cls.VALID_PRESET:
+                value = cls.VALID_PRESET[ split_name ]
+            else:
+                log.debug( 'Invalid preset name specified: %s' % split_name )
+            rval.extend( [ val for val in value if val not in rval ] )
+        return rval
+    
+    @classmethod
+    def get_mapping_by_name( cls, name ):
+        rval = {}
+        for split_name in name.split( ',' ):
+            split_name = split_name.strip()
+            if split_name in cls.MAPPING_PRESET:
+                rval.update( cls.MAPPING_PRESET[ split_name ] )
+            else:
+                log.debug( 'Invalid preset name specified: %s' % split_name )
+        return rval
+    #end class methods
+    
+    def __init__( self ):
+        self._valid_chars = [] #List of valid characters
+        self._mapped_chars = {} #Replace a char with a any number of characters
+        self._invalid_char = self.DEFAULT_INVALID_CHAR #Replace invalid characters with this character
+        self.sanitize = True #Simply pass back the passed in value
+    
+    def restore_text( self, text ):
+        """Restores sanitized text"""
+        if self.sanitize:
+            for key, value in self._mapped_chars.iteritems():
+                text = text.replace( value, key )
+        return text
+    
+    def restore_param( self, value ):
+        if self.sanitize:
+            if isinstance( value, basestring ):
+                return self.restore_text( value )
+            elif isinstance( value, list ):
+                return map( self.restore_text, value )
+            else:
+                raise Exception, 'Unknown parameter type (%s:%s)' % ( type( value ), value )
+        return value
+    
+    def sanitize_text( self, text ):
+        """Restricts the characters that are allowed in a text"""
+        if not self.sanitize:
+            return text
+        rval = []
+        for c in text:
+            if c in self._valid_chars:
+                rval.append( c )
+            elif c in self._mapped_chars:
+                rval.append( self._mapped_chars[ c ] )
+            else:
+                rval.append( self._invalid_char )
+        return ''.join( rval )
+    
+    def sanitize_param( self, value ):
+        """Clean incoming parameters (strings or lists)"""
+        if not self.sanitize:
+            return value
+        if isinstance( value, basestring ):
+            return self.sanitize_text( value )
+        elif isinstance( value, list ):
+            return map( self.sanitize_text, value )
+        else:
+            raise Exception, 'Unknown parameter type (%s:%s)' % ( type( value ), value )
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/tools/util/maf_utilities.py
--- a/lib/galaxy/tools/util/maf_utilities.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/tools/util/maf_utilities.py	Mon Dec 07 14:45:47 2009 -0500
@@ -191,13 +191,16 @@
 def build_maf_index_species_chromosomes( filename, index_species = None ):
     species = []
     species_chromosomes = {}
-    indexes = bx.interval_index_file.Indexes()
+    indexes = bx.interval_index_file.Indexes()
+    blocks = 0
     try:
         maf_reader = bx.align.maf.Reader( open( filename ) )
         while True:
             pos = maf_reader.file.tell()
             block = maf_reader.next()
-            if block is None: break
+            if block is None:
+                break
+            blocks += 1
             for c in block.components:
                 spec = c.src
                 chrom = None
@@ -225,11 +228,11 @@
         #most likely a bad MAF
         log.debug( 'Building MAF index on %s failed: %s' % ( filename, e ) )
         return ( None, [], {} )
-    return ( indexes, species, species_chromosomes )
+    return ( indexes, species, species_chromosomes, blocks )
 
 #builds and returns ( index, index_filename ) for specified maf_file
 def build_maf_index( maf_file, species = None ):
-    indexes, found_species, species_chromosomes = build_maf_index_species_chromosomes( maf_file, species )
+    indexes, found_species, species_chromosomes, blocks = build_maf_index_species_chromosomes( maf_file, species )
     if indexes is not None:
         fd, index_filename = tempfile.mkstemp()
         out = os.fdopen( fd, 'w' )
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/util/__init__.py	Mon Dec 07 14:45:47 2009 -0500
@@ -174,70 +174,16 @@
     [('status', 'on'), ('symbols', 'alpha'), ('symbols', '__lt____gt__'), ('symbols', 'XrmXX!')]
     """
     
-    # HACK: Need top prevent sanitizing certain parameter types. The 
-    #       better solution I think is to more responsibility for 
-    #       sanitizing into the tool parameters themselves so that
-    #       different parameters can be sanitized in different ways.
+    # is NEVER_SANITIZE required now that sanitizing for tool parameters can be controlled on a per parameter basis and occurs via InputValueWrappers?
     NEVER_SANITIZE = ['file_data', 'url_paste', 'URL', 'filesystem_paths']
     
-    def __init__( self, params, safe=True, sanitize=True, tool=None ):
-        if safe:
+    def __init__( self, params, sanitize=True ):
+        if sanitize:
             for key, value in params.items():
-                # Check to see if we should translate certain parameter names.  For example,
-                # in data_source tools, the external data source application may send back 
-                # parameter names like GENOME which is translated to dbkey in Galaxy.
-                # param_trans_dict looks like { "GENOME" : [ "dbkey" "?" ] }
-                new_key = key
-                new_value = value
-                if tool and tool.tool_type == 'data_source':
-                    if key in tool.param_trans_dict:
-                        new_key = tool.param_trans_dict[ key ][0]
-                        if new_key == 'data_type':
-                            try:
-                                # The Galaxy "data_type entry is special in that it can include the ability
-                                # to translate the format to a Galaxy supported format.  In the dict, this entry
-                                # looks something like:  
-                                # {'hgta_outputType': ['data_type', 'bed', {'selectedFields': 'tabular'}] }
-                                format_trans_dict = tool.param_trans_dict[ key ][2]
-                                if value in format_trans_dict:
-                                    new_value = format_trans_dict[ value ]
-                            except:
-                                pass
-                        elif new_key == 'URL':
-                            # As above, the URL can include a set of params from the remote data source
-                            # that must be appended to the URL prior to the post.  In this case, the
-                            # dict entry would look something like:
-                            # ['URL', '', {'q': '', 's': '', 'd': '', 'dbkey': '', 't': ''}]
-                            try:
-                                add_to_url_dict = tool.param_trans_dict[ key ][2]
-                                if new_value.count( '?' ) == 0:
-                                    sep = '?'
-                                else:
-                                    sep = '&'
-                                for param_name, missing_value in add_to_url_dict.items():
-                                    param_value = params.get( param_name, None )
-                                    if not param_value and missing_value:
-                                        param_value = missing_value
-                                    if param_value:
-                                        new_value += '%s%s=%s' % ( sep, param_name, param_value )
-                                        sep = '&'
-                            except:
-                                pass
-                        if not value and not new_value:
-                            new_value = tool.param_trans_dict[ key ][1]
-                if sanitize and not ( key in self.NEVER_SANITIZE or True in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ] ): #sanitize check both ungrouped and grouped parameters by name
-                    self.__dict__[ new_key ] = sanitize_param( new_value )
+                if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: #sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed. 
+                    self.__dict__[ key ] = sanitize_param( value )
                 else:
-                    self.__dict__[ new_key ] = new_value
-            if tool and tool.tool_type == 'data_source':
-                # Add the tool's URL_method to params
-                self.__dict__[ 'URL_method' ] = tool.URL_method
-                for key, value in tool.param_trans_dict.items():
-                    # Make sure that all translated values used in Galaxy are added to the params
-                    galaxy_name = tool.param_trans_dict[ key ][0]
-                    if galaxy_name not in self.__dict__:
-                        # This will set the galaxy_name to the "missing" value
-                        self.__dict__[ galaxy_name ] = tool.param_trans_dict[ key ][1]
+                    self.__dict__[ key ] = value
         else:
             self.__dict__.update(params)
 
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/web/controllers/async.py
--- a/lib/galaxy/web/controllers/async.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/web/controllers/async.py	Mon Dec 07 14:45:47 2009 -0500
@@ -32,7 +32,7 @@
             return trans.response.send_redirect( "/index" )
 
         history = trans.get_history( create=True )
-        params  = util.Params(kwd, safe=False) 
+        params  = util.Params(kwd, sanitize=False) 
         STATUS = params.STATUS
         URL = params.URL
         data_id = params.data_id
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/web/controllers/root.py
--- a/lib/galaxy/web/controllers/root.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/web/controllers/root.py	Mon Dec 07 14:45:47 2009 -0500
@@ -270,7 +270,7 @@
         if trans.app.security_agent.can_access_dataset( roles, data.dataset ):
             if data.state == trans.model.Dataset.states.UPLOAD:
                 return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to edit its metadata." )
-            params = util.Params( kwd, safe=False )
+            params = util.Params( kwd, sanitize=False )
             if params.change:
                 # The user clicked the Save button on the 'Change data type' form
                 if data.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
diff -r b01c8245ef74 -r 14214b45db3f lib/galaxy/web/controllers/tool_runner.py
--- a/lib/galaxy/web/controllers/tool_runner.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/lib/galaxy/web/controllers/tool_runner.py	Mon Dec 07 14:45:47 2009 -0500
@@ -43,7 +43,10 @@
             log.error( "index called with tool id '%s' but no such tool exists", tool_id )
             trans.log_event( "Tool id '%s' does not exist" % tool_id )
             return "Tool '%s' does not exist, kwd=%s " % (tool_id, kwd)
-        params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool )
+        params = util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers
+        #do param translation here, used by datasource tools
+        if tool.input_translator:
+            tool.input_translator.translate( params )
         history = trans.get_history()
         template, vars = tool.handle_input( trans, params.__dict__ )
         if len(params) > 0:
@@ -73,7 +76,7 @@
         # Get the associated job, if any. If this hda was copied from another,
         # we need to find the job that created the origial hda
         job_hda = data
-        while job_hda.copied_from_history_dataset_association:
+        while job_hda.copied_from_history_dataset_association:#should this check library datasets as well?
             job_hda = job_hda.copied_from_history_dataset_association
         if not job_hda.creating_job_associations:
             error( "Could not find the job for this dataset" )
@@ -153,7 +156,7 @@
         tool = self.get_toolbox().tools_by_id.get( tool_id, None )
         if not tool:
             return False # bad tool_id
-        nonfile_params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool )
+        nonfile_params = util.Params( kwd, sanitize=False )
         if kwd.get( 'tool_state', None ) not in ( None, 'None' ):
             encoded_state = util.string_to_object( kwd["tool_state"] )
             tool_state = DefaultToolState()
diff -r b01c8245ef74 -r 14214b45db3f test-data/1.bam
Binary file test-data/1.bam has changed
diff -r b01c8245ef74 -r 14214b45db3f test-data/2.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.sam	Mon Dec 07 14:45:47 2009 -0500
@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1095:605	0	chrM	23	25	36M	*	0	0	AAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT	IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1650:1185	0	chrM	14956	25	36M	*	0	0	ACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT	IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:799:192	16	chrM	8421	25	36M	*	0	0	CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT	II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1082:719	16	chrM	7191	25	36M	*	0	0	TAAATTAACCCATACCAGCACCATAGANNCTCAAGA	<III0EII3+3I29I>III8AIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1746:1180	16	chrM	12013	25	36M	*	0	0	CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT	IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:606:460	0	chrM	4552	25	36M	*	0	0	TTAATTTNNATTATAATAACACTCACAATATTCATA	IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1059:362	16	chrM	7348	25	36M	*	0	0	GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT	II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1483:1161	16	chrM	15080	25	36M	*	0	0	TCCTGATCCTAGCACTCATCCCCACCCNNCACATAT	HIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1273:600	16	chrM	13855	25	36M	*	0	0	GTATTAGACACCCATACCTCAGGATACNNCTCAGTA	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1190:1283	16	chrM	15338	25	36M	*	0	0	TATATCGCACATTACCCTGGTCTTGTANNCCAGAAA	EIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
diff -r b01c8245ef74 -r 14214b45db3f test-data/2.tabular
--- a/test-data/2.tabular	Mon Dec 07 14:45:09 2009 -0500
+++ b/test-data/2.tabular	Mon Dec 07 14:45:47 2009 -0500
@@ -1,10 +1,10 @@
-1   68  4.1
-2   71  4.6
-3   62  3.8
-4   75  4.4
-5   58  3.2
-6   60  3.1
-7   67  3.8
-8   68  4.1
-9   71  4.3
-10  69  3.7
+1	68	4.1
+2	71	4.6
+3	62	3.8
+4	75	4.4
+5	58	3.2
+6	60	3.1
+7	67	3.8
+8	68	4.1
+9	71	4.3
+10	69	3.7
diff -r b01c8245ef74 -r 14214b45db3f test-data/3.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.sam	Mon Dec 07 14:45:47 2009 -0500
@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1513:715	16	chrM	9563	25	36M	*	0	0	CTGACTACCACAACTAAACATCTATGCNNAAAAAAC	I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1698:516	16	chrM	2735	25	36M	*	0	0	TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC	I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1491:637	16	chrM	10864	25	36M	*	0	0	TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC	DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1711:249	16	chrM	10617	25	36M	*	0	0	ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1634:211	0	chrM	9350	25	36M	*	0	0	GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1218:141	16	chrM	14062	25	36M	*	0	0	ACAAAACTAACAACAAAAATAACACTCNNAATAAAC	I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1398:854	16	chrM	3921	25	36M	*	0	0	CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC	IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1310:991	16	chrM	10002	25	36M	*	0	0	CTCCTATGCCTAGAAGGAATAATACTANNACTATTC	I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1716:413	0	chrM	6040	25	36M	*	0	0	GATCCAANNCTTTATCAACACCTATTCTGATTCTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1630:59	16	chrM	12387	25	36M	*	0	0	TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC	FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
diff -r b01c8245ef74 -r 14214b45db3f test-data/chrM.fa
--- a/test-data/chrM.fa	Mon Dec 07 14:45:09 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,335 +0,0 @@
->chrM
-GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA
-GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT
-TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT
-CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA
-AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG
-ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG
-GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA
-ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA
-AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA
-AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA
-TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA
-AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT
-GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC
-CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT
-CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA
-AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT
-TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC
-TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT
-GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT
-CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA
-CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG
-TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA
-TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC
-TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG
-AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG
-ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT
-AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC
-CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT
-ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG
-AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA
-ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA
-AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA
-ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG
-TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA
-ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG
-TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA
-CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA
-TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA
-AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT
-ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC
-AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca
-taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt
-tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg
-cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG
-ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT
-TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC
-CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA
-TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG
-CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG
-TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT
-CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT
-CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT
-AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA
-AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg
-tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt
-caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT
-GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT
-CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG
-GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA
-CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT
-AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC
-CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC
-CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA
-CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG
-TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC
-ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC
-ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA
-ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA
-TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA
-ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG
-GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC
-ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA
-CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC
-TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA
-CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT
-ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact
-acaggaattgaacctgctcctgagaattcaaaatcctccgtgctaccgaa
-ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT
-ACCCCGAAAATGTTGGATTACACCCTTCCCGTACTAATAAATCCCCTTAT
-CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA
-TAAGCTCACACTGACTAATAATCTGAATCGGATTTGAAATAAATCTACTA
-GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC
-CTCCACCAAATATTTTCTAACCCAAGCCACCGCATCAATACTCCTCATAA
-TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA
-GTCTTCAACCCCACAGCGTCCATCATTATAACTTCAGCTCTCGCCATAAA
-ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA
-TCTCATTAACATCAGGTCTCATCCTACTTACATGACAAAAACTAGCCCCA
-ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT
-AACTATAGCCGTACTGTCAATCCTAGTAGGAGGCTGAGGCGGTCTCAACC
-AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA
-TGAATAACAGCTGTCCTAGTATATAACCCAACACTAACAATACTAAACAT
-ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA
-GCTCCTCTACTACAACACTATCACTCTCCCACACATGAAACAAAATACCT
-CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC
-CCCACTATCAGGATTCATACCCAAATGAATAATCATTCAAGAGCTCACCA
-AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC
-AACCTCTACTTCTACATACGACTAACCTATTCCACCTCACTGACCATATT
-CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA
-TTACTCTCTTACCCCCGTTAATTGTTATATCCTCCCTACTCCTCCCCCTA
-ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC
-CAAGAGCCTTCAAAGCTCTAAGCAAGTGAATCCACTTAATTCCTGCATAC
-TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT
-TTTATTAAGCTAAGCCCTTACTAGATTGGTGGGCTACCATCCCACGAAAT
-TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC
-CGCCGCCTAGAAAAAAAGGCGGGAGAAGCCCCGGCAGAAATTGAAGCTGC
-TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG
-AAGAGGATTCCAACCCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAG
-CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA
-GACATCGGCACTCTGTACCTCCTATTCGGCGCTTGAGCTGGAATAGTAGG
-AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC
-TACTAGGAGATGATCAGATCTACAATGTCATTGTAACCGCCCATGCATTC
-GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA
-CTGATTAGTCCCCCTGATAATTGGAGCACCTGATATAGCTTTCCCCCGAA
-TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC
-GCTTCCTCAATAATTGAAGCAGGTGCCGGAACAGGCTGAACCGTATATCC
-TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA
-TTTTCTCTCTCCACCTAGCTGGGGTGTCCTCGATTTTAGGTGCCATCAAC
-TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA
-AACCCCCCTATTCGTTTGATCTGTCCTTATTACGGCAGTACTCCTTCTCC
-TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT
-AACCTGAACACTACTTTCTTCGACCCCGCAGGAGGAGGGGATCCAATCCT
-TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA
-TCCTACCAGGCTTCGGTATAATCTCACACATCGTCACATACTACTCAGGT
-AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT
-TGGCTTTCTAGGCTTCATCGTATGGGCTCACCACATGTTTACAGTAGGGA
-TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT
-ATCCCTACTGGTGTAAAAGTATTCAGCTGACTAGCCACCCTGCACGGAGG
-AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT
-TATTCACAGTAGGAGGTCTAACAGGAATCGTCCTAGCTAACTCATCCCTA
-GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT
-CCTGTCTATAGGAGCAGTCTTCGCCATTATGGGGGGATTTGTACACTGAT
-TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC
-TTTACAATTATATTCGTAGGGGTAAATATAACCTTCTTCCCACAACATTT
-CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT
-ATACAACATGAAATACCATCTCATCCATAGGATCTTTTATCTCACTTACA
-GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG
-AGAAGTGTCTACAGTAGAATTAACCTCAACTAATCTGGAATGACTACACG
-GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA
-AAAtaagaaaggaaggaatcgaaccccctctaactggtttcaagccaata
-tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC
-ATGACTTTGTCAAAGTTAAATTATAGGTTAAACCCCTATATACCTCTATG
-GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA
-AGAACTCCTACACTTCCACGACCACACACTAATAATCGTATTCCTAATTA
-GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC
-CATACCAGCACCATAGATGCTCAAGAAGTAGAGACAATTTGAACGATTTT
-ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT
-ATATAATAGATGAAATCAATAATCCGTCCCTCACAGTCAAAACAATAGGC
-CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT
-TGACTCCTACATGATCCCCACATCAGACCTAAAACCAGGAGAATTACGTC
-TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA
-ATGCTAATTTCATCCGAAGACGTCCTACACTCATGAGCTGTGCCCTCCCT
-AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG
-TGGCCTCTCGACCAGGACTTTACTACGGTCAATGCTCAGAGATCTGCGGA
-TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA
-CTTCGAAGAATGATCTGCATCAATATTATAAAGTCACTAAGAAGCTATTA
-TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT
-GATATGCCACAGTTGGATACATCAACATGATTTATTAATATCGTCTCAAT
-AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT
-ATCCGACACACCCAGAAGTAAAGACAACCAAAATAACAAAACACTCTGCC
-CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA
-ACAATAGTAGGCCTCCCTATTGTAATTCTGATCATCATATTTCCCAGCAT
-CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC
-AACAATGGCTAGTCCAACTTACATCAAAACAAATAATAGCTATCCATAAC
-AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT
-TGGCTCAACAAACTTATTAGGCCTACTACCTCACTCATTTACACCAACAA
-CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA
-GTATTCATAGGCTTTCGTCACAAAACAAAAGCAGCCCTAGCCCACTTTCT
-ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA
-CTATCAGCCTATTTATTCAACCTGTAGCCCTAGCCGTGCGGCTAACCGCT
-AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT
-AGCCCTCATAAGCATCAGCCCCTCAACAGCCCTTATTACGTTTATCATCC
-TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC
-GTATTCACTCTCCTGGTAAGCCTTTACTTACACGACAACACCTAATGACC
-CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC
-AGGAGCCCTATCAGCCCTCCTGATAACATCAGGACTAGCCATGTGATTTC
-ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT
-ACCATATATCAATGATGACGAGACATCATCCGAGAAAGCACATTCCAAGG
-CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT
-TTATTATCTCAGAAGTCTTCTTCTTCTCTGGCTTCTTCTGAGCCTTTTAC
-CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC
-AGGTATCCACCCCTTAAACCCCCTAGAAGTCCCCTTACTCAACACCTCAG
-TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA
-GAAGGAAACCGTAAAAATATGCTCCAAGGCCTATTCATCACAATTTCACT
-AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT
-TTACTATTTCAGATGGAGTATACGGATCAACATTTTTCGTAGCAACAGGG
-TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT
-CCTACGCCAACTAAAATTCCACTTTACATCCAGCCACCACTTCGGATTCG
-AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG
-TACGTCTCTATTTATTGATGAGGATCCTATTCTTTTAGTATTGACCAGTA
-CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA
-AACCTCATACTGACACTCCTCACTAACACATTACTAGCCTCGCTACTCGT
-ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA
-GCCCATATGAATGCGGATTTGACCCTATAGGGTCAGCACGCCTCCCCTTC
-TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA
-AATTGCCCTCCTATTACCCCTTCCATGAGCATCCCAAACAACTAACCTAA
-ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC
-CTAGCCTACGAATGAACCCAAAAAGGACTAGAATGAACTGAGTATGGTAA
-TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT
-TCATAATTACCAACATGTCACTAGTCCATATTAATATCTTCCTAGCATTC
-ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC
-ACTCCTATGCCTAGAAGGAATAATACTATCACTATTCGTCATAGCAACCA
-TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC
-TTACTAGTATTTGCTGCCTGCGAACGAGCTCTAGGATTATCCCTACTAGT
-CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC
-TCCAATGCTAAAAATTATCATTCCCACAATCATACTTATGCCCCTTACAT
-GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA
-TTAATCAGCCTTATCAGCCTATCCCTCCTAAACCAACCTAGCAACAATAG
-CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC
-TGGTGTTGACAACATGACTACTGCCACTAATACTCATAGCCAGCCAACAC
-CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT
-AACCATACTTCAAACTTTCCTAATCATGACTTTTACCGCCACAGAACTAA
-TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC
-ATCACCCGCTGAGGCAACCAAACAGAACGCCTGAACGCAGGCCTCTACTT
-CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT
-CTATCCAAAACCTAACAGGCTCACTAAACTTCCTATTAATTCAATACTGA
-AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG
-TATAATAGCATTCATAGTCAAAATACCGGTATATGGTCTTCACCTCTGAC
-TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA
-GCCATTCTACTAAAACTAGGAGGCTACGGAATACTACGAATTACAACAAT
-ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC
-TGTGAGGAATAATCATAACTAGTTCCATCTGCTTGCGACAAACCGATCTA
-AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT
-AGCCGTCCTCATCCAAACACCATGAAGTTATATAGGAGCTACAGCCCTAA
-TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA
-AATTACGAACGTACCCATAGCCGAACTATAATCCTAGCCCGCGGGCTTCA
-AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA
-ACCTGGCCCTCCCTCCCAGCATTAACCTAATTGGAGAGCTATTCGTAGTA
-ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA
-TATCACCATCACCGCCCTCTACTCCCTATACATACTAATCACAACACAAC
-GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA
-GAAAACGCACTCATGGCCCTCCACATGACTCCCCTACTACTCCTATCACT
-TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA
-AAACACTAGATTGTGGATCTAGAAACAGAAACTTAATATTTCTTATTTAC
-CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA
-TGGCTCTCTCAAACTTTTAAAGGATAGGAGCTATCCGTTGGTCTTAGGAA
-CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC
-CTCATACTAGTTTCACTATTAGTACTAACCCTCCCAATCATATTATCAAT
-CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA
-TCTCATATGCCTTCATTACTAGCCTAATTCCCACTATAATATTTATTCAC
-TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC
-CCTCAAACTATCCCTAAGCTTCAAACTAGATTACTTCTCAATAATTTTCG
-TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA
-TACATGCACTCAGATCCTTACATTACTCGATTTTTTAAATACTTACTTAC
-ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC
-TGTTCATCGGATGGGAGGGAGTAGGCATCATGTCATTCTTACTAATCGGA
-TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT
-TTATAACCGCATCGGGGATATCGGCTTCATCATGGCCATAGCCTGATTCC
-TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC
-AACCTTACCAACCTCCCGCTCCTAGGCCTCCTCCTAGCCGCAACTGGCAA
-ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC
-CTACACCAGTCTCAGCCCTACTCCACTCCAGCACAATAGTTGTAGCAGGC
-GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT
-CCAGTCACTTACCCTATGCCTAGGAGCCATCACCACACTATTCACAGCAA
-TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC
-TCCAGCCAACTAGGCCTGATAATCGTAACCATCGGTATCAATCAACCCTA
-CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT
-TTATATGTTCCGGATCCATTATCCACAGCCTAAATGACGAGCAAGATATC
-CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT
-AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT
-ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC
-TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG
-TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC
-TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC
-CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA
-CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG
-CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG
-ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC
-CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG
-CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC
-TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC
-CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT
-CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG
-TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA
-ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC
-CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA
-CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT
-AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC
-AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG
-TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC
-ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC
-CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG
-AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA
-ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT
-GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC
-GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA
-CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG
-AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT
-ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA
-GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC
-AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG
-GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC
-ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT
-ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT
-ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC
-AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT
-CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT
-CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC
-CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT
-CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA
-ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA
-TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT
-AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC
-CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC
-CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT
-CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT
-CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC
-ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT
-ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC
-TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC
-TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT
-CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC
-CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG
-TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA
-GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC
-AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC
-GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG
-CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT
-TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA
-ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA
-CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT
-CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA
-CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA
-GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac
-ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct
-gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt
-gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc
-acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac
-ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA
-CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT
-GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT
-AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA
-GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT
-TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC
-TTCTTCCCCC
diff -r b01c8245ef74 -r 14214b45db3f test-data/chr_m.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr_m.fasta	Mon Dec 07 14:45:47 2009 -0500
@@ -0,0 +1,335 @@
+>chrM
+GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA
+GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT
+TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT
+CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA
+AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG
+ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG
+GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA
+ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA
+AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA
+AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA
+TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA
+AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT
+GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC
+CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT
+CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA
+AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT
+TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC
+TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT
+GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT
+CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA
+CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG
+TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA
+TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC
+TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG
+AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG
+ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT
+AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC
+CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT
+ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG
+AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA
+ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA
+AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA
+ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG
+TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA
+ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG
+TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA
+CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA
+TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA
+AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT
+ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC
+AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca
+taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt
+tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg
+cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG
+ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT
+TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC
+CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA
+TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG
+CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG
+TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT
+CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT
+CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT
+AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA
+AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg
+tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt
+caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT
+GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT
+CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG
+GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA
+CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT
+AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC
+CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC
+CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA
+CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG
+TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC
+ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC
+ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA
+ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA
+TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA
+ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG
+GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC
+ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA
+CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC
+TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA
+CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT
+ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact
+acaggaattgaacctgctcctgagaattcaaaatcctccgtgctaccgaa
+ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT
+ACCCCGAAAATGTTGGATTACACCCTTCCCGTACTAATAAATCCCCTTAT
+CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA
+TAAGCTCACACTGACTAATAATCTGAATCGGATTTGAAATAAATCTACTA
+GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC
+CTCCACCAAATATTTTCTAACCCAAGCCACCGCATCAATACTCCTCATAA
+TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA
+GTCTTCAACCCCACAGCGTCCATCATTATAACTTCAGCTCTCGCCATAAA
+ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA
+TCTCATTAACATCAGGTCTCATCCTACTTACATGACAAAAACTAGCCCCA
+ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT
+AACTATAGCCGTACTGTCAATCCTAGTAGGAGGCTGAGGCGGTCTCAACC
+AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA
+TGAATAACAGCTGTCCTAGTATATAACCCAACACTAACAATACTAAACAT
+ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA
+GCTCCTCTACTACAACACTATCACTCTCCCACACATGAAACAAAATACCT
+CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC
+CCCACTATCAGGATTCATACCCAAATGAATAATCATTCAAGAGCTCACCA
+AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC
+AACCTCTACTTCTACATACGACTAACCTATTCCACCTCACTGACCATATT
+CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA
+TTACTCTCTTACCCCCGTTAATTGTTATATCCTCCCTACTCCTCCCCCTA
+ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC
+CAAGAGCCTTCAAAGCTCTAAGCAAGTGAATCCACTTAATTCCTGCATAC
+TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT
+TTTATTAAGCTAAGCCCTTACTAGATTGGTGGGCTACCATCCCACGAAAT
+TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC
+CGCCGCCTAGAAAAAAAGGCGGGAGAAGCCCCGGCAGAAATTGAAGCTGC
+TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG
+AAGAGGATTCCAACCCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAG
+CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA
+GACATCGGCACTCTGTACCTCCTATTCGGCGCTTGAGCTGGAATAGTAGG
+AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC
+TACTAGGAGATGATCAGATCTACAATGTCATTGTAACCGCCCATGCATTC
+GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA
+CTGATTAGTCCCCCTGATAATTGGAGCACCTGATATAGCTTTCCCCCGAA
+TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC
+GCTTCCTCAATAATTGAAGCAGGTGCCGGAACAGGCTGAACCGTATATCC
+TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA
+TTTTCTCTCTCCACCTAGCTGGGGTGTCCTCGATTTTAGGTGCCATCAAC
+TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA
+AACCCCCCTATTCGTTTGATCTGTCCTTATTACGGCAGTACTCCTTCTCC
+TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT
+AACCTGAACACTACTTTCTTCGACCCCGCAGGAGGAGGGGATCCAATCCT
+TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA
+TCCTACCAGGCTTCGGTATAATCTCACACATCGTCACATACTACTCAGGT
+AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT
+TGGCTTTCTAGGCTTCATCGTATGGGCTCACCACATGTTTACAGTAGGGA
+TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT
+ATCCCTACTGGTGTAAAAGTATTCAGCTGACTAGCCACCCTGCACGGAGG
+AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT
+TATTCACAGTAGGAGGTCTAACAGGAATCGTCCTAGCTAACTCATCCCTA
+GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT
+CCTGTCTATAGGAGCAGTCTTCGCCATTATGGGGGGATTTGTACACTGAT
+TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC
+TTTACAATTATATTCGTAGGGGTAAATATAACCTTCTTCCCACAACATTT
+CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT
+ATACAACATGAAATACCATCTCATCCATAGGATCTTTTATCTCACTTACA
+GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG
+AGAAGTGTCTACAGTAGAATTAACCTCAACTAATCTGGAATGACTACACG
+GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA
+AAAtaagaaaggaaggaatcgaaccccctctaactggtttcaagccaata
+tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC
+ATGACTTTGTCAAAGTTAAATTATAGGTTAAACCCCTATATACCTCTATG
+GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA
+AGAACTCCTACACTTCCACGACCACACACTAATAATCGTATTCCTAATTA
+GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC
+CATACCAGCACCATAGATGCTCAAGAAGTAGAGACAATTTGAACGATTTT
+ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT
+ATATAATAGATGAAATCAATAATCCGTCCCTCACAGTCAAAACAATAGGC
+CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT
+TGACTCCTACATGATCCCCACATCAGACCTAAAACCAGGAGAATTACGTC
+TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA
+ATGCTAATTTCATCCGAAGACGTCCTACACTCATGAGCTGTGCCCTCCCT
+AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG
+TGGCCTCTCGACCAGGACTTTACTACGGTCAATGCTCAGAGATCTGCGGA
+TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA
+CTTCGAAGAATGATCTGCATCAATATTATAAAGTCACTAAGAAGCTATTA
+TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT
+GATATGCCACAGTTGGATACATCAACATGATTTATTAATATCGTCTCAAT
+AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT
+ATCCGACACACCCAGAAGTAAAGACAACCAAAATAACAAAACACTCTGCC
+CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA
+ACAATAGTAGGCCTCCCTATTGTAATTCTGATCATCATATTTCCCAGCAT
+CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC
+AACAATGGCTAGTCCAACTTACATCAAAACAAATAATAGCTATCCATAAC
+AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT
+TGGCTCAACAAACTTATTAGGCCTACTACCTCACTCATTTACACCAACAA
+CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA
+GTATTCATAGGCTTTCGTCACAAAACAAAAGCAGCCCTAGCCCACTTTCT
+ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA
+CTATCAGCCTATTTATTCAACCTGTAGCCCTAGCCGTGCGGCTAACCGCT
+AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT
+AGCCCTCATAAGCATCAGCCCCTCAACAGCCCTTATTACGTTTATCATCC
+TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC
+GTATTCACTCTCCTGGTAAGCCTTTACTTACACGACAACACCTAATGACC
+CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC
+AGGAGCCCTATCAGCCCTCCTGATAACATCAGGACTAGCCATGTGATTTC
+ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT
+ACCATATATCAATGATGACGAGACATCATCCGAGAAAGCACATTCCAAGG
+CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT
+TTATTATCTCAGAAGTCTTCTTCTTCTCTGGCTTCTTCTGAGCCTTTTAC
+CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC
+AGGTATCCACCCCTTAAACCCCCTAGAAGTCCCCTTACTCAACACCTCAG
+TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA
+GAAGGAAACCGTAAAAATATGCTCCAAGGCCTATTCATCACAATTTCACT
+AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT
+TTACTATTTCAGATGGAGTATACGGATCAACATTTTTCGTAGCAACAGGG
+TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT
+CCTACGCCAACTAAAATTCCACTTTACATCCAGCCACCACTTCGGATTCG
+AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG
+TACGTCTCTATTTATTGATGAGGATCCTATTCTTTTAGTATTGACCAGTA
+CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA
+AACCTCATACTGACACTCCTCACTAACACATTACTAGCCTCGCTACTCGT
+ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA
+GCCCATATGAATGCGGATTTGACCCTATAGGGTCAGCACGCCTCCCCTTC
+TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA
+AATTGCCCTCCTATTACCCCTTCCATGAGCATCCCAAACAACTAACCTAA
+ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC
+CTAGCCTACGAATGAACCCAAAAAGGACTAGAATGAACTGAGTATGGTAA
+TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT
+TCATAATTACCAACATGTCACTAGTCCATATTAATATCTTCCTAGCATTC
+ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC
+ACTCCTATGCCTAGAAGGAATAATACTATCACTATTCGTCATAGCAACCA
+TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC
+TTACTAGTATTTGCTGCCTGCGAACGAGCTCTAGGATTATCCCTACTAGT
+CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC
+TCCAATGCTAAAAATTATCATTCCCACAATCATACTTATGCCCCTTACAT
+GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA
+TTAATCAGCCTTATCAGCCTATCCCTCCTAAACCAACCTAGCAACAATAG
+CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC
+TGGTGTTGACAACATGACTACTGCCACTAATACTCATAGCCAGCCAACAC
+CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT
+AACCATACTTCAAACTTTCCTAATCATGACTTTTACCGCCACAGAACTAA
+TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC
+ATCACCCGCTGAGGCAACCAAACAGAACGCCTGAACGCAGGCCTCTACTT
+CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT
+CTATCCAAAACCTAACAGGCTCACTAAACTTCCTATTAATTCAATACTGA
+AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG
+TATAATAGCATTCATAGTCAAAATACCGGTATATGGTCTTCACCTCTGAC
+TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA
+GCCATTCTACTAAAACTAGGAGGCTACGGAATACTACGAATTACAACAAT
+ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC
+TGTGAGGAATAATCATAACTAGTTCCATCTGCTTGCGACAAACCGATCTA
+AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT
+AGCCGTCCTCATCCAAACACCATGAAGTTATATAGGAGCTACAGCCCTAA
+TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA
+AATTACGAACGTACCCATAGCCGAACTATAATCCTAGCCCGCGGGCTTCA
+AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA
+ACCTGGCCCTCCCTCCCAGCATTAACCTAATTGGAGAGCTATTCGTAGTA
+ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA
+TATCACCATCACCGCCCTCTACTCCCTATACATACTAATCACAACACAAC
+GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA
+GAAAACGCACTCATGGCCCTCCACATGACTCCCCTACTACTCCTATCACT
+TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA
+AAACACTAGATTGTGGATCTAGAAACAGAAACTTAATATTTCTTATTTAC
+CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA
+TGGCTCTCTCAAACTTTTAAAGGATAGGAGCTATCCGTTGGTCTTAGGAA
+CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC
+CTCATACTAGTTTCACTATTAGTACTAACCCTCCCAATCATATTATCAAT
+CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA
+TCTCATATGCCTTCATTACTAGCCTAATTCCCACTATAATATTTATTCAC
+TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC
+CCTCAAACTATCCCTAAGCTTCAAACTAGATTACTTCTCAATAATTTTCG
+TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA
+TACATGCACTCAGATCCTTACATTACTCGATTTTTTAAATACTTACTTAC
+ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC
+TGTTCATCGGATGGGAGGGAGTAGGCATCATGTCATTCTTACTAATCGGA
+TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT
+TTATAACCGCATCGGGGATATCGGCTTCATCATGGCCATAGCCTGATTCC
+TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC
+AACCTTACCAACCTCCCGCTCCTAGGCCTCCTCCTAGCCGCAACTGGCAA
+ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC
+CTACACCAGTCTCAGCCCTACTCCACTCCAGCACAATAGTTGTAGCAGGC
+GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT
+CCAGTCACTTACCCTATGCCTAGGAGCCATCACCACACTATTCACAGCAA
+TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC
+TCCAGCCAACTAGGCCTGATAATCGTAACCATCGGTATCAATCAACCCTA
+CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT
+TTATATGTTCCGGATCCATTATCCACAGCCTAAATGACGAGCAAGATATC
+CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT
+AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT
+ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC
+TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG
+TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC
+TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC
+CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA
+CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG
+CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG
+ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC
+CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG
+CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC
+TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC
+CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT
+CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG
+TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA
+ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC
+CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA
+CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT
+AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC
+AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG
+TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC
+ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC
+CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG
+AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA
+ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT
+GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC
+GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA
+CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG
+AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT
+ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA
+GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC
+AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG
+GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC
+ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT
+ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT
+ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC
+AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT
+CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT
+CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC
+CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT
+CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA
+ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA
+TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT
+AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC
+CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC
+CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT
+CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT
+CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC
+ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT
+ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC
+TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC
+TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT
+CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC
+CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG
+TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA
+GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC
+AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC
+GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG
+CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT
+TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA
+ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA
+CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT
+CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA
+CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA
+GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac
+ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct
+gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt
+gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc
+acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac
+ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA
+CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT
+GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT
+AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA
+GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT
+TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC
+TTCTTCCCCC
diff -r b01c8245ef74 -r 14214b45db3f test-data/joiner_out3.bed
--- a/test-data/joiner_out3.bed	Mon Dec 07 14:45:09 2009 -0500
+++ b/test-data/joiner_out3.bed	Mon Dec 07 14:45:47 2009 -0500
@@ -6,46 +6,46 @@
 chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-	chr11	116124407	116124501	AK057832_cds_0_0_chr11_116124408_r	0	-
 chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+	chr11	116206508	116206563	NM_000040_cds_1_0_chr11_116206509_f	0	+
 chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-	chr11	116211733	116212337	BC005380_cds_0_0_chr11_116211734_r	0	-
-chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+	X	X	X	X	X	X
+chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+	~	~	~	~	~	~
 chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-	chr12	38440094	38440321	NM_052885_cds_0_0_chr12_38440095_r	0	-
 chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+	chr13	112381694	112381953	NM_207440_cds_1_0_chr13_112381695_f	0	+
 chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-	chr14	98710240	98712285	NM_022898_cds_0_0_chr14_98710241_r	0	-
 chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-	chr15	41486872	41487060	BX537418_cds_0_0_chr15_41486873_r	0	-
 chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+	chr15	41673708	41673857	AK223365_cds_0_0_chr15_41673709_f	0	+
 chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-	chr15	41679161	41679250	NM_153700_cds_0_0_chr15_41679162_r	0	-
-chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+	X	X	X	X	X	X
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+	~	~	~	~	~	~
 chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+	chr16	142908	143003	NM_005332_cds_0_0_chr16_142909_f	0	+
-chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-	X	X	X	X	X	X
+chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-	~	~	~	~	~	~
 chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+	chr16	244413	244681	AK057165_cds_2_0_chr16_244414_f	0	+
 chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-	chr16	259268	259383	AB016929_cds_0_0_chr16_259269_r	0	-
 chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-	chr18	23786114	23786321	NM_001792_cds_0_0_chr18_23786115_r	0	-
 chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+	chr18	59406881	59407046	NM_012397_cds_1_0_chr18_59406882_f	0	+
 chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-	chr18	59455932	59456337	AB046400_cds_0_0_chr18_59455933_r	0	-
-chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+	X	X	X	X	X	X
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+	~	~	~	~	~	~
 chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+	chr19	59068595	59069564	BC013995_cds_1_0_chr19_59068596_f	0	+
 chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-	chr19	59236026	59236146	NM_198481_cds_0_0_chr19_59236027_r	0	-
 chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+	chr19	59297998	59298008	NM_004542_cds_0_0_chr19_59297999_f	0	+
-chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-	X	X	X	X	X	X
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-	~	~	~	~	~	~
 chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+	chr2	118288583	118288668	NM_006773_cds_0_0_chr2_118288584_f	0	+
-chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-	X	X	X	X	X	X
-chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+	X	X	X	X	X	X
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-	~	~	~	~	~	~
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+	~	~	~	~	~	~
 chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-	chr2	220229609	220230869	NM_024536_cds_0_0_chr2_220229610_r	0	-
 chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-	chr20	33330413	33330423	NM_181466_cds_0_0_chr20_33330414_r	0	-
 chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+	chr20	33513606	33513792	AF022655_cds_1_0_chr20_33513607_f	0	+
-chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-	X	X	X	X	X	X
-chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+	X	X	X	X	X	X
-chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+	X	X	X	X	X	X
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-	~	~	~	~	~	~
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+	~	~	~	~	~	~
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+	~	~	~	~	~	~
 chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-	chr21	32869641	32870022	NM_018277_cds_3_0_chr21_32869642_r	0	-
 chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+	chr21	33321040	33322012	NM_005806_cds_1_0_chr21_33321041_f	0	+
-chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-	X	X	X	X	X	X
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-	~	~	~	~	~	~
 chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+	chr22	30120223	30120265	NM_004147_cds_0_0_chr22_30120224_f	0	+
 chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-	chr22	30160419	30160661	BC032941_cds_0_0_chr22_30160420_r	0	-
-chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+	X	X	X	X	X	X
-chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-	X	X	X	X	X	X
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+	~	~	~	~	~	~
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-	~	~	~	~	~	~
 chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+	chr5	131424298	131424460	NM_000588_cds_0_0_chr5_131424299_f	0	+
 chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-	chr5	131556601	131556672	BC035813_cds_0_0_chr5_131556602_r	0	-
 chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+	chr5	131621326	131621419	BC003096_cds_0_0_chr5_131621327_f	0	+
-chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-	X	X	X	X	X	X
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-	~	~	~	~	~	~
 chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-	chr6	108299600	108299744	NM_007214_cds_0_0_chr6_108299601_r	0	-
 chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+	chr6	108594662	108594687	NM_003269_cds_0_0_chr6_108594663_f	0	+
 chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-	chr6	108640045	108640151	NM_003795_cds_0_0_chr6_108640046_r	0	-
@@ -57,8 +57,8 @@
 chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-	chr8	118881131	118881317	NM_000127_cds_0_0_chr8_118881132_r	0	-
 chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+	chr9	128764156	128764189	BC051300_cds_0_0_chr9_128764157_f	0	+
 chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-	chr9	128787519	128789136	NM_014908_cds_0_0_chr9_128787520_r	0	-
-chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+	X	X	X	X	X	X
-chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-	X	X	X	X	X	X
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+	~	~	~	~	~	~
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-	~	~	~	~	~	~
 chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+	chrX	122745047	122745924	NM_001167_cds_1_0_chrX_122745048_f	0	+
 chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-	chrX	152648964	152649196	NM_000425_cds_0_0_chrX_152648965_r	0	-
 chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+	chrX	152691446	152691471	AF101728_cds_0_0_chrX_152691447_f	0	+
diff -r b01c8245ef74 -r 14214b45db3f test-data/sam_to_bam_in1.sam
--- a/test-data/sam_to_bam_in1.sam	Mon Dec 07 14:45:09 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-HWI-EAS91_1_30788AAXX:1:1:1513:715	16	chrM	9563	25	36M	*	0	0	CTGACTACCACAACTAAACATCTATGCNNAAAAAAC	I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1698:516	16	chrM	2735	25	36M	*	0	0	TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC	I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1491:637	16	chrM	10864	25	36M	*	0	0	TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC	DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1711:249	16	chrM	10617	25	36M	*	0	0	ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1634:211	0	chrM	9350	25	36M	*	0	0	GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1218:141	16	chrM	14062	25	36M	*	0	0	ACAAAACTAACAACAAAAATAACACTCNNAATAAAC	I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1398:854	16	chrM	3921	25	36M	*	0	0	CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC	IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1310:991	16	chrM	10002	25	36M	*	0	0	CTCCTATGCCTAGAAGGAATAATACTANNACTATTC	I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1716:413	0	chrM	6040	25	36M	*	0	0	GATCCAANNCTTTATCAACACCTATTCTGATTCTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1630:59	16	chrM	12387	25	36M	*	0	0	TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC	FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
diff -r b01c8245ef74 -r 14214b45db3f test-data/sam_to_bam_in2.sam
--- a/test-data/sam_to_bam_in2.sam	Mon Dec 07 14:45:09 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-HWI-EAS91_1_30788AAXX:1:1:1095:605	0	chrM	23	25	36M	*	0	0	AAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT	IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1650:1185	0	chrM	14956	25	36M	*	0	0	ACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT	IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:799:192	16	chrM	8421	25	36M	*	0	0	CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT	II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1082:719	16	chrM	7191	25	36M	*	0	0	TAAATTAACCCATACCAGCACCATAGANNCTCAAGA	<III0EII3+3I29I>III8AIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1746:1180	16	chrM	12013	25	36M	*	0	0	CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT	IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:606:460	0	chrM	4552	25	36M	*	0	0	TTAATTTNNATTATAATAACACTCACAATATTCATA	IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1059:362	16	chrM	7348	25	36M	*	0	0	GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT	II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1483:1161	16	chrM	15080	25	36M	*	0	0	TCCTGATCCTAGCACTCATCCCCACCCNNCACATAT	HIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1273:600	16	chrM	13855	25	36M	*	0	0	GTATTAGACACCCATACCTCAGGATACNNCTCAGTA	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
-HWI-EAS91_1_30788AAXX:1:1:1190:1283	16	chrM	15338	25	36M	*	0	0	TATATCGCACATTACCCTGGTCTTGTANNCCAGAAA	EIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27
diff -r b01c8245ef74 -r 14214b45db3f test-data/sam_to_bam_out1.bam
Binary file test-data/sam_to_bam_out1.bam has changed
diff -r b01c8245ef74 -r 14214b45db3f test-data/sam_to_bam_out2.bam
Binary file test-data/sam_to_bam_out2.bam has changed
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/biomart.xml
--- a/tools/data_source/biomart.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/biomart.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -7,7 +7,7 @@
     TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
     everything including and beyond the first '&' is truncated from URL.  They said they'll let us know when this is fixed at their end.
 -->
-<tool name="BioMart" id="biomart" tool_type="data_source" URL_method="get" version="1.0.1">
+<tool name="BioMart" id="biomart" tool_type="data_source" version="1.0.1">
 	<description>Central server</description>
 	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
 	<inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
@@ -16,16 +16,17 @@
     </inputs>
     <request_param_translation>
         <request_param galaxy_name="URL" remote_name="URL" missing="">
-            <add_to_url>
-                <param_from_source name="_export" missing="1" />
-                <param_from_source name="GALAXY_URL" missing="0" />
-            </add_to_url>
+            <append_param separator="&" first_separator="?" join="=">
+                <value name="_export" missing="1" />
+                <value name="GALAXY_URL" missing="0" />
+            </append_param>
         </request_param>
         <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
-            <data_type_translation>
-                <format galaxy_format="tabular" remote_format="TSV" />
-            </data_type_translation>
+            <value_translation>
+                <value galaxy_value="tabular" remote_value="TSV" />
+            </value_translation>
         </request_param>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
         <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
         <request_param galaxy_name="table" remote_name="table" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/biomart_test.xml
--- a/tools/data_source/biomart_test.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/biomart_test.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -7,7 +7,7 @@
     TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
     everything including and beyond the first '&' is truncated from URL.  They said they'll let us know when this is fixed at their end.
 -->
-<tool name="BioMart" id="biomart_test" tool_type="data_source" URL_method="get" version="1.0.1">
+<tool name="BioMart" id="biomart_test" tool_type="data_source" version="1.0.1">
 	<description>Test server</description>
 	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
 	<inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
@@ -16,16 +16,17 @@
 	</inputs>
     <request_param_translation>
         <request_param galaxy_name="URL" remote_name="URL" missing="">
-            <add_to_url>
-                <param_from_source name="_export" missing="1" />
-                <param_from_source name="GALAXY_URL" missing="0" />
-            </add_to_url>
+            <append_param separator="&" first_separator="?" join="=">
+                <value name="_export" missing="1" />
+                <value name="GALAXY_URL" missing="0" />
+            </append_param>
         </request_param>
         <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
-            <data_type_translation>
-                <format galaxy_format="tabular" remote_format="TSV" />
-            </data_type_translation>
+            <value_translation>
+                <value galaxy_value="tabular" remote_value="TSV" />
+            </value_translation>
         </request_param>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
         <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
         <request_param galaxy_name="table" remote_name="table" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/data_source.py
--- a/tools/data_source/data_source.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/data_source.py	Mon Dec 07 14:45:47 2009 -0500
@@ -12,6 +12,7 @@
     sys.exit()
 
 def check_gzip( filename ):
+    # TODO: This needs to check for BAM files since they are compressed and must remain so ( see upload.py )
     temp = open( filename, "U" )
     magic_check = temp.read( 2 )
     temp.close()
@@ -66,6 +67,7 @@
         out.write( chunk )
     out.close()
     if check_gzip( filename ):
+        # TODO: This needs to check for BAM files since they are compressed and must remain so ( see upload.py )
         fd, uncompressed = tempfile.mkstemp()
         gzipped_file = gzip.GzipFile( filename )
         while 1:
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/epigraph_import.xml
--- a/tools/data_source/epigraph_import.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/epigraph_import.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="EpiGRAPH" id="epigraph_import" tool_type="data_source" URL_method="get">
+<tool name="EpiGRAPH" id="epigraph_import" tool_type="data_source">
     <description> server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH/faces/Login.jsp" check_values="false" method="get">
@@ -12,6 +12,7 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import" />
     </inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="GENOME" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/epigraph_import_test.xml
--- a/tools/data_source/epigraph_import_test.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/epigraph_import_test.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="EpiGRAPH" id="epigraph_import_test" tool_type="data_source" URL_method="get">
+<tool name="EpiGRAPH" id="epigraph_import_test" tool_type="data_source">
     <description> test server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/Login.jsp" check_values="false" method="get">
@@ -12,6 +12,7 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import_test" />
     </inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="GENOME" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/eupathdb.xml
--- a/tools/data_source/eupathdb.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/eupathdb.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -3,7 +3,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post">
+<tool name="EuPathDB" id="eupathdb" tool_type="data_source">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://galaxy.eupathdb.org/eupathdb.galaxy/queries_tools.jsp" check_values="false" method="post"> 
@@ -11,15 +11,16 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" />
     </inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="URL" remote_name="URL" missing="">
-            <add_to_url>
-                <param_from_source name="dbkey" missing="?" />
-                <param_from_source name="wdk_history_id" missing="" />
-                <param_from_source name="wdkReportFormat" missing="tabular" />
-                <param_from_source name="selectedFields" missing="" />
-                <param_from_source name="includeHeader" missing="yes" />
-                <param_from_source name="downloadType" missing="plain" />
-            </add_to_url>
+            <append_param separator="&" first_separator="?" join="=">
+                <value name="dbkey" missing="?" />
+                <value name="wdk_history_id" missing="" />
+                <value name="wdkReportFormat" missing="tabular" />
+                <value name="selectedFields" missing="" />
+                <value name="includeHeader" missing="yes" />
+                <value name="downloadType" missing="plain" />
+            </append_param>
         </request_param>
         <request_param galaxy_name="format" remote_name="wdkReportFormat" missing="tabular" />
         <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/flymine.xml
--- a/tools/data_source/flymine.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/flymine.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="Flymine" id="flymine" tool_type="data_source" URL_method="post">
+<tool name="Flymine" id="flymine" tool_type="data_source">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://www.flymine.org" check_values="false" method="get" target="_top"> 
@@ -12,6 +12,7 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
     </inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/flymine_test.xml
--- a/tools/data_source/flymine_test.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/flymine_test.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="Flymine test" id="flymine_test" tool_type="data_source" URL_method="post">
+<tool name="Flymine test" id="flymine_test" tool_type="data_source">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get" target="_top"> 
@@ -12,6 +12,7 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
     </inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/gramene_mart.xml
--- a/tools/data_source/gramene_mart.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/gramene_mart.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -7,7 +7,7 @@
     TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
     everything including and beyond the first '&' is truncated from URL.  They said they'll let us know when this is fixed at their end.
 -->
-<tool name="GrameneMart" id="gramenemart" tool_type="data_source" URL_method="get" version="1.0.1">
+<tool name="GrameneMart" id="gramenemart" tool_type="data_source" version="1.0.1">
     <description> Central server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top">
@@ -16,16 +16,17 @@
     </inputs>
     <request_param_translation>
         <request_param galaxy_name="URL" remote_name="URL" missing="">
-            <add_to_url>
-                <param_from_source name="_export" missing="1" />
-                <param_from_source name="GALAXY_URL" missing="0" />
-            </add_to_url>
+            <append_param separator="&" first_separator="?" join="=">
+                <value name="_export" missing="1" />
+                <value name="GALAXY_URL" missing="0" />
+            </append_param>
         </request_param>
         <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular">
-            <data_type_translation>
-                <format galaxy_format="tabular" remote_format="TSV" />
-            </data_type_translation> 
+            <value_translation>
+                <value galaxy_value="tabular" remote_value="TSV" />
+            </value_translation> 
         </request_param>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
         <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
         <request_param galaxy_name="table" remote_name="table" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/modmine.xml
--- a/tools/data_source/modmine.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/modmine.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="modMine" id="modmine" tool_type="data_source" URL_method="post">
+<tool name="modMine" id="modmine" tool_type="data_source">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://intermine.modencode.org/" check_values="false" method="get" target="_top"> 
@@ -12,6 +12,7 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modmine" />
     </inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/ratmine.xml
--- a/tools/data_source/ratmine.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/ratmine.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="Ratmine" id="ratmine" tool_type="data_source" URL_method="post">
+<tool name="Ratmine" id="ratmine" tool_type="data_source">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get" target="_top"> 
@@ -12,6 +12,7 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" />
     </inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
         <request_param galaxy_name="organism" remote_name="organism" missing="" />
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/ucsc_tablebrowser.xml
--- a/tools/data_source/ucsc_tablebrowser.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/ucsc_tablebrowser.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source" URL_method="post">
+<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source">
 	<description>table browser</description>
 	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
 	<inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
@@ -16,20 +16,21 @@
 		<param name="hgta_outputType" type="hidden" value="bed" />
 	</inputs>
 	<request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
         <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
 	    <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
 	    <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
 	    <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
-            <data_type_translation>
-                <format galaxy_format="tabular" remote_format="primaryTable" />
-                <format galaxy_format="tabular" remote_format="selectedFields" />
-                <format galaxy_format="wig" remote_format="wigData" />
-                <format galaxy_format="interval" remote_format="tab" />
-                <format galaxy_format="html" remote_format="hyperlinks" />
-                <format galaxy_format="fasta" remote_format="sequence" />
-            </data_type_translation>
+            <value_translation>
+                <value galaxy_value="tabular" remote_value="primaryTable" />
+                <value galaxy_value="tabular" remote_value="selectedFields" />
+                <value galaxy_value="wig" remote_value="wigData" />
+                <value galaxy_value="interval" remote_value="tab" />
+                <value galaxy_value="html" remote_value="hyperlinks" />
+                <value galaxy_value="fasta" remote_value="sequence" />
+            </value_translation>
         </request_param>
 	</request_param_translation>
 	<uihints minwidth="800"/>
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/ucsc_tablebrowser_archaea.xml
--- a/tools/data_source/ucsc_tablebrowser_archaea.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/ucsc_tablebrowser_archaea.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source" URL_method="post">
+<tool name="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source">
 	<description>table browser</description>
 	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
 	<inputs action="http://archaea.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
@@ -16,20 +16,21 @@
 		<param name="hgta_outputType" type="hidden" value="bed" />
 	</inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
         <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
-        <request_param galaxy_name="table" remote_name="hgta_track" missing="" />
-        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
+        <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
+        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
         <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
-            <data_type_translation>
-                <format galaxy_format="tabular" remote_format="primaryTable" />
-                <format galaxy_format="tabular" remote_format="selectedFields" />
-                <format galaxy_format="wig" remote_format="wigdata" />
-                <format galaxy_format="interval" remote_format="tab" />
-                <format galaxy_format="html" remote_format="hyperlinks" />
-                <format galaxy_format="fasta" remote_format="sequence" />
-            </data_type_translation>
+            <value_translation>
+                <value galaxy_value="tabular" remote_value="primaryTable" />
+                <value galaxy_value="tabular" remote_value="selectedFields" />
+                <value galaxy_value="wig" remote_value="wigData" />
+                <value galaxy_value="interval" remote_value="tab" />
+                <value galaxy_value="html" remote_value="hyperlinks" />
+                <value galaxy_value="fasta" remote_value="sequence" />
+            </value_translation>
         </request_param>
     </request_param_translation>
 	<uihints minwidth="800"/>
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/ucsc_tablebrowser_test.xml
--- a/tools/data_source/ucsc_tablebrowser_test.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/ucsc_tablebrowser_test.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
     the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
     initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
 -->
-<tool name="UCSC Test" id="ucsc_table_direct_test1" tool_type="data_source" URL_method="post">
+<tool name="UCSC Test" id="ucsc_table_direct_test1" tool_type="data_source">
 	<description>table browser</description>
 	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
 	<inputs action="http://genome-test.cse.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
@@ -16,20 +16,21 @@
 		<param name="hgta_outputType" type="hidden" value="bed" />
 	</inputs>
     <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="URL" remote_name="URL" missing="" />
         <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
         <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
-        <request_param galaxy_name="table" remote_name="hgta_track" missing="" />
-        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
+        <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
+        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
         <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
-            <data_type_translation>
-                <format galaxy_format="tabular" remote_format="primaryTable" />
-                <format galaxy_format="tabular" remote_format="selectedFields" />
-                <format galaxy_format="wig" remote_format="wigdata" />
-                <format galaxy_format="interval" remote_format="tab" />
-                <format galaxy_format="html" remote_format="hyperlinks" />
-                <format galaxy_format="fasta" remote_format="sequence" />
-            </data_type_translation>
+            <value_translation>
+                <value galaxy_value="tabular" remote_value="primaryTable" />
+                <value galaxy_value="tabular" remote_value="selectedFields" />
+                <value galaxy_value="wig" remote_value="wigData" />
+                <value galaxy_value="interval" remote_value="tab" />
+                <value galaxy_value="html" remote_value="hyperlinks" />
+                <value galaxy_value="fasta" remote_value="sequence" />
+            </value_translation>
         </request_param>
     </request_param_translation>
 	<uihints minwidth="800"/>
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/upload.py
--- a/tools/data_source/upload.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/upload.py	Mon Dec 07 14:45:47 2009 -0500
@@ -4,7 +4,7 @@
 # WARNING: Changes in this tool (particularly as related to parsing) may need
 # to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
 
-import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs
+import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs, binascii
 from galaxy import eggs
 # need to import model before sniff to resolve a circular import dependency
 import galaxy.model
@@ -18,7 +18,6 @@
 def stop_err( msg, ret=1 ):
     sys.stderr.write( msg )
     sys.exit( ret )
-
 def file_err( msg, dataset, json_file ):
     json_file.write( to_json_string( dict( type = 'dataset',
                                            ext = 'data',
@@ -28,7 +27,6 @@
         os.remove( dataset.path )
     except:
         pass
-
 def safe_dict(d):
     """
     Recursively clone json structure with UTF-8 dictionary keys
@@ -40,7 +38,6 @@
         return [safe_dict(x) for x in d]
     else:
         return d
-
 def check_html( temp_name, chunk=None ):
     if chunk is None:
         temp = open(temp_name, "U")
@@ -64,7 +61,6 @@
     if chunk is None:
         temp.close()
     return False
-
 def check_binary( temp_name, chunk=None ):
     if chunk is None:
         temp = open( temp_name, "U" )
@@ -85,21 +81,42 @@
     if chunk is None:
         temp.close()
     return False
-
 def check_gzip( temp_name ):
+    # This is sort of hacky.  BAM is compressed in the BGZF format, and must 
+    # not be uncompressed in upon upload ( it will be detected as gzipped ).
+    # The tuple we're returning from here contains boolean values for
+    # ( is_compressed, is_valid, is_bam ).
     temp = open( temp_name, "U" )
     magic_check = temp.read( 2 )
     temp.close()
     if magic_check != util.gzip_magic:
-        return ( False, False )
+        return ( False, False, False )
     CHUNK_SIZE = 2**15 # 32Kb
     gzipped_file = gzip.GzipFile( temp_name )
     chunk = gzipped_file.read( CHUNK_SIZE )
     gzipped_file.close()
-    if check_html( temp_name, chunk=chunk ) or check_binary( temp_name, chunk=chunk ):
-        return( True, False )
-    return ( True, True )
-
+    if check_html( temp_name, chunk=chunk ):
+        return ( True, False, False )
+    if check_binary( temp_name, chunk=chunk ):
+        # We do support some binary data types, so check if the compressed binary file is valid
+        # We currently only check for [ 'sff', 'bam' ]
+        # TODO: this should be fixed to more easily support future-supported binary data types.
+        # This is currently just copied from the sniff methods.
+        # The first 4 bytes of any bam file is 'BAM\1', and the file is binary. 
+        try:
+            header = gzip.open( temp_name ).read(4)
+            if binascii.b2a_hex( header ) == binascii.hexlify( 'BAM\1' ):
+                return ( True, True, True )
+        except:
+            pass
+        try:
+            header = gzip.open( temp_name ).read(4)
+            if binascii.b2a_hex( header ) == binascii.hexlify( '.sff' ):
+                return ( True, True, False )
+        except:
+            pass
+        return ( True, False, False )
+    return ( True, True, False )
 def check_zip( temp_name ):
     if not zipfile.is_zipfile( temp_name ):
         return ( False, False, None )
@@ -116,14 +133,12 @@
         if ext != test_ext:
             return ( True, False, test_ext )
     return ( True, True, test_ext )
-
 def parse_outputs( args ):
     rval = {}
     for arg in args:
         id, files_path, path = arg.split( ':', 2 )
         rval[int( id )] = ( path, files_path )
     return rval
-
 def add_file( dataset, json_file, output_path ):
     data_type = None
     line_count = None
@@ -153,15 +168,19 @@
         ext = sniff.guess_ext( dataset.path, is_multi_byte=True )
     else:
         # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress
-        is_gzipped, is_valid = check_gzip( dataset.path )
+        is_gzipped, is_valid, is_bam = check_gzip( dataset.path )
         if is_gzipped and not is_valid:
             file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
             return
-        elif is_gzipped and is_valid:
-            # We need to uncompress the temp_name file
+        elif is_gzipped and is_valid and is_bam:
+            ext = 'bam'
+            data_type = 'bam'
+        elif is_gzipped and is_valid and not is_bam:
+            # We need to uncompress the temp_name file, but BAM files must remain compressed
+            # in order for samtools to function on them
             CHUNK_SIZE = 2**20 # 1Mb   
-            fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ) )
-            gzipped_file = gzip.GzipFile( dataset.path )
+            fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False )
+            gzipped_file = gzip.GzipFile( dataset.path, 'rb' )
             while 1:
                 try:
                     chunk = gzipped_file.read( CHUNK_SIZE )
@@ -229,7 +248,7 @@
             if check_html( dataset.path ):
                 file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
                 return
-        if data_type != 'binary' and data_type != 'zip':
+        if data_type != 'bam' and data_type != 'binary' and data_type != 'zip':
             if dataset.space_to_tab:
                 line_count = sniff.convert_newlines_sep2tabs( dataset.path )
             else:
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/wormbase.xml
--- a/tools/data_source/wormbase.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/wormbase.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool name="Wormbase" id="wormbase" tool_type="data_source" URL_method="post">
+<tool name="Wormbase" id="wormbase" tool_type="data_source">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://www.wormbase.org/db/seq/gbgff/c_elegans/" check_values="false" target="_top"> 
@@ -8,14 +8,15 @@
     </inputs>
     <request_param_translation>
         <request_param galaxy_name="URL" remote_name="URL" missing="">
-            <add_to_url>
-                <param_from_source name="d" missing="" />
-                <param_from_source name="dbkey" missing="" />
-                <param_from_source name="q" missing="" />
-                <param_from_source name="s" missing="" />
-                <param_from_source name="t" missing="" />
-            </add_to_url>
+            <append_param separator="&" first_separator="?" join="=">
+                <value name="d" missing="" />
+                <value name="dbkey" missing="" />
+                <value name="q" missing="" />
+                <value name="s" missing="" />
+                <value name="t" missing="" />
+            </append_param>
         </request_param>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
     </request_param_translation>
     <uihints minwidth="800"/>
diff -r b01c8245ef74 -r 14214b45db3f tools/data_source/wormbase_test.xml
--- a/tools/data_source/wormbase_test.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/data_source/wormbase_test.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool name="Wormbase" id="wormbase_test" tool_type="data_source" URL_method="post">
+<tool name="Wormbase" id="wormbase_test" tool_type="data_source">
 	<description>test server</description>
 	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
 	<inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" target="_top"> 
@@ -8,14 +8,15 @@
 	</inputs>
     <request_param_translation>
         <request_param galaxy_name="URL" remote_name="URL" missing="">
-            <add_to_url>
-                <param_from_source name="d" missing="" />
-                <param_from_source name="dbkey" missing="" />
-                <param_from_source name="q" missing="" />
-                <param_from_source name="s" missing="" />
-                <param_from_source name="t" missing="" />
-            </add_to_url>
+            <append_param separator="&" first_separator="?" join="=">
+                <value name="d" missing="" />
+                <value name="dbkey" missing="" />
+                <value name="q" missing="" />
+                <value name="s" missing="" />
+                <value name="t" missing="" />
+            </append_param>
         </request_param>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
         <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
     </request_param_translation>
 	<uihints minwidth="800"/>
diff -r b01c8245ef74 -r 14214b45db3f tools/emboss_5/emboss_fuzznuc.xml
--- a/tools/emboss_5/emboss_fuzznuc.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/emboss_5/emboss_fuzznuc.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -1,12 +1,20 @@
-<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.0">
+<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
   <description>Nucleic acid pattern search</description>
-  <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
+  <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
     <param name="pattern" size="5" type="text" value="">
       <label>Search pattern</label>
+      <sanitizer>
+        <valid initial="string.printable">
+         <remove value="'"/>
+        </valid>
+        <mapping initial="none">
+          <add source="'" target=""/>
+        </mapping>
+      </sanitizer>
     </param>
     <param name="mismatch" size="5" type="text" value="0">
       <label>Number of mismatches</label>
diff -r b01c8245ef74 -r 14214b45db3f tools/filters/grep.py
--- a/tools/filters/grep.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/filters/grep.py	Mon Dec 07 14:45:47 2009 -0500
@@ -13,9 +13,11 @@
 # -v	        true or false (output NON-matching lines)
 
 import sys
+import os
 import re
 import string
 import commands
+from tempfile import NamedTemporaryFile
 
 # This function is exceedingly useful, perhaps package for reuse?
 def getopts(argv):
@@ -72,17 +74,15 @@
                  '[' :'__ob__',
                  ']' :'__cb__',
 		 '{' :'__oc__',
-                 '}' :'__cc__',
-
+                 '}' :'__cc__'
                  }
-
+    
+    #with new sanitizing we only need to replace for single quote, but this needs to remain for backwards compatibility
     for key, value in mapped_chars.items():
         pattern = pattern.replace(value, key)
-
-    pattern = pattern.replace('\'', '')
-
-    fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$")
-    invertRegEx = re.compile("(true)|(false)")
+    
+    fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$") #why?
+    invertRegEx = re.compile("(true)|(false)") #why?
 
     if not fileRegEx.match(outputfile):
 	print "Illegal output filename."
@@ -94,16 +94,29 @@
 	print "Illegal invert option."
 	return -7
 
-    # grep
+    # invert grep search?
     if invert == "true":
-	invertflag = " -v"
+        invertflag = " -v"
+        print "Not matching pattern: %s" % pattern
     else:
-	invertflag = ""
-
-    commandline = "grep -E"+invertflag+" '"+pattern+"' "+inputfile+" > "+outputfile
-
+        invertflag = ""
+        print "Matching pattern: %s" % pattern
+    
+    #Create temp file holding pattern
+    #By using a file to hold the pattern, we don't have worry about sanitizing grep commandline and can include single quotes in pattern
+    pattern_file_name = NamedTemporaryFile().name
+    open( pattern_file_name, 'w' ).write( pattern )
+    
+    #generate grep command
+    commandline = "grep -E %s -f %s %s > %s" % ( invertflag, pattern_file_name, inputfile, outputfile )
+    
+    #run grep
     errorcode, stdout = commands.getstatusoutput(commandline)
     
+    #remove temp pattern file
+    os.unlink( pattern_file_name )
+    
+    #return error code
     return errorcode
 
 if __name__ == "__main__":
diff -r b01c8245ef74 -r 14214b45db3f tools/filters/grep.xml
--- a/tools/filters/grep.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/filters/grep.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -1,4 +1,4 @@
-<tool id="Grep1" name="Select">
+<tool id="Grep1" name="Select" version="1.0.1">
   <description>lines that match an expression</description>
   <command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert</command>
   <inputs>
@@ -7,7 +7,16 @@
       <option value="false">Matching</option>
       <option value="true">NOT Matching</option>
     </param>
-    <param name="pattern" size="40" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)"/>
+    <param name="pattern" size="40" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
+      <sanitizer>
+        <valid initial="string.printable">
+         <remove value="'"/>
+        </valid>
+        <mapping initial="none">
+          <add source="'" target="__sq__"/>
+        </mapping>
+      </sanitizer>
+    </param>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input"/>
diff -r b01c8245ef74 -r 14214b45db3f tools/filters/joiner.xml
--- a/tools/filters/joiner.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/filters/joiner.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -1,4 +1,4 @@
-<tool id="join1" name="Join two Queries" version="2.0.1">
+<tool id="join1" name="Join two Queries" version="2.0.2">
   <description>side by side on a specified field</description>
   <command interpreter="python">join.py $input1 $input2 $field1 $field2 $out_file1 $unmatched $partial --index_depth=3 --buffer=50000000 --fill_options_file=$fill_options_file</command>
   <inputs>
diff -r b01c8245ef74 -r 14214b45db3f tools/plotting/xy_plot.xml
--- a/tools/plotting/xy_plot.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/plotting/xy_plot.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -94,9 +94,7 @@
   <outputs>
     <data format="pdf" name="out_file1" />
   </outputs>
-    <!--
-        TODO: figure out how to change the submit_form() method to correctly handle refreshing the 
-        form when the input for refresh is within a repeat construct ( like this tool )
+
     <tests>
         <test>
             <param name="main" value="Example XY Plot"/>
@@ -106,13 +104,12 @@
             <param name="xcol" value="1"/>
             <param name="ycol" value="2"/>
             <param name="type" value="line"/>
-            <param name="lty" value="dashed"/>
+            <param name="lty" value="2"/>
             <param name="col" value="2"/>
             <param name="lwd" value="1.0"/>
             <output name="out_file1" file="XY_Plot_1_out.pdf"/>
         </test>
     </tests>
-    -->
 <help>
 .. class:: infomark
 
diff -r b01c8245ef74 -r 14214b45db3f tools/samtools/sam_to_bam.py
--- a/tools/samtools/sam_to_bam.py	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/samtools/sam_to_bam.py	Mon Dec 07 14:45:47 2009 -0500
@@ -1,31 +1,27 @@
 #! /usr/bin/python
-
 """
-Converts SAM data to BAM format.
-
-usage: %prog [options]
-   -i, --input1=i: SAM file to be converted
-   -d, --dbkey=d: dbkey value
-   -r, --ref_file=r: Reference file if choosing from history
-   -o, --output1=o: BAM output
-   -x, --index_dir=x: Index directory
-
-usage: %prog input_file dbkey ref_list output_file
+Converts SAM data to sorted BAM data.
+usage: sam_to_bam.py [options]
+   --input1: SAM file to be converted
+   --dbkey: dbkey value
+   --ref_file: Reference file if choosing from history
+   --output1: output dataset in bam format
+   --index_dir: GALAXY_DATA_INDEX_DIR
 """
 
-import os, sys, tempfile
+import optparse, os, sys, subprocess, tempfile, shutil, gzip
 from galaxy import eggs
 import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.cookbook import doc_optparse
+from galaxy import util
 
 def stop_err( msg ):
     sys.stderr.write( "%s\n" % msg )
     sys.exit()
 
-def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
-    seq_file = "%s/sam_fa_indices.loc" % GALAXY_DATA_INDEX_DIR
+def check_seq_file( dbkey, cached_seqs_pointer_file ):
     seq_path = ''
-    for line in open( seq_file ):
+    for line in open( cached_seqs_pointer_file ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( "#" ) and line.startswith( 'index' ):
             fields = line.split( '\t' )
@@ -38,48 +34,80 @@
  
 def __main__():
     #Parse Command Line
-    options, args = doc_optparse.parse( __doc__ )
-    seq_path = check_seq_file( options.dbkey, options.index_dir )
+    parser = optparse.OptionParser()
+    parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
+    parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' )
+    parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
+    parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
+    parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
+    ( options, args ) = parser.parse_args()
+
+    cached_seqs_pointer_file = "%s/sam_fa_indices.loc" % options.index_dir
+    if not os.path.exists( cached_seqs_pointer_file ):
+        stop_err( "The required file (%s) does not exist." % cached_seqs_pointer_file )
+    # If found for the dbkey, seq_path will look something like /depot/data2/galaxy/equCab2/sam_index/equCab2.fa,
+    # and the equCab2.fa file will contain fasta sequences.
+    seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
     tmp_dir = tempfile.gettempdir()
-    os.chdir(tmp_dir)
-    tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir)
-    tmpf1fai = '%s.fai' % tmpf1.name
-    tmpf2 = tempfile.NamedTemporaryFile(dir=tmp_dir)
-    tmpf3 = tempfile.NamedTemporaryFile(dir=tmp_dir)
-    tmpf3bam = '%s.bam' % tmpf3.name
     if options.ref_file == "None":
-        full_path = "%s.fai" % seq_path 
-        if not os.path.exists( full_path ):
-            stop_err( "No sequences are available for '%s', request them by reporting this error." % options.dbkey )
-        cmd1 = "cp %s %s; cp %s %s" % (seq_path, tmpf1.name, full_path, tmpf1fai)
+        # We're using locally cached reference sequences( e.g., /depot/data2/galaxy/equCab2/sam_index/equCab2.fa ).
+        # The indexes for /depot/data2/galaxy/equCab2/sam_index/equCab2.fa will be contained in
+        # a file named /depot/data2/galaxy/equCab2/sam_index/equCab2.fa.fai
+        fai_index_file_path = "%s.fai" % seq_path 
+        if not os.path.exists( fai_index_file_path ):
+            stop_err( "No sequences are available for build (%s), request them by reporting this error." % options.dbkey )
     else:
-        cmd1 = "cp %s %s; samtools faidx %s 2>/dev/null" % (options.ref_file, tmpf1.name, tmpf1.name) 
-    cmd2 = "samtools view -bt %s -o %s %s 2>/dev/null" % (tmpf1fai, tmpf2.name, options.input1)   
-    cmd3 = "samtools sort %s %s 2>/dev/null" % (tmpf2.name, tmpf3.name)
-    cmd4 = "cp %s %s" % (tmpf3bam, options.output1)
-    # either create index based on fa file or copy provided index to temp directory 
+        try:
+            # Create indexes for history reference ( e.g., ~/database/files/000/dataset_1.dat ) using samtools faidx, which will:
+            # - index reference sequence in the FASTA format or extract subsequence from indexed reference sequence
+            # - if no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk
+            # - if regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format
+            # - the input file can be compressed in the RAZF format.
+            # IMPORTANT NOTE: a real weakness here is that we are creating indexes for the history dataset
+            # every time we run this tool.  It would be nice if we could somehow keep track of user's specific
+            # index files so they could be re-used.
+            fai_index_file_path = os.path.join( tmp_dir, os.path.basename( options.ref_file ) )
+            # At this point, fai_index_file_path will look something like /tmp/dataset_13.dat
+            os.symlink( options.ref_file, fai_index_file_path )
+            command = "samtools faidx %s 2>/dev/null" % fai_index_file_path
+            proc = subprocess.Popen( args=command, shell=True )
+            proc.wait()
+        except Exception, e:
+            stop_err( 'Error creating indexes from reference (%s), %s' % ( options.ref_file, str( e ) ) )
     try:
-        os.system(cmd1)
-    except Exception, eq:
-        stop_err("Error creating the reference list index.\n" + str(eq))
-    # create original bam file
+        # Extract all alignments from the input SAM file to BAM format ( since no region is specified, all the alignments will be extracted ).
+        tmp_aligns_file = tempfile.NamedTemporaryFile()
+        tmp_aligns_file_name = tmp_aligns_file.name
+        tmp_aligns_file.close()
+        # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning,
+        # and the docs do not currently state that this occurs ( very bad ).
+        command = "samtools view -bt %s -o %s %s 2>/dev/null" % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) 
+        proc = subprocess.Popen( args=command, shell=True )
+        proc.wait()
+    except Exception, e:
+        stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
     try:
-        os.system(cmd2)
-    except Exception, eq:
-        stop_err("Error running view command.\n" + str(eq))
-    # sort original bam file to produce sorted output bam file
-    try:
-        os.system(cmd3)
-        os.system(cmd4)
-    except Exception, eq:
-        stop_err("Error sorting data and creating output file.\n" + str(eq))
-    # cleanup temp files
-    tmpf1.close()
-    tmpf2.close()
-    tmpf3.close()
-    if os.path.exists(tmpf1fai):
-        os.remove(tmpf1fai)
-    if os.path.exists(tmpf3bam):
-        os.remove(tmpf3bam)
+        # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
+        # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
+        # into memory ( controlled by option -m ).
+        tmp_sorted_aligns_file = tempfile.NamedTemporaryFile()
+        tmp_sorted_aligns_file_name = tmp_sorted_aligns_file.name
+        tmp_sorted_aligns_file.close()
+        command = "samtools sort %s %s 2>/dev/null" % ( tmp_aligns_file_name, tmp_sorted_aligns_file_name )
+        proc = subprocess.Popen( args=command, shell=True )
+        proc.wait()
+    except Exception, e:
+        stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) )
+    # Move tmp_aligns_file_name to our output dataset location
+    sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name
+    shutil.move( sorted_bam_file, options.output1 )
+    if options.ref_file != "None":
+        # Remove the symlink from /tmp/dataset_13.dat to ~/database/files/000/dataset_13.dat
+        os.unlink( fai_index_file_path )
+        # Remove the index file
+        index_file_name = '%s.fai' % fai_index_file_path
+        os.unlink( index_file_name )
+    # Remove the tmp_aligns_file_name
+    os.unlink( tmp_aligns_file_name )
 
 if __name__=="__main__": __main__()
diff -r b01c8245ef74 -r 14214b45db3f tools/samtools/sam_to_bam.xml
--- a/tools/samtools/sam_to_bam.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/samtools/sam_to_bam.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -1,32 +1,29 @@
 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.0.0">
   <description>converts SAM format to BAM format</description>
   <command interpreter="python">
-    sam_to_bam.py 
-        --input1=$source.input1
-        --dbkey=${input1.metadata.dbkey} 
-        #if $source.indexSource == "history":
-         --ref_file=$ref_file
-        #else
-         --ref_file="None"
-        #end if
-        --output1=$output1
-        --index_dir=${GALAXY_DATA_INDEX_DIR}
+sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} 
+#if $source.index_source == "history":
+--ref_file=$source.ref_file
+#else
+--ref_file="None"
+#end if
+--output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR}
   </command>
   <inputs>
     <conditional name="source">
-      <param name="indexSource" type="select" label="Choose the source for the reference list">
-        <option value="built_in">Built-in</option>
+      <param name="index_source" type="select" label="Choose the source for the reference list">
+        <option value="cached">Locally cached</option>
         <option value="history">History</option>
       </param>
-      <when value="built_in">
+      <when value="cached">
         <param name="input1" type="data" format="sam" label="SAM File to Convert">
            <validator type="unspecified_build" />
            <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
         </param>
       </when>
       <when value="history">
-        <param name="input1" type="data" format="sam" label="SAM File to Convert" />
-        <param name="ref_file" type="data" format="fasta" label="Choose the reference file" />
+        <param name="input1" type="data" format="sam" label="Convert SAM file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
   </inputs>
@@ -34,19 +31,16 @@
     <data name="output1" format="bam"/>
   </outputs>
   <tests>
+    <!--
+    # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning,
+    # and the docs do not currently state that this occurs ( very bad ).
+    -->
     <test>
-      <param name="indexSource" value="history" /> 
-      <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
-      <param name="ref_file" value="chrM.fa" ftype="fasta" />
+      <param name="index_source" value="history" /> 
+      <param name="input1" value="3.sam" ftype="sam" />
+      <param name="ref_file" value="chr_m.fasta" ftype="fasta" />
       <output name="output1" file="sam_to_bam_out1.bam" />
     </test>
-<!--  chrM is not a built-in dbkey (in the builds.txt list) so can't be tested
-    <test>
-      <param name="indexSource" value="built_in" />
-      <param name="input1" value="sam_to_bam_in2.sam" ftype="sam" dbkey="chrM" />
-      <output name="output1" file="sam_to_bam_out2.bam" />
-    </test>
--->
   </tests>
   <help>
 
diff -r b01c8245ef74 -r 14214b45db3f tools/sr_mapping/bowtie_wrapper.xml
--- a/tools/sr_mapping/bowtie_wrapper.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/sr_mapping/bowtie_wrapper.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -338,7 +338,7 @@
     </test>
     <test>
       <param name="genomeSource" value="history" />
-      <param name="ownFile" value="chrM.fa" />
+      <param name="ownFile" value="chr_m.fasta" />
       <param name="index_settings" value="index_pre_set" />
       <param name="sPaired" value="paired" />
       <param name="input1" ftype="fastqsanger" value="bowtie_in2.fastq" />
@@ -349,7 +349,7 @@
     </test>
     <test>
       <param name="genomeSource" value="history" />
-      <param name="ownFile" value="chrM.fa" />
+      <param name="ownFile" value="chr_m.fasta" />
       <param name="index_settings" value="index_full" />
       <param name="auto_b" value="set" />
       <param name="packed" value="unpacked" />
diff -r b01c8245ef74 -r 14214b45db3f tools/sr_mapping/lastz_wrapper.xml
--- a/tools/sr_mapping/lastz_wrapper.xml	Mon Dec 07 14:45:09 2009 -0500
+++ b/tools/sr_mapping/lastz_wrapper.xml	Mon Dec 07 14:45:47 2009 -0500
@@ -125,10 +125,13 @@
         <requirement type="binary">lastz</requirement>
     </requirements>
     <tests>
-        <test> <!-- Lastz command: lastz phiX.2bit/PHIX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam 
-        			You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data 
-        			You will have to replace all the pluses before the commands with 2 dashes, 
-        			as double-dash can't appear in an XML comment -->
+        <test>
+            <!--
+            Lastz command:
+            lastz phiX.2bit/PHIX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam 
+            You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data.  You will have to replace all the pluses before the
+            commands with 2 dashes, as double-dash can't appear in an XML comment.
+            -->
             <param name="input2" value="b1.fasta" ftype="fasta" />
             <param name="ref_source" value="cached" />
             <param name="input1_2bit" value="phiX" />
@@ -156,10 +159,13 @@
             <param name="num_threads" value="4" />
             <output name="output1" file="lastz_wrapper_out2.sam" />
         </test>
-        <test> <!-- Lastz command: lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular 
-        			phiX.fasta and b1.fasta are located in galaxy's test-data 
-        			You will have to replace all the pluses before the commands with 2 dashes, 
-        			as double-dash can't appear in an XML comment -->
+        <test>
+            <!--
+            Lastz command:
+            lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular 
+        	phiX.fasta and b1.fasta are located in galaxy's test-data.  You will have to replace all the pluses before the commands with 2 dashes, 
+            as double-dash can't appear in an XML comment.
+            -->
             <param name="input2" value="b1.fasta" ftype="fasta" />
             <param name="ref_source" value="history" />
             <param name="input1" value="phiX.fasta" ftype="fasta" />
@@ -173,14 +179,7 @@
             <param name="num_threads" value="4" />
             <output name="output1" file="lastz_wrapper_out3.tabular" />
         </test>
-        <test> <!-- Lastz command: first you will need to split the file phiX_split.fasta into two files, 
-        			phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:
-        			lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular 
-        			lastz phiX2.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular 
-        			You need to point to phiX1.fasta and phiX2.fasta somewhere on your system. 
-        			phiX_split.fasta and b1.fasta are located in galaxy's test-data 
-        			You will have to replace all the asterisks before the commands with 2 dashes, 
-        			as double-dash can't appear in an XML comment -->
+        <test>
             <param name="input2" value="b1.fasta" ftype="fasta" />
             <param name="ref_source" value="history" />
             <param name="input1" value="phiX_split.fasta" ftype="fasta"  />

    

[galaxy-dev] [hg] galaxy 3153: Merge with 24f195c617da80ae71dd8281b7517973301...

Greg Von Kuster