# HG changeset patch
# User devteam
# Date 1391804849 18000
# Node ID 0bd6b2cb3b2a65520fdcc48bcad7fa02bc6cadf3

Uploaded archive containing files for version 1.03.52.

diff -r 000000000000 -r 0bd6b2cb3b2a lastz/lastz_wrapper.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/lastz_wrapper.py	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,378 @@
+#!/usr/bin/env python
+
+"""
+Runs Lastz
+Written for Lastz v. 1.03.52.
+"""
+import optparse, os, subprocess, shutil, sys, tempfile, threading, time
+from Queue import Queue
+
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( 'bx-python' )
+from bx.seq.twobit import *
+from bx.seq.fasta import FastaReader
+from galaxy.util.bunch import Bunch
+
+STOP_SIGNAL = object()
+SLOTS = 128
+
+def stop_err( msg ):
+    sys.stderr.write( "%s" % msg )
+    sys.exit()
+
+def stop_queues( lastz, combine_data ):
+    """
+    Send STOP_SIGNAL to all worker threads.  This method should only be called if
+    an error has been encountered.
+    """
+    for t in lastz.threads:
+        lastz.put( STOP_SIGNAL, True )
+    combine_data.put( STOP_SIGNAL, True )
+
+
+class BaseQueue( object ):
+
+    def __init__( self, num_threads, slots=-1 ):
+        """Initialize the queue and worker threads."""
+        self.queue = Queue( slots )
+        self.threads = []
+        for i in range( num_threads ):
+            worker = threading.Thread( target=self.run_next )
+            worker.start()
+            self.threads.append( worker )
+
+    def run_next( self ):
+        """Run the next job, waiting until one is available if necessary."""
+        while True:
+            job = self.queue.get()
+            if job is STOP_SIGNAL:
+                return self.shutdown()
+            self.run_job( job )
+            time.sleep( 1 )
+
+    def run_job( self, job ):
+        stop_err( 'Not Implemented' )
+
+    def put( self, job, block=False ):
+        """Add a job to the queue."""
+        self.queue.put( job, block )
+
+    def shutdown( self ):
+        return
+
+
+class LastzJobQueue( BaseQueue ):
+    """
+    A queue that runs commands in parallel.  Blocking is done so the queue will
+    not consume much memory.
+    """
+
+    def run_job( self, job ):
+        # Execute the job's command
+        proc = subprocess.Popen( args=job.command, shell=True, stderr=subprocess.PIPE, )
+        proc.wait()
+        stderr = proc.stderr.read()
+        proc.wait()
+        if stderr:
+            stop_queues( self, job.combine_data_queue )
+            stop_err( stderr )
+        job.combine_data_queue.put( job )
+
+
+class CombineDataQueue( BaseQueue ):
+    """
+    A queue that concatenates files in serial.  Blocking is not done since this
+    queue is not expected to grow larger than the command queue.
+    """
+
+    def __init__( self, output_filename, num_threads=1 ):
+        BaseQueue.__init__( self, num_threads )
+        self.CHUNK_SIZE = 2**20 # 1Mb
+        self.output_file = open( output_filename, 'wb' )
+
+    def run_job( self, job ):
+        in_file = open( job.output, 'rb' )
+        while True:
+            chunk = in_file.read( self.CHUNK_SIZE )
+            if not chunk:
+                in_file.close()
+                break
+            self.output_file.write( chunk )
+        for file_name in job.cleanup:
+            os.remove( file_name )
+
+    def shutdown( self ):
+        self.output_file.close()
+        return
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '', '--threads', dest='threads', help='The number of threads to use' )
+    parser.add_option( '', '--ref_name', dest='ref_name', help='The reference name to change all output matches to' )
+    parser.add_option( '', '--ref_source', dest='ref_source', help='Whether the reference is self, cached or from the history' )
+    parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
+    parser.add_option( '', '--mirror', dest='mirror', help='Do or do not report mirror image of all gap-free alignments' )
+    parser.add_option( '', '--source_select', dest='source_select', help='Whether to used pre-set or cached reference file' )
+    parser.add_option( '', '--input1', dest='input1', help='The name of the reference file if using history or reference base name if using cached' )
+    parser.add_option( '', '--input2', dest='input2', help='The reads file to align' )
+    parser.add_option( '', '--strand', dest='strand', help='Which strand of the read to search, if specifying all parameters' )
+    parser.add_option( '', '--match_reward', dest='match_reward', help='Score values for a match (reward)' )
+    parser.add_option( '', '--match_penalty', dest='match_penalty', help='Score values for a mismatch (penalty), same as reward when not specified (but reward is)' )
+    parser.add_option( '', '--gapped', dest='gapped', help='Perform gapped extension of HSPs (or seeds if gapped-free extension is not performed) after first reducing them to anchor points' )
+    parser.add_option( '', '--gap_open', dest='gap_open', help='Score penalties for opening a gap' )
+    parser.add_option( '', '--gap_extend', dest='gap_extend', help='Score penalties for extending a gap' )
+    parser.add_option( '', '--ambiguous', dest='ambiguous', help='Treat as ambiguous nucleotides' )
+    parser.add_option( '', '--step', dest='step', help='Offset between the starting positions of successive target words considered for potential seeds' )
+    parser.add_option( '', '--masking', dest='masking', help='Dynamically mask the target sequence by excluding any positions that appear in too many alignments from further consideration for seeds' )
+    parser.add_option( '', '--seed', dest='seed', help='Offset between the starting positions of successive target words considered for potential seeds' )
+    parser.add_option( '', '--match_length', dest='match_length', help='Seeds require bp word of this length with matches in all positions' )
+    parser.add_option( '', '--transition', dest='transition', help='Transition settings, affects the number of allowed transition substitutions in each seed' )
+    parser.add_option( '', '--xdrop', dest='xdrop', help='Find HSPs using the xdrop extension method with the given termination threshold instead of using the exact match method' )
+    parser.add_option( '', '--hspthresh', dest='hspthresh', help='Score threshold for the x-drop extension method' )
+    parser.add_option( '', '--entropy', dest='entropy', help='Whether to adjust for entropy when qualifying HSPs in the x-drop extension method' )
+    parser.add_option( '', '--chain', dest='chain', help='Perform chaining of HSPs with no penalties' )
+    parser.add_option( '', '--ydrop', dest='ydrop', help='Set the threshold for terminating gapped extension' )
+    parser.add_option( '', '--ytrim', dest='ytrim', help='Trim back to peak score if y-drop extension encounters end of sequence' )
+    parser.add_option( '', '--gappedthresh', dest='gappedthresh', help='Threshold for gapped extension.  Alignments scoring lower are discarded.' )
+    parser.add_option( '', '--filter', dest='filter', help='Filter alignments.' )
+    parser.add_option( '', '--identity_min', dest='identity_min', help='Minimum for filtering alignments by their percent identity.' )
+    parser.add_option( '', '--identity_max', dest='identity_max', help='Maximum for filtering alignments by their percent identity.' )
+    parser.add_option( '', '--coverage_min', dest='coverage_min', help='Minimum for filtering alignments by how much of the input sequence they cover.' )
+    parser.add_option( '', '--coverage_max', dest='coverage_max', help='Maximum for filtering alignments by how much of the input sequence they cover.' )
+    parser.add_option( '', '--nmatch_min', dest='nmatch_min', help='Minimum for filtering alignments by how many bases they match.' )
+    parser.add_option( '', '--nmismatch_max', dest='nmismatch_max', help='Maximum for filtering alignments by the number of mismatches.' )
+    parser.add_option( '', '--trivial', dest='trivial', help='Do or do not output a trivial self-alignment block if the target and query sequences are identical.' )
+    parser.add_option( '', '--inner', dest='inner', help='Perform additional alignment between the gapped alignment blocks using (presumably) more sensitive alignment parameters.' )
+    parser.add_option( '', '--shortcuts_for_yasra', dest='shortcuts_for_yasra', help='Shortcut options to support the Yasra mapping assembler' )
+    parser.add_option( '', '--out_format', dest='format', help='The format of the output file (sam, diffs, or tabular (general))' )
+    parser.add_option( '', '--output', dest='output', help='The output file' )
+    parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' )
+    ( options, args ) = parser.parse_args()
+    # Output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='lastz -v', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Lastz version\n' )
+
+    if options.ref_name:
+        ref_name = '[nickname=%s]' % options.ref_name
+    else:
+        ref_name = ''
+    set_options = ''
+    # Commonly-used preset options
+    if options.source_select == 'pre_set':
+        # Handle ref_source
+        if options.ref_source == 'self':
+            # --mirror is available only if ref_source selection is --self
+            if options.mirror == 'yes':
+                set_options += '--nomirror '
+    else:
+        # Full set of user-specified options
+        # Handle ref_source
+        if options.ref_source == 'self':
+            # --mirror is available only if ref_source selection is --self
+            if options.mirror == 'yes':
+                set_options += '--nomirror '
+        else:
+            # Using --self automatically enables this option
+            if options.trivial == 'no':
+                set_options += '--notrivial '
+        # Handle --match
+        if options.match_reward not in [ "", "0" ]:
+            if options.match_penalty in [ "", "0" ]:
+                match_penalty = options.match_reward
+            else:
+                match_penalty = options.match_penalty
+            set_options += '--match=%s,%s ' % ( options.match_reward, match_penalty )
+        # Handle --gapped
+        if options.gapped == 'yes':
+            set_options += '--gapped '
+            if options.gap_open not in [ "" ]:
+                if options.gap_extend in [ "" ]:
+                    set_options += '--gap=%s ' % options.gap_open
+                else:
+                    set_options += '--gap=%s,%s ' % ( options.gap_open, options.gap_extend )
+            # Handle --ydrop
+            if options.ydrop not in [ "", "0" ]:
+                set_options += '--ydrop=%s ' % options.ydrop
+            # Handle --ytrim
+            if options.ytrim == 'no':
+                set_options += '--noytrim '
+            # Handle --gappedthresh
+            if options.gappedthresh not in [ "", "0" ]:
+                set_options += '--gappedthresh=%s ' % options.gappedthresh
+            # Handle --inner
+            if options.inner not in [ "" ]:
+                set_options += '--inner=%s ' % options.inner
+        else:
+            set_options += '--nogapped '
+        # Handle --step
+        if options.step not in [ "", "0" ]:
+            set_options += '--step=%s ' % options.step
+        # Handle --masking
+        if options.masking not in [ '0' ]:
+            set_options += '--masking=%s ' % options.masking
+        # Handle --seed
+        if options.seed not in [ "no" ]:
+            if options.seed == 'match':
+                set_options += '--seed=match%s ' % options.match_length
+            else:
+                set_options += '--seed=%s ' % options.seed
+        # Handle --transition
+        if options.transition == '0':
+            set_options += '--notransition '
+        else:
+            set_options += '--transition=%s ' % options.transition
+        # Handle --xdrop
+        if options.xdrop not in [ "", "0" ]:
+            set_options += '--xdrop=%s ' % options.xdrop
+        # handle --hspthresh
+        if options.hspthresh not in [ "", "0" ]:
+            set_options += '--hspthresh=%s ' % options.hspthresh
+        # Handle --entropy
+        if options.entropy == 'no':
+            set_options += '--noentropy '
+        else:
+            set_options += '--entropy '
+        # Handle --chain
+        if options.chain == 'no':
+            set_options += '--nochain '
+        else:
+            set_options += '--chain '
+        # Handle --filter
+        if options.filter not in [ "no" ]:
+            if options.filter == 'identity':
+                identity_min = options.identity_min
+                if options.identity_max in [ "", "0" ] or options.identity_max <= identity_min:
+                    identity_max = '100'
+                else:
+                    identity_max = options.identity_max
+                set_options += '--filter=identity:%s..%s ' % ( identity_min, identity_max )
+            elif options.filter == 'coverage':
+                coverage_min = options.coverage_min
+                if options.coverage_max in [ "", "0" ] or options.coverage_max <= coverage_min:
+                    coverage_max = '100'
+                else:
+                    coverage_max = options.coverage_max
+                set_options += '--filter=coverage:%s..%s ' % ( coverage_min, coverage_max )
+            elif options.filter == 'nmatch':
+                set_options += '--filter=nmatch:%s% ' % options.nmatch_min
+            elif options.filter == 'nmismatch':
+                set_options += '--filter=nmismatch:0..%s ' % options.nmismatch_max
+    # Handle --strand
+    set_options += '--strand=%s ' % options.strand
+    # Handle --ambiguous
+    if options.ambiguous not in [ "no" ]:
+        set_options += '--ambiguous=%s ' % options.ambiguous
+    # Handle --shortcuts_for_yasra
+    if options.shortcuts_for_yasra not in [ 'none' ]:
+        set_options += '--%s ' % ( options.shortcuts_for_yasra )
+    # Specify input2 and add [fullnames] modifier if output format is diffs
+    if options.format == 'diffs':
+        input2 = '%s[fullnames]' % options.input2
+    else:
+        input2 = options.input2
+    if options.format == 'tabular':
+        # Change output format to general if it's tabular and add field names for tabular output
+        format = 'general-'
+        tabular_fields = ':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'
+    elif options.format == 'sam':
+        # We currently need to keep headers.
+        format = 'sam'
+        tabular_fields = ''
+    else:
+        format = options.format
+        tabular_fields = ''
+    # Set up our queues
+    threads = int( options.threads )
+    lastz_job_queue = LastzJobQueue( threads, slots=SLOTS )
+    combine_data_queue = CombineDataQueue( options.output )
+    if str( options.ref_source ) in [ 'history', 'self' ]:
+        # Reference is a fasta dataset from the history or the dataset containing the target sequence itself,
+        # so split job across the number of sequences in the dataset ( this could be a HUGE number ).
+        try:
+            # Ensure there is at least 1 sequence in the dataset ( this may not be necessary ).
+            error_msg = "The reference dataset is missing metadata.  Click the pencil icon in the history item and 'auto-detect' the metadata attributes."
+            ref_sequences = int( options.ref_sequences )
+            if ref_sequences < 1:
+                stop_queues( lastz_job_queue, combine_data_queue )
+                stop_err( error_msg )
+        except:
+            stop_queues( lastz_job_queue, combine_data_queue )
+            stop_err( error_msg )
+        seqs = 0
+        fasta_reader = FastaReader( open( options.input1 ) )
+        while True:
+            # Read the next sequence from the reference dataset
+            seq = fasta_reader.next()
+            if not seq:
+                break
+            seqs += 1
+            # Create a temporary file to contain the current sequence as input to lastz
+            tmp_in_fd, tmp_in_name = tempfile.mkstemp( suffix='.in' )
+            tmp_in = os.fdopen( tmp_in_fd, 'wb' )
+            # Write the current sequence to the temporary input file
+            tmp_in.write( '>%s\n%s\n' % ( seq.name, seq.text ) )
+            tmp_in.close()
+            # Create a 2nd temporary file to contain the output from lastz execution on the current sequence
+            tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' )
+            os.close( tmp_out_fd )
+            # Generate the command line for calling lastz on the current sequence
+            command = 'lastz %s%s %s %s --format=%s%s > %s' % ( tmp_in_name, ref_name, input2, set_options, format, tabular_fields, tmp_out_name )
+            # Create a job object
+            job = Bunch()
+            job.command = command
+            job.output = tmp_out_name
+            job.cleanup = [ tmp_in_name, tmp_out_name ]
+            job.combine_data_queue = combine_data_queue
+            # Add another job to the lastz_job_queue.  Execution will wait at this point if the queue is full.
+            lastz_job_queue.put( job, block=True )
+        # Make sure the value of sequences in the metadata is the same as the number of
+        # sequences read from the dataset.  According to Bob, this may not be necessary.
+        if ref_sequences != seqs:
+            stop_queues( lastz_job_queue, combine_data_queue )
+            stop_err( "The value of metadata.sequences (%d) differs from the number of sequences read from the reference (%d)." % ( ref_sequences, seqs ) )
+    else:
+        # Reference is a locally cached 2bit file, split job across number of chroms in 2bit file
+        tbf = TwoBitFile( open( options.input1, 'r' ) )
+        for chrom in tbf.keys():
+            # Create a temporary file to contain the output from lastz execution on the current chrom
+            tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' )
+            os.close( tmp_out_fd )
+            command = 'lastz %s/%s%s %s %s --format=%s%s >> %s' % \
+                ( options.input1, chrom, ref_name, input2, set_options, format, tabular_fields, tmp_out_name )
+            # Create a job object
+            job = Bunch()
+            job.command = command
+            job.output = tmp_out_name
+            job.cleanup = [ tmp_out_name ]
+            job.combine_data_queue = combine_data_queue
+            # Add another job to the lastz_job_queue.  Execution will wait at this point if the queue is full.
+            lastz_job_queue.put( job, block=True )
+    # Stop the lastz_job_queue.
+    for t in lastz_job_queue.threads:
+        lastz_job_queue.put( STOP_SIGNAL, True )
+    # Although all jobs are submitted to the queue, we can't shut down the combine_data_queue
+    # until we know that all jobs have been submitted to its queue.  We do this by checking
+    # whether all of the threads in the lastz_job_queue have terminated.
+    while threading.activeCount() > 2:
+        time.sleep( 1 )
+    # Now it's safe to stop the combine_data_queue.
+    combine_data_queue.put( STOP_SIGNAL )
+
+if __name__=="__main__": __main__()
diff -r 000000000000 -r 0bd6b2cb3b2a lastz/lastz_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/lastz_wrapper.xml	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,569 @@
+<tool id="lastz_wrapper_2" name="Lastz" version="1.03.52">
+    <requirements>
+        <requirement type="package" version="1.03.52">lastz</requirement>
+    </requirements>
+    <description> map short reads against reference sequence</description>
+    <command interpreter="python">
+        lastz_wrapper.py
+        --threads="\${GALAXY_SLOTS:-4}"
+        #if str( $seq_name.how_to_name ) == "yes":
+            --ref_name="${seq_name.ref_name}"
+        #end if
+        --ref_source="${source.ref_source}"
+        --source_select="${params.source_select}"
+        --out_format="${out_format}"
+        --input2="${input2}"
+        #if str( $source.ref_source ) == "history":
+            --input1="${source.input1}"
+            --ref_sequences="${input1.metadata.sequences}"
+            --trivial="${source.trivial}"
+        #else if str( $source.ref_source ) == "self":
+            --input1="${input2}"
+            --ref_sequences="${input2.metadata.sequences}"
+            --mirror="${source.mirror}"
+        #else:
+            --input1="${source.input1_2bit.fields.path}"
+            --ref_sequences="None"
+            --trivial="${source.trivial}"
+        #end if
+        --shortcuts_for_yasra="${params.shortcuts_for_yasra}"
+        --strand="${params.strand}"
+        --ambiguous="${params.ambiguous}"
+        #if str( $params.source_select ) == "full":
+            --match_reward="${params.match_reward}"
+            --match_penalty="${params.match_penalty}"
+            --gapped="${params.gapped_extension.gapped}"
+            #if str( $params.gapped_extension.gapped ) == "yes":
+                --gap_open="${params.gapped_extension.gap_open}"
+                --gap_extend="${params.gapped_extension.gap_extend}"
+                --ydrop="${params.gapped_extension.ydrop}"
+                --ytrim="${params.gapped_extension.ytrim}"
+                --gappedthresh="${params.gapped_extension.gappedthresh}"
+                --inner="${params.gapped_extension.inner}"
+            #end if
+            --step="${params.step}"
+            --masking="${params.masking}"
+            --seed="${params.seeding_settings.seed}"
+            #if str( $params.seeding_settings.seed ) == "match":
+                --match_length="${params.seeding_settings.match_length}"
+            #end if
+            --transition="${params.transition}"
+            --xdrop="${params.xdrop}"
+            --hspthresh="${params.hspthresh}"
+            --entropy="${params.entropy}"
+            --chain="${params.chain}"        
+            --filter="${params.back_end_filter.filter}"
+            #if str( $params.back_end_filter.filter ) == "identity":
+                --identity_min="${params.back_end_filter.identity_min}"
+                --identity_max="${params.back_end_filter.identity_max}"
+            #else if str( $params.back_end_filter.filter ) == "coverage":
+                --coverage_min="${params.back_end_filter.coverage_min}"
+                --coverage_max="${params.back_end_filter.coverage_max}"
+            #else if str( $params.back_end_filter.filter ) == "nmatch":
+                --nmatch_min="${params.back_end_filter.nmatch_min}"
+            #else if str( $params.back_end_filter.filter ) == "nmismatch":
+                --nmismatch_max="${params.back_end_filter.nmismatch_max}"
+            #end if
+        #end if
+        --output="${output1}"
+        --lastzSeqsFileDir="${GALAXY_DATA_INDEX_DIR}"
+    </command>
+    <inputs>
+        <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
+        <conditional name="source">
+            <param name="ref_source" type="select" label="Against reference sequences that are">
+                <option value="cached">locally cached</option>
+                <option value="history">in your history</option>
+                <option value="self">in self</option>
+            </param>
+            <when value="cached">
+                <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                    <options from_data_table="lastz_seqs" />
+                </param>
+                <param name="trivial" type="select" label="Output a trivial self-alignment block if the target and query sequences are identical">
+                    <option value="yes">Yes</option>
+                    <option value="no">No</option>
+                </param>
+            </when>
+            <when value="history">
+                <param name="input1" type="data" format="fasta" label="Select a reference dataset" />
+                <param name="trivial" type="select" label="Output a trivial self-alignment block if the target and query sequences are identical">
+                    <option value="yes">Yes</option>
+                    <option value="no">No</option>
+                </param>
+            </when>
+            <when value="self">
+                <param name="mirror" type="select" label="Report mirror image of all gap-free alignments?" help="If no, only one copy of each meaningful alignment block in a self-alignment will be produced">
+                    <option value="yes">Yes</option>
+                    <option value="no">No</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="out_format" type="select" label="Output format">
+            <option value="sam">SAM</option>
+            <option value="diffs">Polymorphisms</option>
+            <option value="tabular">Tabular</option>
+        </param>
+        <conditional name="params">
+            <param name="source_select" type="select" label="Lastz settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
+                <option value="pre_set">Commonly used</option>
+                <option value="full">Full Parameter List</option>
+            </param>
+            <when value="pre_set">
+                <param name="strand" type="select" label="Strand to search">
+                    <option value="both">Both</option>
+                    <option value="plus">Search forward strand only (the one in the reference)</option>
+                    <option value="minus">Search the reverse complement strand only (opposite of the reference)</option>
+                </param>
+                <param name="ambiguous" type="select" label="Treat as ambiguous nucleotides?">
+                    <option value="no">No</option>
+                    <option value="n">Treat N as an ambiguous nucleotide</option>
+                    <option value="iupac">Treat any IUPAC-IUB as a completely ambiguous nucleotide</option>
+                </param>
+                <param name="shortcuts_for_yasra" type="select" label="Select mapping mode">
+                    <option value="none">Do not set</option>
+                    <option value="yasra98">Roche-454 98% identity</option>
+                    <option value="yasra95">Roche-454 95% identity</option>
+                    <option value="yasra90">Roche-454 90% identity</option>
+                    <option value="yasra85">Roche-454 85% identity</option>
+                    <option value="yasra75">Roche-454 75% identity</option>
+                    <option value="yasra95short">Illumina 95% identity</option>
+                    <option value="yasra85short">Illumina 85% identity</option>
+                </param>
+            </when>
+            <when value="full">
+                <param name="strand" type="select" label="Strand to search">
+                    <option value="both">Both</option>
+                    <option value="plus">Search forward strand only (the one in the reference)</option>
+                    <option value="minus">Search the reverse complement strand only (opposite of the reference)</option>
+                </param>
+                <param name="ambiguous" type="select" label="Treat as ambiguous nucleotides?">
+                    <option value="no">No</option>
+                    <option value="n">Treat N as an ambiguous nucleotide</option>
+                    <option value="iupac">Treat any IUPAC-IUB as a completely ambiguous nucleotide</option>
+                </param>
+                <param name="shortcuts_for_yasra" type="select" label="Select mapping mode">
+                    <option value="none">Do not set</option>
+                    <option value="yasra98">Roche-454 98% identity</option>
+                    <option value="yasra95">Roche-454 95% identity</option>
+                    <option value="yasra90">Roche-454 90% identity</option>
+                    <option value="yasra85">Roche-454 85% identity</option>
+                    <option value="yasra75">Roche-454 75% identity</option>
+                    <option value="yasra95short">Illumina 95% identity</option>
+                    <option value="yasra85short">Illumina 85% identity</option>
+                </param>
+                <param name="match_reward" type="integer" size="10" value="" optional="true" label="Score values for a match (reward)">
+                    <validator type="in_range" message="Positive integer required" min="1" />
+                </param>
+                <param name="match_penalty" type="integer" size="10" value="" optional="true" label="Score values for a mismatch (penalty)" help="same as reward when not specified (but reward is)">
+                    <validator type="in_range" message="Positive integer required" min="1" />
+                </param>
+                <conditional name="gapped_extension">
+                    <param name="gapped" type="select" label="Perform gapped extension of HSPs (or seeds if gapped-free extension is not performed)?" help="after first reducing them to anchor points">
+                        <option value="no">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="yes">
+                        <param name="gap_open" type="integer" size="10" value="" optional="true" label="Score penalties for opening a gap">
+                            <validator type="in_range" message="Positive integer required" min="1" />
+                        </param>
+                        <param name="gap_extend" type="integer" size="10" value="" optional="true" label="Score penalties for extending a gap">
+                            <validator type="in_range" message="Positive integer required" min="1" />
+                        </param>
+                        <param name="ydrop" type="integer" size="10" value="" optional="true" label="y-drop threshold for terminating gapped extension" help="Restricts the end points of each local alignment">
+                            <validator type="in_range" message="Positive integer required" min="1" />
+                        </param>
+                        <param name="ytrim" type="select" label="Trim back to peak score if y-drop extension encounters end of sequence">
+                            <option value="yes">Yes</option>
+                            <option value="no">No</option>
+                        </param>
+                        <param name="gappedthresh" type="integer" size="10" value="" optional="true" label="Threshold for gapped extension" help="Alignments scoring lower are discarded">
+                            <validator type="in_range" message="Positive integer required" min="1" />
+                        </param>
+                        <param name="inner" type="integer" size="10" value="" optional="true" label="Perform additional alignment between the gapped alignment blocks" help="using presumably more sensitive alignment parameters">
+                            <validator type="in_range" message="Positive integer required" min="1" />
+                        </param>
+                    </when>
+                </conditional>
+                <param name="step" type="integer" size="10" value="" optional="true" label="Offset between the starting positions of successive target words considered for potential seeds">
+                    <validator type="in_range" message="Positive integer required" min="1" />
+                </param>
+                <param name="masking" type="integer" size="10" value="0" label="Dynamically mask the target sequence" help="Zero indicates no masking">
+                    <validator type="in_range" message="Non-negative integer required" min="0" />
+                </param>
+                <conditional name="seeding_settings">
+                    <param name="seed" type="select" label="Select seeding hit settings" help="allows you set word size and number of mismatches">
+                        <option value="no">No</option>
+                        <option value="match">Set length of bp word with matches in all positions</option>
+                        <option value="12of19">Require a 19 bp word with matches in 12 specific positions</option>
+                    </param>
+                    <when value="match">
+                        <param name="match_length" type="integer" size="10" value="" label="Length of bp word with matches in all positions">
+                            <validator type="in_range" message="Positive integer required" min="1" />
+                        </param>
+                    </when>
+                </conditional>
+                <param name="transition" type="select" label="Select transition settings" help="affects the number of allowed transition substitutions">
+                    <option value="0">Don't allow any transitions in seed hits</option>
+                    <option value="1">Allow one transition in each seed hit</option>
+                    <option value="2">Allow two transitions in each seed hit</option>
+                </param>
+                <param name="xdrop" type="integer" size="10" value="" optional="true" label="x-drop extension termination threshold" help="find HSPs using the x-drop extension method with this termination threshold">
+                    <validator type="in_range" message="Positive integer required" min="1" />
+                </param>
+                <param name="hspthresh" type="integer" size="10" value="" optional="true" label="Score threshold for the x-drop extension method" help="HSPs scoring lower are discarded">
+                    <validator type="in_range" message="Positive integer required" min="1" />
+                </param>
+                <param name="entropy" type="select" label="Adjust for entropy when qualifying HSPs in the x-drop extension method">
+                    <option value="no">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <param name="chain" type="select" label="Perform chaining of HSPs with no penalties">
+                    <option value="no">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <conditional name="back_end_filter">
+                    <param name="filter" type="select" label="Filter alignments">
+                        <option value="no">No</option>
+                        <option value="identity">by their percent identity</option>
+                        <option value="coverage">by how much of the input sequence they cover</option>
+                        <option value="nmatch">by how many bases match</option>
+                        <option value="nmismatch">by the number of mismatches</option>
+                    </param>
+                    <when value="identity">
+                        <param name="identity_min" type="integer" size="10" value="0" label="Minimum percentage identity">
+                            <validator type="in_range" message="Non-negative integer required" min="0" max="100" />
+                        </param>
+                        <param name="identity_max" type="integer" size="10" value="" optional="true" label="Maximum percentage identity">
+                            <validator type="in_range" message="Non-negative integer required" min="0" max="100" />
+                        </param>
+                    </when>
+                    <when value="coverage">
+                        <param name="coverage_min" type="integer" size="10" value="0" label="Minimum percentage coverage">
+                            <validator type="in_range" message="Non-negative integer required" min="0" max="100" />
+                        </param>
+                        <param name="coverage_max" type="integer" size="10" value="" optional="true" label="Maximum percentage coverage">
+                            <validator type="in_range" message="Non-negative integer required" min="0" max="100" />
+                        </param>
+                    </when>
+                    <when value="nmatch">
+                        <param name="nmatch_min" type="integer" size="10" value="0" label="Minimum percentage of query length for matching bases">
+                            <validator type="in_range" message="Non-negative integer required" min="0" max="100" />
+                        </param>
+                    </when>
+                    <when value="nmismatch">
+                        <param name="nmismatch_max" type="integer" size="10" value="0" label="Maximum number of mismatched bases">
+                            <validator type="in_range" message="Non-negative integer required" min="0" />
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        <conditional name="seq_name">
+            <param name="how_to_name" type="select" label="Modify the reference name?">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="ref_name" type="text" size="25" value="Type sequence name here" label="Enter name for the Reference sequence"/>
+            </when>
+            <when value="no" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output1" label="${tool.name} on ${on_string}: mapped reads">
+            <change_format>
+                <when input="out_format" value="sam" format="sam" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <!--
+            Since the input file include more than 1 sequence, the output must be sorted in 
+            order for functional test to pass.  This is done using the sort="True" attribute on the output.
+            
+            The output1 file for this test was produced using the following command line call produced by the lastz_wrapper.py script:
+            GALAXY_SLOTS="1"; export GALAXY_SLOTS;
+            PACKAGE_BASE=/tool_dependencies/lastz/1.03.52/devteam/lastz/ccc73a16422f; export PACKAGE_BASE;
+            . /Users/gvk/workspace/tool_dependencies/lastz/1.03.52/devteam/lastz/ccc73a16422f/env.sh;
+            python /localhost/repos/devteam/lastz/ccc73a16422f/lastz/lastz_wrapper.py
+                \-\-threads="${GALAXY_SLOTS:-4}"
+                \-\-ref_source="history"
+                \-\-source_select="pre_set"
+                \-\-out_format="sam"
+                \-\-input2="b1.fasta"
+                \-\-input1="phiX_split.fasta"
+                \-\-ref_sequences="2" \-\-trivial="yes"
+                \-\-shortcuts_for_yasra="none"
+                \-\-strand="both"
+                \-\-ambiguous="no"
+                \-\-output="/database/files/000/dataset_XX.dat"
+                \-\-lastzSeqsFileDir="/galaxy-central/tool-data"
+            
+            From the command line without using Galaxy, the above command would probably be something like this:
+            lastz b1.fasta[multiple] phiX_split.fasta \-\-format="sam" \-\-strand="both" \-\-output="lastz_wrapper_out0.sam"
+            -->
+            <param name="input2" value="b1.fasta" ftype="fasta" />
+            <param name="ref_source" value="history" />
+            <param name="input1" value="phiX_split.fasta" ftype="fasta"  />
+            <param name="trivial" value="yes" />
+            <param name="out_format" value="sam" />
+            <param name="source_select" value="pre_set" />
+            <param name="strand" value="both" />
+            <param name="ambiguous" value="no" />
+            <param name="how_to_name" value="no" />
+            <output name="output1" file="lastz_wrapper_out0.sam" sort="True" />
+        </test>
+        <test>
+            <!--
+            GALAXY_SLOTS="1"; export GALAXY_SLOTS;
+            PACKAGE_BASE=/tool_dependencies/lastz/1.03.52/devteam/lastz/ccc73a16422f; export PACKAGE_BASE;
+            . /tool_dependencies/lastz/1.03.52/devteam/lastz/ccc73a16422f/env.sh;
+            python /localhost/repos/devteam/lastz/ccc73a16422f/lastz/lastz_wrapper.py
+                \-\-threads="${GALAXY_SLOTS:-4}"
+                \-\-ref_source="history"
+                \-\-source_select="full"
+                \-\-out_format="sam"
+                \-\-input2="b1.fasta"
+                \-\-input1="phiX_split.fasta"
+                \-\-ref_sequences="2"
+                \-\-trivial="no"
+                \-\-shortcuts_for_yasra="none"
+                \-\-strand="plus"
+                \-\-ambiguous="no"
+                \-\-match_reward=""
+                \-\-match_penalty=""
+                \-\-gapped="no"
+                \-\-step=""
+                \-\-masking="0"
+                \-\-seed="no"
+                \-\-transition="1"
+                \-\-xdrop=""
+                \-\-hspthresh=""
+                \-\-entropy="no"
+                \-\-chain="no"
+                \-\-filter="identity"
+                \-\-identity_min="0"
+                \-\-identity_max="100"
+                \-\-output="/database/files/000/dataset_XX.dat"
+                \-\-lastzSeqsFileDir="/galaxy-central/tool-data"
+            -->
+            <param name="input2" value="b1.fasta" ftype="fasta" />
+            <param name="ref_source" value="history" />
+            <param name="input1" value="phiX_split.fasta" ftype="fasta"  />
+            <param name="trivial" value="no" />
+            <param name="out_format" value="sam" />
+            <param name="source_select" value="full" />
+            <param name="strand" value="plus" />
+            <param name="seed" value="12of19" />
+            <param name="transition" value="1" />
+            <param name="entropy" value="no" />
+            <param name="chain" value="no" />
+            <param name="filter" value="identity" />
+            <param name="identity_min" value="0" />
+            <param name="identity_max" value="100" />
+            <output name="output1" file="lastz_wrapper_out1.sam" />
+        </test>
+    </tests>
+    <help>
+        
+**What it does**
+        
+**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. This Galaxy version of LASTZ is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive documentation on LASTZ available here_.
+
+ .. _here: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00.html
+ 
+------
+
+**Input formats**
+
+LASTZ accepts reference and reads in FASTA format. However, because Galaxy supports implicit format conversion the tool will recognize fastq and other method specific formats.
+
+------
+
+**Outputs**
+
+LASTZ generates one output. Depending on the choice you make in the *Select output format* drop-down, LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.
+
+**SAM output**
+
+SAM has 12 columns::
+
+                                   1     2     3         4   5    6  7         8     9                                    10                                     11  12
+  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  HWI-EAS91_1_30788AAXX:1:2:1670:915    99  chr9  58119878  60  36M  =  58120234   392  GACCCCTACCCCACCGTGCTCTGGATCTCAGTGTTT   IIIIIIIIIIIIIIIIEIIIIIII7IIIIIIIIIII  XT:A:U  NM:i:0  SM:i:37  AM:i:37  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:36
+  HWI-EAS91_1_30788AAXX:1:2:1670:915   147  chr9  58120234  60  36M  =  58119878  -392  ATGAGTCGAATTCTATTTTCCAAACTGTTAACAAAA   IFIIDI;IIICIIIIIIIIIIIIIIIIIIIIIIIII  XT:A:U  NM:i:0  SM:i:37  AM:i:37  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:36
+
+
+where::
+
+     Column  Description
+  ---------  ---------------------------------------------------------------------   
+   1. QNAME  Query (pair) NAME
+   2. FLAG   bitwise FLAG
+   3. RNAME  Reference sequence NAME
+   4. POS    1-based leftmost POSition/coordinate of clipped sequence
+   5. MAPQ   MAPping Quality (Phred-scaled)
+   6. CIGAR  extended CIGAR string
+   7. MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
+   8. MPOS   1-based Mate POSition
+   9. ISIZE  Inferred insert SIZE
+  10. SEQ    query SEQuence on the same strand as the reference
+  11. QUAL   query QUALity (ASCII-33 gives the Phred base quality)
+  12. OPT    variable OPTional fields in the format TAG:VTYPE:VALUE, tab-separated
+  
+The flags are as follows::
+
+    Flag  Description
+  ------  -------------------------------------
+  0x0001  the read is paired in sequencing
+  0x0002  the read is mapped in a proper pair
+  0x0004  the query sequence itself is unmapped
+  0x0008  the mate is unmapped
+  0x0010  strand of the query (1 for reverse)
+  0x0020  strand of the mate
+  0x0040  the read is the first read in a pair
+  0x0080  the read is the second read in a pair
+  0x0100  the alignment is not primary
+
+**Polymorphism (SNP or differences) output**
+
+Polymorphism output contains 14 columns::
+
+     1     2     3  4     5                                   6   7   8  9  10  11 12                                   13                                    14
+  --------------------------------------------------------------------------------------------------------------------------------------------------------------
+  chrM  2490  2491  +  5386  HWI-EAS91_1_306UPAAXX:6:1:486:822   10  11  -  36  C  A  ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC  ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC
+  chrM  2173  2174  +  5386  HWI-EAS91_1_306UPAAXX:6:1:259:1389  26  27  +  36  G  T  GCGTACTTATTCGCCACCATGATTATGACCAGTGTT  GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
+
+where::
+
+  1. (chrM)   - Reference sequence id
+  2. (2490)   - Start position of the difference in the reference
+  3. (2491)   - End position of the difference in the reference
+  4. (+)      - Strand of the reference (always plus)
+  5. (5386)   - Length of the reference sequence
+  6. (HWI...) - read id
+  7. (10)     - Start position of the difference in the read
+  8. (11)     - End position of the difference in the read
+  9. (+)      - Strand of the read
+ 10. (36)     - Length of the read
+ 11. (C)      - Nucleotide in the reference
+ 12. (A)      - Nucleotide in the read
+ 13. (ACC...) - Reference side os the alignment
+ 14. (ACC...) - Read side of the alignment
+ 
+**Tabular output**
+
+Tabular output is a tab-separated format with 30 columns::
+
+   1        2  3     4     5     6     7   8                 9              10  11   12   13   14   15   16   17   18  19                20                21   22     23      24      25    26    27    28    29  30
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  14  PHIX174  +  5386  4648  4647  4661  14  ATTTTCGTGATATT    EYKX4VC01BV8HS  +   204  154  153  167  154  153  167  14  ATTTTCGTGATATT    ..............    14M  14/14  100.0%  14/204  6.9%  0/14  0.0%  4494  NA
+  16  PHIX174  +  5386  3363  3362  3378  16  GACGCCGGATTTGAGA  EYKX4VC01AWJ88  -   259   36   35   51  209  208  224  16  GACGCCGGATTTGAGA  ................  16M  16/16  100.0%  16/259  6.2%  0/16  0.0%  3327  NA
+
+The following columns are present::
+
+             Field  Meaning
+  ----------------  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+   1.        score  Score of the alignment block. The scale and meaning of this number will vary, depending on the final stage performed and other command-line options.
+   2.        name1  Name of the target sequence.
+   3.      strand1  Target sequence strand, either "+" or "−".
+   4.        size1  Size of the entire target sequence.
+   5.       start1  Starting position of the alignment block in the target, origin-one.
+   6.      zstart1  Starting position of the alignment block in the target, origin-zero.
+   7.         end1  Ending position of the alignment block in the target, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
+   8.      length1  Length of the alignment block in the target (excluding gaps).
+   9.        text1  Aligned characters in the target, including gap characters.
+  10.        name2  Name of the query sequence.
+  11.      strand2  Query sequence strand, either "+" or "−".
+  12.        size2  Size of the entire query sequence.
+  13.       start2  Starting position of the alignment block in the query, origin-one.
+  14.      zstart2  Starting position of the alignment block in the query, origin-zero.
+  15.         end2  Ending position of the alignment block in the query, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
+  16.      start2+  Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-one. Note that if strand2 is "−", then this is the other end of the block from start2.
+  17.     zstart2+  Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-zero. Note that if strand2 is "−", then this is the other end of the block from zstart2.
+  18.        end2+  Ending position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). Note that if strand2 is "−", then this is the other end of the block from end2.
+  19.      length2  Length of the alignment block in the query (excluding gaps).
+  20.        text2  Aligned characters in the query, including gap characters.
+  21.         diff  Differences between what would be written for text1 and text2. Matches are written as . (period), transitions as : (colon), transversions as X, and gaps as - (hyphen).
+  22.        cigar  A CIGAR-like representation of the alignment's path through the Dynamic Programming matrix. This is the short representation, without spaces, described in the Ensembl CIGAR specification.
+  23./24. identity  Fraction of aligned bases in the block that are matches (see Identity). This is written as two fields. The first field is a fraction, written as &lt;n&gt;/&lt;d&gt;. The second field contains the same value, computed as a percentage.
+  25./26. coverage  Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (see Coverage). This is written as two fields. The first field is a fraction, written as &lt;n&gt;/&lt;d&gt;. The second field contains the same value, computed as a percentage.
+  27./28.  gaprate  Rate of gaps (also called indels) in the alignment block. This is written as two fields. The first field is a fraction, written as &lt;n&gt;/&lt;d&gt;, with the numerator being the number of alignment columns containing gaps and the denominator being the number without gaps. The second field contains the same value, computed as a percentage.
+  29.     diagonal  The diagonal of the start of the alignment block in the dynamic programming matrix, expressed as an identifying number start1-start2.
+  30.      shingle  A measurement of the shingle overlap between the target and the query. This is intended for the case where both the target and query are relatively short, and their ends are expected to overlap.  
+
+-------
+
+**LASTZ Settings**
+
+There are two setting modes: (1) **Commonly used settings** and (2) **Full Parameter List**.
+
+**Commonly used settings**
+
+There are seven modes::
+
+  Illumina-Solexa/AB-SOLiD 95% identity
+  Illumina-Solexa/AB-SOLiD 85% identity
+  Roche-454 98% identity
+  Roche-454 95% identity
+  Roche-454 90% identity
+  Roche-454 85% identity
+  Roche-454 75% identity
+
+When deciding which one to use, consider the following: a 36 bp read with two differences will be 34/36 = 94% identical to the reference.  
+
+**Full Parameter List**
+
+This mode gives you fuller control over lastz. The description of these and other parameters is found at the end of this page. Note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu.
+
+------
+
+**Modify the reference name?**
+
+This option allows you to set the name of the reference sequence manually. This is helpful when, for example, you would like to make the reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at the UCSC Genome Browser.
+
+------
+
+**LASTZ parameter list**
+
+This is the list of LASTZ options that are available in this interface::
+
+  target                         File containing target sequence (fasta or nib).
+  query                          File containing query sequences (fasta or nib).
+  --self                         The selected target is the file containing both the target sequence and query sequences.
+  --nomirror                     Do not report mirror image of all gap-free alignments (default is "mirror" for self-alignments only).
+  --strand=both                  Search both strands.
+  --strand=plus                  Search + strand only (matching strand of query spec).
+  --strand=minus                 Search - strand only (opposite strand of query spec) (default is both strands are searched).
+  --match=&lt;reward&gt;[,&lt;penalty&gt;]   Set the score values for a match (+&lt;reward&gt;) and mismatch (-&lt;penalty&gt;).
+  --gapped                       Perform gapped extension of HSPs (or seeds if gap-free extension is not performed) after first reducing them to anchor points.
+  --nogapped                     Skip the gapped extension stage.
+  --gap=&lt;[open,]extend&gt;          Set gap open and extend penalties.  This option is valid only if gapped extension is being performed.
+  --ambiguous=n                  Treat N as an ambiguous nucleotide (default is N is treated as a sequence splicing character).
+  --ambiguous=iupac              Treat any ambiguous IUPAC-IUB character as a completely ambiguous nucleotide.
+  --step=&lt;offset&gt;                Offset between the starting positions of successive target words considered for potential seeds.  This does not apply to the query words which always use a step size of 1.
+  --masking=&lt;count&gt;              Dynamically mask the target sequence by excluding any positions that appear in too many alignments from further consideration for seeds.
+  --seed=12of19                  Seeds require a 19 bp word with matches in 12 specific positions.
+  --seed=match&lt;length&gt;           Seeds require a &lt;length&gt; bp word with matches in all positions.
+  --transition[=1,2]             Allow one or two transitions in a seed hit (default is that a transition is allowed).
+  --notransition                 Don't allow any match positions in seeds to be satisfied by transitions.
+  --xdrop=&lt;dropoff&gt;                Find HSPs using the xdrop extension method with the given termination threshold instead of using the exact match method.
+  --hspthresh=&lt;score&gt;            Set the score threshold for the x-drop extension method.  HSPs scoring lower are discarded.
+  --entropy                      Adjust for entropy when qualifying HSPs in the x-drop extension method.
+  --noentropy                    Don't adjust for entropy when qualifying HSPs in the x-drop extension method.
+  --chain                        Perform chaining of HSPs with no penalties.
+  --nochain                      Don't perform chaining of HSPs with no penalties.
+  --ydrop=&lt;dropoff&gt;              Set the threshold for terminating gapped extension.  This restricts the endpoints of each local alignment by limiting the local region around each anchor in which extension is performed.
+  --ytrim                        Trim back to peak score if y-drop extension encounters end of sequence.
+  --noytrim                      Don't trim back to peak score if y-drop extension encounters end of sequence.
+  --gappedthresh=&lt;score&gt;         Threshold for gapped extension.  Alignments scoring lower are discarded.
+  --filter=identity=&lt;min&gt;[..&lt;max&gt;]      Filter alignments by their percent identity, 0&lt;=min&lt;=max&lt;=100.  Identity is the percentage of aligned bases that are matches.
+  --filter=coverage=&lt;min&gt;[..&lt;max&gt;]      Filter alignments by how much of the input sequence they cover, 0&lt;=min&lt;=max&lt;=100.  Coverage is the percentage of the [shorted of the] entire target or query sequence included in the alignment block.
+  --filter=nmatch&lt;min&gt;     Filter alignments by how many bases match with the threshold specified as a percentage of the query length.
+  --filter=nmismatch0..&lt;max&gt;     Filter alignments by the number of mismatches, allowing no more than &lt;max&gt; mismatched bases.
+  --notrivial                    Don't output a trivial self-alignment block if the target and query sequences are identical.
+  --inner=&lt;score&gt;                Perform additional alignment between the gapped alignment blocks using (presumably) more sensitive alignment parameters.
+    </help>
+</tool>
diff -r 000000000000 -r 0bd6b2cb3b2a lastz/test-data/b1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/test-data/b1.fasta	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,1000 @@
+>HWI-EAS91_1_306UPAAXX:6:1:1503:1160
+GGTGGTCTATAGTGTTATTAATATCAAGTTGGGGGG
+>HWI-EAS91_1_306UPAAXX:6:1:1564:1179
+GCGAGCAGTAGACTCCTTCTGTTGATAAGCAAGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1704:1082
+GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1588:1797
+GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1304:1526
+GTAGTTGAAATGGTAATAAGACGACCAATCTGACCT
+>HWI-EAS91_1_306UPAAXX:6:1:1490:1582
+GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC
+>HWI-EAS91_1_306UPAAXX:6:1:1356:1339
+GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:1311:853
+GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:1257:1552
+GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC
+>HWI-EAS91_1_306UPAAXX:6:1:1486:1402
+GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC
+>HWI-EAS91_1_306UPAAXX:6:1:1028:1081
+GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT
+>HWI-EAS91_1_306UPAAXX:6:1:1167:752
+GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC
+>HWI-EAS91_1_306UPAAXX:6:1:1507:1113
+GTCAACGTTATATTTTGATAGTTTGACGGTTAATTC
+>HWI-EAS91_1_306UPAAXX:6:1:1654:1311
+GGATGAAAATGCTCACAATGACAAATCTGTCCACGG
+>HWI-EAS91_1_306UPAAXX:6:1:1386:1060
+GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1070:1356
+GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG
+>HWI-EAS91_1_306UPAAXX:6:1:787:1032
+GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA
+>HWI-EAS91_1_306UPAAXX:6:1:834:1017
+GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1703:1155
+GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT
+>HWI-EAS91_1_306UPAAXX:6:1:1406:593
+GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC
+>HWI-EAS91_1_306UPAAXX:6:1:1411:886
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:923:972
+GCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1279:1004
+GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCT
+>HWI-EAS91_1_306UPAAXX:6:1:1070:840
+GGTTGTCAGCGTCATAAGAGGTTTTACCTCCAAATG
+>HWI-EAS91_1_306UPAAXX:6:1:1595:1040
+GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1002:559
+GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG
+>HWI-EAS91_1_306UPAAXX:6:1:999:974
+GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC
+>HWI-EAS91_1_306UPAAXX:6:1:896:982
+GTGGCTGGAGACAAATAATCTCTTTAATAACCTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1366:741
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC
+>HWI-EAS91_1_306UPAAXX:6:1:749:1469
+GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT
+>HWI-EAS91_1_306UPAAXX:6:1:1010:592
+GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1393:650
+GTGACTCATATCTAAACCAGTCCTTGACGAACGTGC
+>HWI-EAS91_1_306UPAAXX:6:1:1238:1731
+GAGAAATAAAAGTCTGAAACATGATTAAACTCCTAA
+>HWI-EAS91_1_306UPAAXX:6:1:1629:908
+GATGCGGTTATCCATCTGCTTATGGAAGCCAAGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1560:849
+GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG
+>HWI-EAS91_1_306UPAAXX:6:1:1029:783
+GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1152:1324
+GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:1614:2042
+GAAATGCCACAAGCCTCAATAGCAGGTTTAAGAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1398:439
+GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG
+>HWI-EAS91_1_306UPAAXX:6:1:955:616
+GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC
+>HWI-EAS91_1_306UPAAXX:6:1:1672:753
+GAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1195:1293
+GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC
+>HWI-EAS91_1_306UPAAXX:6:1:1074:755
+GCAAGAGTAAACATAGTGCCATGCTCAGGAACAAAG
+>HWI-EAS91_1_306UPAAXX:6:1:984:499
+GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1452:1833
+GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT
+>HWI-EAS91_1_306UPAAXX:6:1:863:710
+GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT
+>HWI-EAS91_1_306UPAAXX:6:1:885:649
+GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC
+>HWI-EAS91_1_306UPAAXX:6:1:917:1214
+GACAGATGTATCCATCTGAATGCAATGAAGAAAACC
+>HWI-EAS91_1_306UPAAXX:6:1:892:1254
+GCTCAGGAAATGCAGCAGCAAGATAATCACGAGTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1555:1005
+GCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1637:1413
+GATGCTGTTCAACCACTAATAGGTAAGAAATCATGT
+>HWI-EAS91_1_306UPAAXX:6:1:1102:1567
+GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA
+>HWI-EAS91_1_306UPAAXX:6:1:799:1337
+GTATATGCACAAAATGAGATGCTTGCTTATCAACAG
+>HWI-EAS91_1_306UPAAXX:6:1:1353:1843
+GCAGACCCATAATGTCAATAGATGTGGTAGAAGTCG
+>HWI-EAS91_1_306UPAAXX:6:1:1196:789
+GCGGCATACGCTCGGCGCCAGTTTGAATATTAGACA
+>HWI-EAS91_1_306UPAAXX:6:1:1056:1676
+GTAAAATACTGACCAGCCGTTTGAGCTTGAGTAAGC
+>HWI-EAS91_1_306UPAAXX:6:1:1349:1836
+GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1027:788
+GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT
+>HWI-EAS91_1_306UPAAXX:6:1:990:1283
+GCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGC
+>HWI-EAS91_1_306UPAAXX:6:1:904:939
+GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1732:793
+GTCAACATACATATCACCATTATCGAACTCAACGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1355:2003
+GTTAGACCAAACCATGAAACCAACATAAACATTATT
+>HWI-EAS91_1_306UPAAXX:6:1:1337:977
+GCACCAGAAACAAAACTAGGGGCGGCCTCATCAGGG
+>HWI-EAS91_1_306UPAAXX:6:1:1605:1175
+GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT
+>HWI-EAS91_1_306UPAAXX:6:1:1763:1192
+GACAGGCCGTTTGAATGTTGACGGGATGAACATAAT
+>HWI-EAS91_1_306UPAAXX:6:1:722:483
+GTTATTATACCGTCAAGGACTGTGTGACTATTGACT
+>HWI-EAS91_1_306UPAAXX:6:1:1760:1136
+GCAAAGCATTGGGATTATCATAAAACGCCTCTAATC
+>HWI-EAS91_1_306UPAAXX:6:1:1088:798
+GGAAACCTGCTGTTGCTTGGAAAGATTGGTGTTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:633:1076
+GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:673:754
+GTCATGGAAGCGATAAAACTCTGCAGGTTGGATATT
+>HWI-EAS91_1_306UPAAXX:6:1:1759:2019
+GTAAAGGACGGTTGTCAGCGTCATAAGAGGTTTTAC
+>HWI-EAS91_1_306UPAAXX:6:1:1064:1797
+GCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGG
+>HWI-EAS91_1_306UPAAXX:6:1:1112:1669
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT
+>HWI-EAS91_1_306UPAAXX:6:1:510:1447
+GCATTAAGCTCAGGAAATGCAGCAGCAAGATAATCA
+>HWI-EAS91_1_306UPAAXX:6:1:877:1573
+GTGCTATTGCTGGCGGTATTTCTTCTTCTTTTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:870:542
+GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC
+>HWI-EAS91_1_306UPAAXX:6:1:966:384
+GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA
+>HWI-EAS91_1_306UPAAXX:6:1:1186:1903
+GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1632:1742
+GCATCACCCATGCCTACAGTATTGTTATCGGTAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1521:559
+GAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGCC
+>HWI-EAS91_1_306UPAAXX:6:1:683:454
+GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:112:1280
+GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGTC
+>HWI-EAS91_1_306UPAAXX:6:1:891:381
+GACCAGGGCGAGCGCCAGAACGTTTTTTACCTTTAG
+>HWI-EAS91_1_306UPAAXX:6:1:1348:958
+GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1785:1915
+GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG
+>HWI-EAS91_1_306UPAAXX:6:1:1418:42
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1421:743
+GGTCAACGCTACCTGTAGGAAGTGTCCGCATAAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1079:790
+GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT
+>HWI-EAS91_1_306UPAAXX:6:1:663:740
+GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1245:413
+GTTTGAATGTTGACGGGATGAACATAATAAGCAATG
+>HWI-EAS91_1_306UPAAXX:6:1:1378:1035
+GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGG
+>HWI-EAS91_1_306UPAAXX:6:1:903:1746
+GTACGGGGAAGGACGTCAATAGTCACACAGTCCTTG
+>HWI-EAS91_1_306UPAAXX:6:1:1713:1134
+GGCGTACGGGGAAGGACGTCAATAGTCACACAGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:1246:1887
+GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG
+>HWI-EAS91_1_306UPAAXX:6:1:872:1731
+GGGCGGCCTCATCAGGGTTAGGAACATTAGAGCCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1714:1582
+GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:1785:763
+GNCGAGAAATAAAANNNTGAAACATGATTAAANTCC
+>HWI-EAS91_1_306UPAAXX:6:1:1684:542
+GAAAAGACAGAATCTCTTCCAAGAGCTTGATGCGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1581:1665
+GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT
+>HWI-EAS91_1_306UPAAXX:6:1:901:1581
+GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1128:239
+GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC
+>HWI-EAS91_1_306UPAAXX:6:1:969:441
+GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG
+>HWI-EAS91_1_306UPAAXX:6:1:630:1087
+GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC
+>HWI-EAS91_1_306UPAAXX:6:1:606:1852
+GGAGACAAATAATCTCTTTAATAACCTGATTCAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:489:1315
+GAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAC
+>HWI-EAS91_1_306UPAAXX:6:1:465:1983
+GAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAA
+>HWI-EAS91_1_306UPAAXX:6:1:559:1028
+GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC
+>HWI-EAS91_1_306UPAAXX:6:1:1655:1413
+GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG
+>HWI-EAS91_1_306UPAAXX:6:1:980:605
+GCCGTTTGAATGTTGACGGGATGAACATAATAAGCA
+>HWI-EAS91_1_306UPAAXX:6:1:1629:1865
+GAAAAGCGGCATGGTCAATATAACCAGTAGTGTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1180:1920
+GCACTCCGTGGACAGATTTGTCATTGTGAGCATTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1116:383
+GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG
+>HWI-EAS91_1_306UPAAXX:6:1:906:2041
+GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA
+>HWI-EAS91_1_306UPAAXX:6:1:1514:157
+GTCAATAGATGTGGTAGAAGTCGTCATTTGGCGTGG
+>HWI-EAS91_1_306UPAAXX:6:1:1032:1857
+GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT
+>HWI-EAS91_1_306UPAAXX:6:1:638:609
+GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAT
+>HWI-EAS91_1_306UPAAXX:6:1:74:750
+GATAATCACGAGTATCCTTTCCTTTATCATCTTCAT
+>HWI-EAS91_1_306UPAAXX:6:1:486:822
+GTTGACGATGTAGCTTTAGGTGTCTTTAAAACAGGT
+>HWI-EAS91_1_306UPAAXX:6:1:899:473
+GAACAGCATCGGACTCAGATAGTAATCCACGCTCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1613:197
+GTGACATTCAGAAGGGTAATAAGAACGAACCATAAA
+>HWI-EAS91_1_306UPAAXX:6:1:326:1747
+GTTGAGGCTTTCGTTTATTGTACGCTTTGCTTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1487:526
+GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+>HWI-EAS91_1_306UPAAXX:6:1:629:665
+GAAATGCAGCAGCAAGATAATCACGAGTATCCTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:766:744
+GGCCGTCAACATACATATCACCATTATCGAACTCAA
+>HWI-EAS91_1_306UPAAXX:6:1:391:1771
+GTGGTTGATATTTTTCATGGTATTGATAAATCTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:591:1102
+GCTTTGCGTGACTATTTTCGTGATATTGTTCGTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:917:664
+GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG
+>HWI-EAS91_1_306UPAAXX:6:1:217:737
+GTTCAGTTGTTGCATTGGAATATTCAGTTTAAATTT
+>HWI-EAS91_1_306UPAAXX:6:1:1047:839
+GACCATTCAAAGGATAAACATCATAGGCAGTCGGGG
+>HWI-EAS91_1_306UPAAXX:6:1:558:1040
+GCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1207:524
+GCCAATACCATCAGCTTTACCGTCTTTCCAGAAATT
+>HWI-EAS91_1_306UPAAXX:6:1:708:1634
+GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:576:1851
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG
+>HWI-EAS91_1_306UPAAXX:6:1:906:460
+GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:693:1260
+GCGAAAGGTCGCAAAGTAAGAGCTTCTCGAGCTGCG
+>HWI-EAS91_1_306UPAAXX:6:1:1373:286
+GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:762:41
+GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT
+>HWI-EAS91_1_306UPAAXX:6:1:475:1091
+GTCACACAGTCCTTGACGGTATAATAACCACCATCT
+>HWI-EAS91_1_306UPAAXX:6:1:791:627
+GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC
+>HWI-EAS91_1_306UPAAXX:6:1:336:1791
+GAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1483:943
+GCACGTAATTTTTGACGCACGTTTTCTTCTGCGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:641:1071
+GATGGGCATACTGTAACCATAAGGCCACGTATTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:196:755
+GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT
+>HWI-EAS91_1_306UPAAXX:6:1:463:1398
+GTCATAAGAGGTTTTACCTCCAAATGAAGAAATAAC
+>HWI-EAS91_1_306UPAAXX:6:1:1559:460
+GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1625:1561
+GAGGAGTGGCATTAACACCATCCTTCATGAACTTAC
+>HWI-EAS91_1_306UPAAXX:6:1:1729:1588
+GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT
+>HWI-EAS91_1_306UPAAXX:6:1:945:393
+GGCCTCATCAGGGTTAGGAACATTAGAGCCTTGAAT
+>HWI-EAS91_1_306UPAAXX:6:1:298:1391
+GTAAAGTTAGACCAAACCATGAAACCAACATAAACA
+>HWI-EAS91_1_306UPAAXX:6:1:1270:1500
+GAATTACTACTGCTTGTTTACGAATTAAATATATGT
+>HWI-EAS91_1_306UPAAXX:6:1:481:1546
+GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG
+>HWI-EAS91_1_306UPAAXX:6:1:473:1729
+GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:801:1831
+GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT
+>HWI-EAS91_1_306UPAAXX:6:1:536:639
+GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT
+>HWI-EAS91_1_306UPAAXX:6:1:259:938
+GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG
+>HWI-EAS91_1_306UPAAXX:6:1:907:1513
+GGCATGGGTGATGCTGGTATTAAATCTGCCATTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:372:1409
+GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG
+>HWI-EAS91_1_306UPAAXX:6:1:485:1626
+GATGGCAGCAACGGAAACCATAACGAGCATCATCTT
+>HWI-EAS91_1_306UPAAXX:6:1:583:1679
+GCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAG
+>HWI-EAS91_1_306UPAAXX:6:1:690:1610
+GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:257:918
+GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT
+>HWI-EAS91_1_306UPAAXX:6:1:818:33
+GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCTG
+>HWI-EAS91_1_306UPAAXX:6:1:541:1242
+GGGATTATCATAAAACGCCTCTAATCGGTCGTCAGC
+>HWI-EAS91_1_306UPAAXX:6:1:1014:279
+GTAAAAATGTCTACAGTAGAGTCAATAGCAAGGCCC
+>HWI-EAS91_1_306UPAAXX:6:1:672:1790
+GGCCGTTTGAATGTTGACGGGATGAACATAATAAGC
+>HWI-EAS91_1_306UPAAXX:6:1:708:464
+GGAGACAAATAATCTCTTTAATAACCTGATTCAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:633:1486
+GGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:328:696
+GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:259:1389
+GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
+>HWI-EAS91_1_306UPAAXX:6:1:1315:41
+GCTTTCCGTGATGTCACAGCCTGCTTTGATGTGTCG
+>HWI-EAS91_1_306UPAAXX:6:1:1647:549
+GCTTAATCCAACTTACCAAGCTGGGTTACGACGCGC
+>HWI-EAS91_1_306UPAAXX:6:1:300:886
+GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:317:1411
+GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCTT
+>HWI-EAS91_1_306UPAAXX:6:1:321:1819
+GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:631:70
+GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC
+>HWI-EAS91_1_306UPAAXX:6:1:624:1040
+GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT
+>HWI-EAS91_1_306UPAAXX:6:1:662:1187
+GGGAGAGGAGTGGCATTAACACCATCCTTCATGACC
+>HWI-EAS91_1_306UPAAXX:6:1:1440:1959
+GAATCAGCGGTATGGCTCCTCTCCTATTTTTGCTTC
+>HWI-EAS91_1_306UPAAXX:6:1:458:1629
+GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT
+>HWI-EAS91_1_306UPAAXX:6:1:216:790
+GGGATGAAAATGCTCACAATGACAAATCTGTCCACG
+>HWI-EAS91_1_306UPAAXX:6:1:1407:1174
+TTACCTATTAGTGGTTGAACAGCATCGGACTCAGAT
+>HWI-EAS91_1_306UPAAXX:6:1:999:1790
+GTCCTGCGTGTAGCGAACTGCGATGGGCATACTGTC
+>HWI-EAS91_1_306UPAAXX:6:1:141:1994
+GGCTTTTTTATGGTTCGTTCTTATTACCCTTCTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:225:465
+GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC
+>HWI-EAS91_1_306UPAAXX:6:1:649:1760
+GACCCATAATGTCAATAGATGTGGTAGAAGTCGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:300:986
+GTTGAACACGACCAGAAAACTGGCCTAACGACGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:478:605
+GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC
+>HWI-EAS91_1_306UPAAXX:6:1:622:395
+GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGG
+>HWI-EAS91_1_306UPAAXX:6:1:1701:574
+GTAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCC
+>HWI-EAS91_1_306UPAAXX:6:1:646:59
+GGAAGTGTCCGCATAAAATGCACCGCATGGAAATGT
+>HWI-EAS91_1_306UPAAXX:6:1:284:2031
+GACAGAATCGTTAGTTGATGGCGAAAGGTCGCAAAG
+>HWI-EAS91_1_306UPAAXX:6:1:22:1009
+GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT
+>HWI-EAS91_1_306UPAAXX:6:1:47:1826
+GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG
+>HWI-EAS91_1_306UPAAXX:6:1:1025:1236
+TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT
+>HWI-EAS91_1_306UPAAXX:6:1:773:591
+GAGCAGGAAAGCGAGGGTATCCCACAAAGTCCAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:1753:527
+GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC
+>HWI-EAS91_1_306UPAAXX:6:1:426:1717
+GTAGCGCCAATATGAGAAGAGCCATACCGCTGATTC
+>HWI-EAS91_1_306UPAAXX:6:1:959:818
+TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC
+>HWI-EAS91_1_306UPAAXX:6:1:459:1344
+GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT
+>HWI-EAS91_1_306UPAAXX:6:1:973:1367
+TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:201:871
+GATTAGAGGCGTTTTATGATAATCCCAATGCTTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:713:1672
+GGCGTACGGGGAAGGACGTCAATAGTCACACAGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:444:1435
+TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGTG
+>HWI-EAS91_1_306UPAAXX:6:1:288:1136
+GCCTTCCATGATGAGACAGGCCGTTTTAATTTTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1653:225
+GCAAGGCCACGACGCAATGGAGAAAGACGGAGAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:537:1764
+GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA
+>HWI-EAS91_1_306UPAAXX:6:1:196:1854
+GTATCGAGGCTCTTAAACCTGCTATTTAGGCTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:312:1707
+GCGTCATAAGAGGTTTTACCTCCAAATGAAGAAATA
+>HWI-EAS91_1_306UPAAXX:6:1:651:183
+GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:295:694
+GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT
+>HWI-EAS91_1_306UPAAXX:6:1:330:1895
+GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG
+>HWI-EAS91_1_306UPAAXX:6:1:590:331
+GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT
+>HWI-EAS91_1_306UPAAXX:6:1:481:1687
+GCAGATTGCGATAAACGGTCACATTAAATTTAACCT
+>HWI-EAS91_1_306UPAAXX:6:1:1112:1279
+TGTGCATATACCTGGTCTTTCGTATTCTGTCGTGAT
+>HWI-EAS91_1_306UPAAXX:6:1:1099:1216
+TTAGAGCGCATGACAAGTAAAGGACGGTTGTCAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:221:1238
+GTATCCTTTCCTTTATCATCGGCAGACTTTTCACCT
+>HWI-EAS91_1_306UPAAXX:6:1:1015:364
+GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
+>HWI-EAS91_1_306UPAAXX:6:1:735:1806
+TGTTATTAATATCAAGTTGGGGGAGCACATTGTAGC
+>HWI-EAS91_1_306UPAAXX:6:1:320:411
+GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGTG
+>HWI-EAS91_1_306UPAAXX:6:1:1273:1031
+TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA
+>HWI-EAS91_1_306UPAAXX:6:1:1456:1088
+AATAATCAGCGTGACATTCAGAAGGGTAATAAGAAC
+>HWI-EAS91_1_306UPAAXX:6:1:1365:307
+GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:478:252
+GATGCGGTTATCCATCTGCTTATTGAAGCCAAGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:915:1232
+TATTAATAACACTATAGACCACCGCCCCGAAGGGGC
+>HWI-EAS91_1_306UPAAXX:6:1:680:1357
+TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGC
+>HWI-EAS91_1_306UPAAXX:6:1:238:1279
+GCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTA
+>HWI-EAS91_1_306UPAAXX:6:1:1583:35
+GCAAATTAGCATAAGCAGCTTGCAGACCCATAATGT
+>HWI-EAS91_1_306UPAAXX:6:1:502:283
+GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:418:1730
+GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:596:647
+GCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTA
+>HWI-EAS91_1_306UPAAXX:6:1:92:1591
+GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC
+>HWI-EAS91_1_306UPAAXX:6:1:430:1938
+GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:212:527
+GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT
+>HWI-EAS91_1_306UPAAXX:6:1:594:942
+GACGACATTAGAAATATCCTTTGCAGTAGCGCCAAT
+>HWI-EAS91_1_306UPAAXX:6:1:169:1774
+GCCTTCCATGATGAGACAGGCCGTTTTAATTTTTAC
+>HWI-EAS91_1_306UPAAXX:6:1:1090:210
+GGAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGC
+>HWI-EAS91_1_306UPAAXX:6:1:589:96
+GGCGGCCCCATCAGGGTTAGGAACATTAGAGCCTTG
+>HWI-EAS91_1_306UPAAXX:6:1:1477:1231
+TAGGAACATTAGAGCCTTGAATGGCAGATTTAATAC
+>HWI-EAS91_1_306UPAAXX:6:1:707:1076
+TCTGACGTTCGTGATGAGTTTGTATCTTTTTCTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:749:1715
+GAACATAATAAGCAATGACGGCAGCAATAAACTCAA
+>HWI-EAS91_1_306UPAAXX:6:1:1738:1884
+GCTCACCTTTAGCATCAACAGGCCACAACCAACCAG
+>HWI-EAS91_1_306UPAAXX:6:1:1160:1088
+TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC
+>HWI-EAS91_1_306UPAAXX:6:1:517:119
+GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT
+>HWI-EAS91_1_306UPAAXX:6:1:1472:716
+TGGTAATGGTGGTTTTCTTCATTTCATTCAGTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:281:441
+GAGCAGTAGACTCCTTCTGTTGATAAGCAAGCATCT
+>HWI-EAS91_1_306UPAAXX:6:1:1101:324
+AATACCATCAGCTTTACCGTCTTTCCAGAAATTGTT
+>HWI-EAS91_1_306UPAAXX:6:1:1225:1494
+TTCTCAAATCCGGCGTCAACCATACCAGCAGAGGAA
+>HWI-EAS91_1_306UPAAXX:6:1:1509:1025
+TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:592:510
+GATACCAATAAAATCCCTAAGCATTTGTTTCTGGTT
+>HWI-EAS91_1_306UPAAXX:6:1:324:1729
+GAACAAAGAAACGCGGCACAGAATGTTTATAGGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:128:1925
+GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC
+>HWI-EAS91_1_306UPAAXX:6:1:786:893
+TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGC
+>HWI-EAS91_1_306UPAAXX:6:1:248:955
+GCTACAATGTGCTCCCCCAACTTGATATTAATAACA
+>HWI-EAS91_1_306UPAAXX:6:1:388:1127
+GATATTGGTCGTATGGTTCTTGCTGCCTAGTGTCTC
+>HWI-EAS91_1_306UPAAXX:6:1:721:1156
+TCTGGTTGGTTGTGGCCTTTTTATGCTAAATGTTAG
+>HWI-EAS91_1_306UPAAXX:6:1:1564:1468
+TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG
+>HWI-EAS91_1_306UPAAXX:6:1:750:77
+GGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTA
+>HWI-EAS91_1_306UPAAXX:6:1:405:487
+GTTGGATTAAGCACTCCGTGGACAGATTTGTCATTT
+>HWI-EAS91_1_306UPAAXX:6:1:836:1204
+TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:224:1548
+GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC
+>HWI-EAS91_1_306UPAAXX:6:1:931:1015
+TTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGT
+>HWI-EAS91_1_306UPAAXX:6:1:329:579
+GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT
+>HWI-EAS91_1_306UPAAXX:6:1:260:1145
+GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC
+>HWI-EAS91_1_306UPAAXX:6:1:1523:1253
+TTGGTAAAATACTGACCAGCCGTTTGAGCTTGAGTA
+>HWI-EAS91_1_306UPAAXX:6:1:326:1271
+GACCACTCGCGATTCAATCATGACTTCGTGATAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:213:622
+GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA
+>HWI-EAS91_1_306UPAAXX:6:1:274:712
+GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG
+>HWI-EAS91_1_306UPAAXX:6:1:1549:627
+TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGT
+>HWI-EAS91_1_306UPAAXX:6:1:1714:737
+TCTTTCGTATTCTGGCGTGAAGTCGCCGACTGAATG
+>HWI-EAS91_1_306UPAAXX:6:1:760:1217
+TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:174:768
+GTTGGCTGACGACCGATTAGAGGCGTTTTTTTATAT
+>HWI-EAS91_1_306UPAAXX:6:1:172:1412
+GGTCGGCAGATTGCGATAAACGTTCACATTAAATTT
+>HWI-EAS91_1_306UPAAXX:6:1:1393:869
+TTCATCCCGTCAACATTCAAACGGCCTGTCTCATCT
+>HWI-EAS91_1_306UPAAXX:6:1:301:481
+GTTATAGATATTCAAATAACCCTGAAACAAATGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:648:1093
+TAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTT
+>HWI-EAS91_1_306UPAAXX:6:1:1233:591
+TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:540:1415
+TTATTAAAGAGATTATTTTTCTCCAGCCACTTATGT
+>HWI-EAS91_1_306UPAAXX:6:1:151:1792
+GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA
+>HWI-EAS91_1_306UPAAXX:6:1:748:1378
+TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT
+>HWI-EAS91_1_306UPAAXX:6:1:1526:1479
+TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:985:1093
+TAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCTT
+>HWI-EAS91_1_306UPAAXX:6:1:480:1378
+TCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:903:753
+TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1697:1737
+GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT
+>HWI-EAS91_1_306UPAAXX:6:1:803:1037
+TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT
+>HWI-EAS91_1_306UPAAXX:6:1:1727:1244
+TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT
+>HWI-EAS91_1_306UPAAXX:6:1:253:1162
+GCATTTAGTAGCGGTAAAGTTTGACCAAACCATTAT
+>HWI-EAS91_1_306UPAAXX:6:1:216:856
+GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT
+>HWI-EAS91_1_306UPAAXX:6:1:825:886
+TCCCACAAAGTCCAGCGTACCATAAACGCAAGCCTC
+>HWI-EAS91_1_306UPAAXX:6:1:1699:962
+TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT
+>HWI-EAS91_1_306UPAAXX:6:1:1210:625
+TCAGATAGTAATCCACGCTCTTTTAAAATGTCAACA
+>HWI-EAS91_1_306UPAAXX:6:1:538:616
+TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT
+>HWI-EAS91_1_306UPAAXX:6:1:184:1849
+GCTCACCTTTAGCATCAACAGGCCACAACCAACCAG
+>HWI-EAS91_1_306UPAAXX:6:1:1636:1103
+TATCTGACTTTTTGTTAACGTATTTAGCCACATAGA
+>HWI-EAS91_1_306UPAAXX:6:1:605:223
+GGTTATTTGAATATCTATAACAACTATTTTAAATCG
+>HWI-EAS91_1_306UPAAXX:6:1:256:1052
+GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC
+>HWI-EAS91_1_306UPAAXX:6:1:300:1515
+GCCATGATGGTGGTTATTATACCGTCAAGGACTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1684:1320
+TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA
+>HWI-EAS91_1_306UPAAXX:6:1:1186:895
+TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1463:754
+TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:808:1053
+TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG
+>HWI-EAS91_1_306UPAAXX:6:1:960:1218
+TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:521:1646
+GGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCA
+>HWI-EAS91_1_306UPAAXX:6:1:289:1885
+GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
+>HWI-EAS91_1_306UPAAXX:6:1:471:170
+GGTCAGTTCCATCAACATCATAGCCAGATGCCCAGA
+>HWI-EAS91_1_306UPAAXX:6:1:828:754
+TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT
+>HWI-EAS91_1_306UPAAXX:6:1:924:1679
+TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
+>HWI-EAS91_1_306UPAAXX:6:1:837:901
+TGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCG
+>HWI-EAS91_1_306UPAAXX:6:1:543:16
+GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1482:578
+TCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATA
+>HWI-EAS91_1_306UPAAXX:6:1:1254:1668
+TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT
+>HWI-EAS91_1_306UPAAXX:6:1:1402:898
+TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC
+>HWI-EAS91_1_306UPAAXX:6:1:764:1534
+TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT
+>HWI-EAS91_1_306UPAAXX:6:1:681:1079
+TGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAA
+>HWI-EAS91_1_306UPAAXX:6:1:672:1350
+TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1266:493
+TGACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGC
+>HWI-EAS91_1_306UPAAXX:6:1:118:238
+GACGGTATAATAACCACCATCATGGCGACCATTCAA
+>HWI-EAS91_1_306UPAAXX:6:1:699:433
+TTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTC
+>HWI-EAS91_1_306UPAAXX:6:1:708:1387
+TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC
+>HWI-EAS91_1_306UPAAXX:6:1:498:1085
+TTATGATAATCCCAATGCTTTGCGTGACTATTTTCT
+>HWI-EAS91_1_306UPAAXX:6:1:1101:1301
+TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAT
+>HWI-EAS91_1_306UPAAXX:6:1:261:213
+GAATGGTCGCCATGATGGTGGTTATTATACCGTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:1287:1267
+TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGT
+>HWI-EAS91_1_306UPAAXX:6:1:744:331
+TTAATGGATGAATTGGCACAATGCTACAATGTGCTC
+>HWI-EAS91_1_306UPAAXX:6:1:614:814
+TGTCAGCGTCATAAGAGGTTTTACCTCCAAATGAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1362:1063
+TAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAG
+>HWI-EAS91_1_306UPAAXX:6:1:1238:1508
+TCAACTAACGATTCTGTCAAAAACTGACGCGTTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:904:1130
+TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT
+>HWI-EAS91_1_306UPAAXX:6:1:465:216
+GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:844:628
+TAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGC
+>HWI-EAS91_1_306UPAAXX:6:1:684:1444
+TATCCCACAAAGTCCAGCGTACCATAAACGCAAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:515:1373
+TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT
+>HWI-EAS91_1_306UPAAXX:6:1:764:1667
+TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:1722:598
+TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCT
+>HWI-EAS91_1_306UPAAXX:6:1:670:1188
+TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT
+>HWI-EAS91_1_306UPAAXX:6:1:1682:1705
+TAGCCACATAGAAACCAACAGCCATATAACTGGTAG
+>HWI-EAS91_1_306UPAAXX:6:1:1008:1616
+TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC
+>HWI-EAS91_1_306UPAAXX:6:1:490:1220
+TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCT
+>HWI-EAS91_1_306UPAAXX:6:1:891:1437
+TAATGGTGATATGTATGTTTACGTCCATAAGGCTGT
+>HWI-EAS91_1_306UPAAXX:6:1:1310:321
+TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGT
+>HWI-EAS91_1_306UPAAXX:6:1:827:1597
+TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC
+>HWI-EAS91_1_306UPAAXX:6:1:1062:1158
+TAGAGTCAATAGCAAGGCCACGACGCAATGGAGAAA
+>HWI-EAS91_1_306UPAAXX:6:1:1419:208
+TGGCGCATAATCTCGGAAACCTGCTGTTGCTTGGAA
+>HWI-EAS91_1_306UPAAXX:6:1:691:1018
+AAATATCAACCACACCAGAAGCAGCATCAGTGACGA
+>HWI-EAS91_1_306UPAAXX:6:1:374:113
+GATAAAGCTGTTGCCGATACTTGGAACAATTTCTGT
+>HWI-EAS91_1_306UPAAXX:6:1:1720:784
+TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1424:1394
+ATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1063:1760
+TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1235:729
+TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA
+>HWI-EAS91_1_306UPAAXX:6:1:167:1507
+TAGTGTTATTAATATCAAGTTTTTGGAGCACATTGT
+>HWI-EAS91_1_306UPAAXX:6:1:717:1569
+TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT
+>HWI-EAS91_1_306UPAAXX:6:1:610:765
+TTCAGCGCCTTCCATGATGAGACAGGCCGTTTGAAT
+>HWI-EAS91_1_306UPAAXX:6:1:663:380
+TAAACATTCTGTGCCGCGTTTCTTTGTTCCTTATCT
+>HWI-EAS91_1_306UPAAXX:6:1:790:1358
+TTATCACCTTATTGAAGGCTTATCATTCATTTAGGT
+>HWI-EAS91_1_306UPAAXX:6:1:965:1633
+TAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGCT
+>HWI-EAS91_1_306UPAAXX:6:1:673:319
+TTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAT
+>HWI-EAS91_1_306UPAAXX:6:1:684:371
+TAGCGGTAAAGTTAGACCAAACCATGAAACCAACAT
+>HWI-EAS91_1_306UPAAXX:6:1:1147:1444
+ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC
+>HWI-EAS91_1_306UPAAXX:6:1:983:678
+ATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCG
+>HWI-EAS91_1_306UPAAXX:6:1:1608:1119
+TCACGCGGCGGCAAGTTGCCATACAAAACAGGGTCG
+>HWI-EAS91_1_306UPAAXX:6:1:1048:1193
+TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1265:1429
+ATATTTTTCATGGTATTGATAAAGCTGTTGCCGATT
+>HWI-EAS91_1_306UPAAXX:6:1:1607:1677
+TGTTGCTTGGAAAGATTGGTGTTTTCCATAATAGAC
+>HWI-EAS91_1_306UPAAXX:6:1:1087:1421
+ACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATC
+>HWI-EAS91_1_306UPAAXX:6:1:324:490
+GCACCAAACATAAATCACCTCACTTAAGTGGCTGGG
+>HWI-EAS91_1_306UPAAXX:6:1:1596:614
+TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGT
+>HWI-EAS91_1_306UPAAXX:6:1:343:83
+GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC
+>HWI-EAS91_1_306UPAAXX:6:1:203:667
+GCATGAATGTGCTTAATAGAGGCCAAGGCGGTCTAG
+>HWI-EAS91_1_306UPAAXX:6:1:34:480
+GGCAAGTTGCCATACAAAACAGGGTCGCCAGCAATT
+>HWI-EAS91_1_306UPAAXX:6:1:606:1743
+TAGCGACAGCTTGGTTTTTAGTGAGTTGTTCCATTC
+>HWI-EAS91_1_306UPAAXX:6:1:254:1391
+TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:1568:1750
+TAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1538:869
+TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA
+>HWI-EAS91_1_306UPAAXX:6:1:255:38
+GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1543:1555
+TAAAACGCCTCTAATCGGTCGTCAGCCAACGTGAGG
+>HWI-EAS91_1_306UPAAXX:6:1:1365:733
+AGAATCAGCGGTATGGCTCTTCTCCTTTTTTCGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1604:943
+TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1574:1632
+TCAGTATGCAAATTAGCATAAGCAGCTTGCAGACCC
+>HWI-EAS91_1_306UPAAXX:6:1:565:1799
+TCTTGGTCAGTATGCAAATTAGCATAAGCAGCTTGC
+>HWI-EAS91_1_306UPAAXX:6:1:1004:380
+TATTGACTCTACTGTAGACATTTTTACTTTTTATTT
+>HWI-EAS91_1_306UPAAXX:6:1:1345:965
+ATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1704:756
+TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG
+>HWI-EAS91_1_306UPAAXX:6:1:310:1346
+TATAACGTTGACGATGTAGCTTTAGTTTTCTTTAAA
+>HWI-EAS91_1_306UPAAXX:6:1:900:1858
+TTTACCGCTTCGGCGTTATAACCTCACACTCAATCT
+>HWI-EAS91_1_306UPAAXX:6:1:1250:1741
+TAAATCCAAAACGGCAGAAGCCTGAATGAGCTTAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1170:1317
+TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:149:1896
+GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC
+>HWI-EAS91_1_306UPAAXX:6:1:1504:494
+TGTCTACAGTAGAGTCAATAGCAAGGCCACGACGCC
+>HWI-EAS91_1_306UPAAXX:6:1:395:256
+GTCCATATCTGACTTTTTGTTAACGTATTTATCCAC
+>HWI-EAS91_1_306UPAAXX:6:1:1110:1109
+ACCGCTTCGGCGTTATAACCTCACACTCAATCTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:895:649
+TTCTGCACGTAATTTTTGACGCACGTTTTCTTCTGC
+>HWI-EAS91_1_306UPAAXX:6:1:827:1378
+TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1051:1587
+TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG
+>HWI-EAS91_1_306UPAAXX:6:1:1656:1549
+AACCTGCTGTTGCTTGGAAAGATTGGTGTTTTCCAT
+>HWI-EAS91_1_306UPAAXX:6:1:366:150
+GGTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAA
+>HWI-EAS91_1_306UPAAXX:6:1:955:1792
+ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA
+>HWI-EAS91_1_306UPAAXX:6:1:1340:1403
+ATAAAATGCACCGCATGGAAATGAAGACGGCCATTA
+>HWI-EAS91_1_306UPAAXX:6:1:1693:1017
+TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGT
+>HWI-EAS91_1_306UPAAXX:6:1:1099:1572
+AATTTTTACCGCTTCGGCGTTATAACCTCACACTCA
+>HWI-EAS91_1_306UPAAXX:6:1:218:1148
+TATGCAAATTAGCATAAGCAGCTTGCAGACCCATAT
+>HWI-EAS91_1_306UPAAXX:6:1:403:614
+TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC
+>HWI-EAS91_1_306UPAAXX:6:1:1651:646
+TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC
+>HWI-EAS91_1_306UPAAXX:6:1:1566:499
+TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG
+>HWI-EAS91_1_306UPAAXX:6:1:825:951
+ACAGGCCGTTTGAATGTTTACGGGGTGTACATAATA
+>HWI-EAS91_1_306UPAAXX:6:1:1745:1865
+TTAACTTCTGCGTCATGGAAGCGATAAAACTCTGCG
+>HWI-EAS91_1_306UPAAXX:6:1:973:1992
+TAGTAATTCCTGCTTTATCAAGATAATTTTTCGACT
+>HWI-EAS91_1_306UPAAXX:6:1:171:1653
+TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT
+>HWI-EAS91_1_306UPAAXX:6:1:397:363
+TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT
+>HWI-EAS91_1_306UPAAXX:6:1:1336:1155
+ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG
+>HWI-EAS91_1_306UPAAXX:6:1:685:629
+AGTATGCAAATTAGCATAAGCAGCTTGCAGACCCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1409:510
+ACATAATAAGCAATGACGGCAGCAATAAACTCAACA
+>HWI-EAS91_1_306UPAAXX:6:1:1631:998
+AACCATCAGCATGAGCCTGTCGCATTGCATTCATCC
+>HWI-EAS91_1_306UPAAXX:6:1:260:1698
+TTATTATGTTCATCCCGTCAACATTCAAACTGCCTT
+>HWI-EAS91_1_306UPAAXX:6:1:578:971
+TTAACGCTACTAAATTCCGCGGATTGGTTTCGTTGT
+>HWI-EAS91_1_306UPAAXX:6:1:1613:642
+ATAGAAATTTCACGCGGCGGCAAGTTGCCATACAAA
+>HWI-EAS91_1_306UPAAXX:6:1:237:650
+GACGGTATAATAACCACCATCATGGCGACCATTCAA
+>HWI-EAS91_1_306UPAAXX:6:1:1100:1875
+TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG
+>HWI-EAS91_1_306UPAAXX:6:1:352:32
+GTACCATAAACGCAAGCCTCAACGCAGCGACGAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:443:229
+GCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAAC
+>HWI-EAS91_1_306UPAAXX:6:1:1131:731
+AGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCT
+>HWI-EAS91_1_306UPAAXX:6:1:133:1089
+AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA
+>HWI-EAS91_1_306UPAAXX:6:1:65:1307
+TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT
+>HWI-EAS91_1_306UPAAXX:6:1:905:1493
+TCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTT
+>HWI-EAS91_1_306UPAAXX:6:1:733:540
+TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAT
+>HWI-EAS91_1_306UPAAXX:6:1:161:1707
+TAATGTCGTCACTGATGCTGCTTCTGTTGTTGTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:380:1861
+TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC
+>HWI-EAS91_1_306UPAAXX:6:1:1761:566
+TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1486:651
+TGGCGGTATTTCTTCTTCTCTTTCTTGTTGCGCCCT
+>HWI-EAS91_1_306UPAAXX:6:1:508:1380
+TCCATCAACATCATAGCCAGATGCCCAGAGATTAGA
+>HWI-EAS91_1_306UPAAXX:6:1:1763:855
+TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1553:553
+TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA
+>HWI-EAS91_1_306UPAAXX:6:1:1424:507
+TCCACTGCAACAACTGAACGGACTGGAAACACTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:988:135
+TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC
+>HWI-EAS91_1_306UPAAXX:6:1:810:1918
+TTTTCATCCCGAAGTTGCGGCTCATTCTGATTCTGT
+>HWI-EAS91_1_306UPAAXX:6:1:588:559
+TCTGGTTGAACGGCGTCGCGTCGTAACCCAGCTTGG
+>HWI-EAS91_1_306UPAAXX:6:1:1264:1214
+ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC
+>HWI-EAS91_1_306UPAAXX:6:1:1000:1475
+TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG
+>HWI-EAS91_1_306UPAAXX:6:1:1389:160
+TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT
+>HWI-EAS91_1_306UPAAXX:6:1:422:1296
+TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGT
+>HWI-EAS91_1_306UPAAXX:6:1:1273:856
+TAGCCATAGCACCAGAAACAAAACTAGGGGCGGCCT
+>HWI-EAS91_1_306UPAAXX:6:1:450:969
+TGTTTTCCATAATAGACGCAACGCGAGCAGTAGACT
+>HWI-EAS91_1_306UPAAXX:6:1:1202:828
+ATCGTCAACGTTATATTTTGATAGTTTGACGTTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1721:1800
+GGGTTAGGGACATTAGAGCCTTGACTGACTGAGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:228:2019
+TTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTG
+>HWI-EAS91_1_306UPAAXX:6:1:1579:1214
+ACGTTTGGTCAGTTCCATCAACATCATAGCCAGATG
+>HWI-EAS91_1_306UPAAXX:6:1:429:1055
+TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1359:1689
+AAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAA
+>HWI-EAS91_1_306UPAAXX:6:1:1474:1056
+TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC
+>HWI-EAS91_1_306UPAAXX:6:1:105:1818
+TTGGGGATTGAGAAAGAGTAGAAATGCCACAAGCCT
+>HWI-EAS91_1_306UPAAXX:6:1:208:1538
+TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+>HWI-EAS91_1_306UPAAXX:6:1:1361:1623
+AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA
+>HWI-EAS91_1_306UPAAXX:6:1:595:1670
+TGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACA
+>HWI-EAS91_1_306UPAAXX:6:1:6:1885
+TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:706:1085
+TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG
+>HWI-EAS91_1_306UPAAXX:6:1:1307:825
+AGCGGTAAAGTTAGACCAAACCATGAAACCAACATA
+>HWI-EAS91_1_306UPAAXX:6:1:762:802
+TGGCATTAACACCATCCTTCATGAACTTAATCCACT
+>HWI-EAS91_1_306UPAAXX:6:1:1657:506
+TTGCGACCCTCGGCAGCAAGAACCATACGACCAATT
+>HWI-EAS91_1_306UPAAXX:6:1:184:811
+TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC
+>HWI-EAS91_1_306UPAAXX:6:1:1469:1718
+TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTT
+>HWI-EAS91_1_306UPAAXX:6:1:815:1640
+TGGCGGCGATTGCGTACCCGACGACCCAAATTAGGG
+>HWI-EAS91_1_306UPAAXX:6:1:1580:1388
+AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG
+>HWI-EAS91_1_306UPAAXX:6:1:1617:1554
+TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGA
+>HWI-EAS91_1_306UPAAXX:6:1:1544:431
+TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA
+>HWI-EAS91_1_306UPAAXX:6:1:1604:1541
+TCAGTGACGACATTAGAAATATCCTTTGCAGTAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:1485:741
+ATCAAACGCTGAATAGTAAAGCCTCTACGCGATTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1226:393
+TGCCACAAGCCTCAATAGCAGGTTTAAGAGCCTCGA
+>HWI-EAS91_1_306UPAAXX:6:1:1506:973
+ATTAGGGTCAACGCTACCTGTAGGAAGTGTCCGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:890:1838
+TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC
+>HWI-EAS91_1_306UPAAXX:6:1:453:1527
+TAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACT
+>HWI-EAS91_1_306UPAAXX:6:1:1056:570
+ACATTGTAGCATTGTGCCAATTCATCCATTAACTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1736:74
+TATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGT
+>HWI-EAS91_1_306UPAAXX:6:1:169:1896
+GTATGCAAATTAGCATAAGCAGCTTGCAGACCCATA
+>HWI-EAS91_1_306UPAAXX:6:1:259:949
+TGAGGATAAATTATGTCTAATATTCAAACTTGCTCC
+>HWI-EAS91_1_306UPAAXX:6:1:1205:893
+ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT
+>HWI-EAS91_1_306UPAAXX:6:1:732:1335
+TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT
+>HWI-EAS91_1_306UPAAXX:6:1:667:664
+TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG
+>HWI-EAS91_1_306UPAAXX:6:1:535:587
+TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT
+>HWI-EAS91_1_306UPAAXX:6:1:412:446
+GTGTGGTTGATATTTTTCATGGTATTGATAAAGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:507:1599
+TTGCTGGCGGTTTTTCTTTTTTTTTTTTTTTTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:575:1818
+TAAAATGCACCGCATGGAAATGAAGACGGCCATTAG
+>HWI-EAS91_1_306UPAAXX:6:1:1568:1428
+ACCAGTTATATGGCTGGTTGTTTTTTTTTTTTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1417:982
+AACAAGAGAATCTCTACCATGAACAAAATGTGACTC
+>HWI-EAS91_1_306UPAAXX:6:1:280:1340
+GGCCAAACCAGTGGCGATGGCCGCGCTGGAGGTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:966:144
+TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1391:1987
+TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT
+>HWI-EAS91_1_306UPAAXX:6:1:1280:278
+ATGGAAATGAAGACGGCCATTAGCTGTACCATACTC
+>HWI-EAS91_1_306UPAAXX:6:1:631:858
+TGATATTGGTCGTATGGTTCTTGCTTCCGTGGGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:518:573
+TTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:54:981
+TTGACATTTTAAAAGAGCGTGGATTACTATCTGATT
+>HWI-EAS91_1_306UPAAXX:6:1:218:1165
+TATTGACTCTACTGTAGACATTTTTACTTTTTATTT
+>HWI-EAS91_1_306UPAAXX:6:1:1727:1530
+TCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCA
+>HWI-EAS91_1_306UPAAXX:6:1:519:657
+TGAACAGCATCGGACTCAGATAGTAATCCACGCTCT
+>HWI-EAS91_1_306UPAAXX:6:1:939:967
+ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC
+>HWI-EAS91_1_306UPAAXX:6:1:299:1060
+TATAACTGGTAGCTTTAAGCGGCTCACCTTTAGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:438:665
+TAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1303:1971
+AGCATTGTGCCAATTCATCCATTAACTTCTCAGTAA
+>HWI-EAS91_1_306UPAAXX:6:1:214:1264
+TCAGCACCAACAGAAACAACCTGATTAGCGGCGTTG
+>HWI-EAS91_1_306UPAAXX:6:1:1454:1423
+AACGGAAAACATCCTTCATAGAAATTTCACGCGGCG
+>HWI-EAS91_1_306UPAAXX:6:1:1633:340
+TTCCATAATAGACGCAACGCGAGCAGTAGACTCCTT
+>HWI-EAS91_1_306UPAAXX:6:1:671:1196
+ATACGAAAAGACAGAATCTCTTCCAAGAGCTTGATG
diff -r 000000000000 -r 0bd6b2cb3b2a lastz/test-data/lastz_wrapper_out0.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/test-data/lastz_wrapper_out0.sam	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,416 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:phiX1	LN:2310
+HWI-EAS91_1_306UPAAXX	0	phiX1	229	255	36M	*	0	0	GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2071	255	36M	*	0	0	GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1067	255	1H35M	*	0	0	GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1788	255	36M	*	0	0	GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1193	255	36M	*	0	0	GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1590	255	36M	*	0	0	AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1701	255	36M	*	0	0	GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1683	255	36M	*	0	0	CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1665	255	36M	*	0	0	CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	513	255	36M	*	0	0	GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1229	255	36M	*	0	0	GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	615	255	36M	*	0	0	GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	257	255	36M	*	0	0	GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1888	255	36M	*	0	0	GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1828	255	36M	*	0	0	CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	22	255	36M	*	0	0	GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	358	255	35M1H	*	0	0	GATGCTGTTCAACCACTAATAGGTAAGAAATCATG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1775	255	36M	*	0	0	GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1554	255	36M	*	0	0	CGACTTCTACCACATCTATTGACATTATGGGTCTGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1002	255	36M	*	0	0	TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1265	255	36M	*	0	0	GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1332	255	36M	*	0	0	GCACGATTAACCCTGATACCAATAAAATCCCTAAGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1670	255	36M	*	0	0	GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	640	255	36M	*	0	0	ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1674	255	36M	*	0	0	GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1082	255	36M	*	0	0	CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1115	255	36M	*	0	0	GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	636	255	36M	*	0	0	GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	852	255	36M	*	0	0	CTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	632	255	36M	*	0	0	CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1719	255	36M	*	0	0	GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	379	255	36M	*	0	0	GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2160	255	36M	*	0	0	GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1508	255	1H35M	*	0	0	TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	635	255	36M	*	0	0	TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1294	255	1H35M	*	0	0	TAACACTACTGGTTATATTGACCATGCCGCTTTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	772	255	36M	*	0	0	GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1224	255	36M	*	0	0	GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1544	255	3H33M	*	0	0	CGCCAAATGACGACTTCTACCACATCTATTGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	204	255	35M1H	*	0	0	GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	332	255	36M	*	0	0	AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1193	255	36M	*	0	0	GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	157	255	36M	*	0	0	CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1091	255	36M	*	0	0	ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	798	255	1H35M	*	0	0	GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1655	255	36M	*	0	0	GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1249	255	1H35M	*	0	0	TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	789	255	35M1H	*	0	0	GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	305	255	36M	*	0	0	GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1461	255	36M	*	0	0	AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	220	255	36M	*	0	0	GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1172	255	1H35M	*	0	0	GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	636	255	36M	*	0	0	GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1014	255	36M	*	0	0	AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2148	255	36M	*	0	0	GCGTACTTATTCGCCACCATGATTATTACCAGTGTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1590	255	36M	*	0	0	AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	242	255	36M	*	0	0	GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	338	255	36M	*	0	0	GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1112	255	36M	*	0	0	GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1254	255	2H34M	*	0	0	TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	348	255	36M	*	0	0	ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1552	255	1H35M	*	0	0	GACGACTTCTACCACATCTATTGACATTATGGGTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1764	255	36M	*	0	0	AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1529	255	36M	*	0	0	GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	177	255	36M	*	0	0	CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	156	255	36M	*	0	0	GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	227	255	36M	*	0	0	TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	574	255	36M	*	0	0	CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1514	255	36M	*	0	0	GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1657	255	36M	*	0	0	TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2071	255	36M	*	0	0	GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1626	255	36M	*	0	0	GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	2217	255	36M	*	0	0	AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1690	255	36M	*	0	0	CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1082	255	36M	*	0	0	CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1521	255	35M1H	*	0	0	TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	945	255	36M	*	0	0	TAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1575	255	36M	*	0	0	ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2099	255	36M	*	0	0	GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	524	255	36M	*	0	0	TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1252	255	36M	*	0	0	GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1116	255	36M	*	0	0	GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	613	255	36M	*	0	0	TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	289	255	36M	*	0	0	TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1800	255	36M	*	0	0	AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	624	255	36M	*	0	0	GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1877	255	1H35M	*	0	0	CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1214	255	36M	*	0	0	GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2254	255	35M1H	*	0	0	GACCACTCGCGATTCAATCATGACTTCGTGATAAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	2222	255	36M	*	0	0	AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	646	255	35M1H	*	0	0	TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1364	255	36M	*	0	0	AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1613	255	1H35M	*	0	0	ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1045	255	35M1H	*	0	0	TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1588	255	36M	*	0	0	GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	339	255	36M	*	0	0	TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1946	255	36M	*	0	0	GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	727	255	36M	*	0	0	GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	555	255	36M	*	0	0	GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	485	255	36M	*	0	0	TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	318	255	36M	*	0	0	TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	910	255	36M	*	0	0	TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1843	255	36M	*	0	0	TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1082	255	36M	*	0	0	CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1728	255	36M	*	0	0	TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2225	255	36M	*	0	0	TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2059	255	36M	*	0	0	TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	388	255	36M	*	0	0	TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	2128	255	36M	*	0	0	TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	154	255	36M	*	0	0	TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	411	255	35M1H	*	0	0	TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	521	255	35M1H	*	0	0	TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1662	255	36M	*	0	0	CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	533	255	36M	*	0	0	CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	195	255	35M1H	*	0	0	TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2239	255	36M	*	0	0	TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1313	255	36M	*	0	0	GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1545	255	36M	*	0	0	GCCAAATGACGACTTCTACCACATCTATTGACATTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	557	255	36M	*	0	0	GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1249	255	36M	*	0	0	TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	206	255	36M	*	0	0	TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	900	255	36M	*	0	0	TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1155	255	36M	*	0	0	TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	989	255	36M	*	0	0	TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1207	255	36M	*	0	0	TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2116	255	36M	*	0	0	TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	660	255	36M	*	0	0	ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1536	255	36M	*	0	0	AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	2112	255	1H35M	*	0	0	TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1948	255	36M	*	0	0	CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2212	255	35M1H	*	0	0	TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1940	255	1H35M	*	0	0	ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1274	255	1H35M	*	0	0	GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1707	255	36M	*	0	0	TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1582	255	36M	*	0	0	GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1588	255	36M	*	0	0	GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	441	255	36M	*	0	0	ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1012	255	36M	*	0	0	TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	161	255	36M	*	0	0	GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1165	255	1H35M	*	0	0	GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	801	255	36M	*	0	0	GCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1587	255	36M	*	0	0	TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	496	255	36M	*	0	0	TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	441	255	36M	*	0	0	ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1579	255	1H35M	*	0	0	TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	54	255	36M	*	0	0	AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	680	255	1H35M	*	0	0	CATGGAAGGCGCTGAATTTACGGAAAACATTATTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	231	255	36M	*	0	0	TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1580	255	36M	*	0	0	ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	611	255	36M	*	0	0	TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1957	255	36M	*	0	0	TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	540	255	1H35M	*	0	0	GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	584	255	36M	*	0	0	TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1728	255	36M	*	0	0	TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1721	255	36M	*	0	0	TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1954	255	36M	*	0	0	TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	962	255	36M	*	0	0	TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	2175	255	36M	*	0	0	ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2004	255	36M	*	0	0	TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2154	255	36M	*	0	0	TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1093	255	35M1H	*	0	0	TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1734	255	36M	*	0	0	CATCTGGCTATGATGTTGATGGAACTGACCAAACGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1522	255	36M	*	0	0	TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	409	255	36M	*	0	0	AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1867	255	36M	*	0	0	TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1242	255	36M	*	0	0	AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	527	255	35M1H	*	0	0	TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2100	255	36M	*	0	0	AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1002	255	36M	*	0	0	TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	10	255	1H35M	*	0	0	CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1579	255	36M	*	0	0	TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	349	255	36M	*	0	0	TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	286	255	36M	*	0	0	GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	680	255	1H35M	*	0	0	CATGGAAGGCGCTGAATTTACGGAAAACATTATTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	320	255	34M2H	*	0	0	TTGACATTTTAAAAGAGCGTGGATTACTATCTGA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	521	255	36M	*	0	0	TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	333	255	36M	*	0	0	AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	72	255	36M	*	0	0	ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX1	1974	255	36M	*	0	0	CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT	*
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:phiX2	LN:3076
+HWI-EAS91_1_306UPAAXX	16	phiX2	1212	255	36M	*	0	0	ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	358	255	36M	*	0	0	GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1938	255	36M	*	0	0	GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	553	255	36M	*	0	0	GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	247	255	36M	*	0	0	GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2842	255	36M	*	0	0	GGATGAAAATGCTCACAATGACAAATCTGTCCACGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2574	255	36M	*	0	0	GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2742	255	36M	*	0	0	GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2599	255	36M	*	0	0	GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	553	255	36M	*	0	0	GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	816	255	1H35M	*	0	0	GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1110	255	36M	*	0	0	GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	569	255	36M	*	0	0	ATAAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2161	255	36M	*	0	0	GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1788	255	36M	*	0	0	ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2789	255	36M	*	0	0	GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1944	255	36M	*	0	0	GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1098	255	36M	*	0	0	GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1733	255	36M	*	0	0	GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2250	255	36M	*	0	0	GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1124	255	1H35M	*	0	0	GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2229	255	36M	*	0	0	GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1398	255	36M	*	0	0	GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1016	255	36M	*	0	0	GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1866	255	36M	*	0	0	GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	247	255	36M	*	0	0	GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	967	255	36M	*	0	0	ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1282	255	36M	*	0	0	AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1194	255	36M	*	0	0	GTATATGCACAAAATGAGATGCTTGCTTATCAACAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1316	255	36M	*	0	0	GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1262	255	36M	*	0	0	GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1944	255	36M	*	0	0	GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1860	255	36M	*	0	0	GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	809	255	36M	*	0	0	CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	440	255	35M1H	*	0	0	GTTATTATACCGTCAAGGACTGTGTGACTATTGAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2296	255	36M	*	0	0	GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1263	255	36M	*	0	0	GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2795	255	36M	*	0	0	GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1785	255	36M	*	0	0	CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2241	255	36M	*	0	0	GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	974	255	36M	*	0	0	TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1695	255	36M	*	0	0	GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	169	255	36M	*	0	0	GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	735	255	1H35M	*	0	0	GCTACCGATAACAATACTGTAGGCATGGGTGATGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2962	255	36M	*	0	0	GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2581	255	36M	*	0	0	GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2473	255	36M	*	0	0	ATTTTATGCGGACACTTCCTACAGGTAGCGTTGACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1309	255	36M	*	0	0	GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2145	255	36M	*	0	0	GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	654	255	35M1H	*	0	0	GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	453	255	36M	*	0	0	CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	456	255	36M	*	0	0	GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	790	255	36M	*	0	0	AAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1816	255	36M	*	0	0	ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1716	255	36M	*	0	0	GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	311	255	36M	*	0	0	GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	439	255	36M	*	0	0	GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	563	255	36M	*	0	0	CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1553	255	36M	*	0	0	TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2877	255	36M	*	0	0	GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1886	255	36M	*	0	0	GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2847	255	36M	*	0	0	AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2530	255	36M	*	0	0	GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	171	255	36M	*	0	0	ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1668	255	36M	*	0	0	TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2555	255	36M	*	0	0	GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	961	255	36M	*	0	0	GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1864	255	36M	*	0	0	TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	428	255	36M	*	0	0	GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	393	255	1H35M	*	0	0	CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	633	255	36M	*	0	0	ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1551	255	36M	*	0	0	AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	783	255	36M	*	0	0	GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	841	255	36M	*	0	0	GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2482	255	36M	*	0	0	GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1539	255	36M	*	0	0	GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	433	255	1H35M	*	0	0	GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	705	255	36M	*	0	0	GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2556	255	36M	*	0	0	CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2094	255	36M	*	0	0	GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2852	255	36M	*	0	0	GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	951	255	36M	*	0	0	GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	786	255	36M	*	0	0	ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1149	255	36M	*	0	0	GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1389	255	36M	*	0	0	GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	756	255	35M1H	*	0	0	GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2118	255	36M	*	0	0	GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1690	255	36M	*	0	0	CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	884	255	36M	*	0	0	GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2286	255	36M	*	0	0	GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	563	255	36M	*	0	0	CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	379	255	36M	*	0	0	GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2881	255	35M1H	*	0	0	GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	660	255	36M	*	0	0	GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2841	255	36M	*	0	0	GGGATGAAAATGCTCACAATGACAAATCTGTCCACG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2578	255	1H35M	*	0	0	ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2723	255	36M	*	0	0	GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2640	255	36M	*	0	0	CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2174	255	36M	*	0	0	GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2457	255	1H35M	*	0	0	CATTTCCATGCGGTGCATTTTATGCGGACACTTCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	267	255	36M	*	0	0	GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	711	255	36M	*	0	0	GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1421	255	36M	*	0	0	GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	126	255	36M	*	0	0	TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	400	255	36M	*	0	0	GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2296	255	34M2H	*	0	0	GATTAGAGGCGTTTTATGATAATCCCAATGCTTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	456	255	36M	*	0	0	GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	940	255	36M	*	0	0	GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1972	255	36M	*	0	0	GCTACAATGTGCTCCCCCAACTTGATATTAATAACA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1826	255	34M2H	*	0	0	GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2104	255	36M	*	0	0	TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1678	255	36M	*	0	0	GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1893	255	36M	*	0	0	GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1788	255	36M	*	0	0	ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1997	255	35M1H	*	0	0	TATTAATAACACTATAGACCACCGCCCCGAAGGGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	379	255	36M	*	0	0	GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1518	255	36M	*	0	0	GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1446	255	36M	*	0	0	ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	789	255	36M	*	0	0	CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	772	255	36M	*	0	0	GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2626	255	36M	*	0	0	CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2380	255	36M	*	0	0	GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1210	255	36M	*	0	0	AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1548	255	36M	*	0	0	AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1034	255	36M	*	0	0	TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2767	255	36M	*	0	0	GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	453	255	1H35M	*	0	0	CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1972	255	36M	*	0	0	GCTACAATGTGCTCCCCCAACTTGATATTAATAACA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2797	255	36M	*	0	0	TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2858	255	1H35M	*	0	0	AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	646	255	36M	*	0	0	TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1319	255	36M	*	0	0	TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	169	255	36M	*	0	0	GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	691	255	36M	*	0	0	GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2357	255	35M1H	*	0	0	TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1154	255	36M	*	0	0	CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2601	255	35M1H	*	0	0	TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2627	255	36M	*	0	0	TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1364	255	36M	*	0	0	CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2635	255	36M	*	0	0	TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1003	255	36M	*	0	0	TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2626	255	36M	*	0	0	CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2695	255	36M	*	0	0	TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	858	255	36M	*	0	0	GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	428	255	33M3H	*	0	0	GCCATGATGGTGGTTATTATACCGTCAAGGACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1789	255	36M	*	0	0	TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	264	255	36M	*	0	0	TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	143	255	36M	*	0	0	TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2869	255	36M	*	0	0	TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1058	255	36M	*	0	0	CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1001	255	36M	*	0	0	GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2729	255	36M	*	0	0	TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	444	255	36M	*	0	0	TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1307	255	36M	*	0	0	GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	418	255	36M	*	0	0	TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	465	255	36M	*	0	0	GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1907	255	36M	*	0	0	TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2309	255	35M1H	*	0	0	TTATGATAATCCCAATGCTTTGCGTGACTATTTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	420	255	35M1H	*	0	0	GAATGGTCGCCATGATGGTGGTTATTATACCGTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1950	255	36M	*	0	0	TTAATGGATGAATTGGCACAATGCTACAATGTGCTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1864	255	36M	*	0	0	TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2671	255	36M	*	0	0	CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	11	255	35M1H	*	0	0	TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1778	255	35M1H	*	0	0	TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1277	255	36M	*	0	0	TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1477	255	36M	*	0	0	TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1524	255	35M1H	*	0	0	GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1402	255	36M	*	0	0	TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	506	255	36M	*	0	0	ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2866	255	36M	*	0	0	ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1162	255	36M	*	0	0	CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1507	255	35M1H	*	0	0	ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1253	255	36M	*	0	0	GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1888	255	1H35M	*	0	0	ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	597	255	1H35M	*	0	0	CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	533	255	35M1H	*	0	0	TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2064	255	36M	*	0	0	GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2763	255	36M	*	0	0	GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2124	255	36M	*	0	0	TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2130	255	36M	*	0	0	TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1610	255	36M	*	0	0	GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2277	255	1H35M	*	0	0	CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	388	255	36M	*	0	0	ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	857	255	36M	*	0	0	TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2268	255	36M	*	0	0	TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1260	255	36M	*	0	0	ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2444	255	36M	*	0	0	TAATGGCCGTCTTCATTTCCATGCGGTGCATTTTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1822	255	36M	*	0	0	TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2465	255	36M	*	0	0	TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1882	255	36M	*	0	0	ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2222	255	1H35M	*	0	0	GATGAATGCAATGCGACAGGCTCATGCTGATGGTT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	418	255	36M	*	0	0	TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1669	255	36M	*	0	0	TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2374	255	36M	*	0	0	AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1380	255	36M	*	0	0	AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1542	255	1H35M	*	0	0	ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	547	255	35M1H	*	0	0	TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2348	255	35M1H	*	0	0	TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	132	255	36M	*	0	0	TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2816	255	1H35M	*	0	0	CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2896	255	36M	*	0	0	CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	569	255	36M	*	0	0	ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	817	255	36M	*	0	0	AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1234	255	36M	*	0	0	AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1290	255	36M	*	0	0	CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1753	255	36M	*	0	0	AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1085	255	36M	*	0	0	TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1672	255	36M	*	0	0	TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	505	255	36M	*	0	0	TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2349	255	1H35M	*	0	0	ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	126	255	36M	*	0	0	TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2507	255	36M	*	0	0	CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	452	255	36M	*	0	0	TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2645	255	36M	*	0	0	TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1451	255	36M	*	0	0	CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2189	255	36M	*	0	0	GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1729	255	36M	*	0	0	TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2478	255	36M	*	0	0	ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2071	255	36M	*	0	0	AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1946	255	36M	*	0	0	GAAGTTAATGGATGAATTGGCACAATGCTACAATGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1552	255	36M	*	0	0	ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	968	255	36M	*	0	0	TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2298	255	36M	*	0	0	TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2443	255	36M	*	0	0	CTAATGGCCGTCTTCATTTCCATGCGGTGCATTTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	540	255	36M	*	0	0	TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2430	255	36M	*	0	0	GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	157	255	1H35M	*	0	0	CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	446	255	36M	*	0	0	ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	2647	255	36M	*	0	0	ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1939	255	36M	*	0	0	TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	282	255	36M	*	0	0	CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1230	255	36M	*	0	0	AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA	*
+HWI-EAS91_1_306UPAAXX	16	phiX2	1820	255	36M	*	0	0	CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT	*
diff -r 000000000000 -r 0bd6b2cb3b2a lastz/test-data/lastz_wrapper_out1.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/test-data/lastz_wrapper_out1.sam	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,247 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:phiX1	LN:2310
+HWI-EAS91_1_306UPAAXX	0	phiX1	229	255	36M	*	0	0	GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2071	255	36M	*	0	0	GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1788	255	36M	*	0	0	GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1193	255	36M	*	0	0	GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1701	255	36M	*	0	0	GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	513	255	36M	*	0	0	GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1229	255	36M	*	0	0	GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	615	255	36M	*	0	0	GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1888	255	36M	*	0	0	GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	22	255	36M	*	0	0	GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	358	255	35M1H	*	0	0	GATGCTGTTCAACCACTAATAGGTAAGAAATCATG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1775	255	36M	*	0	0	GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1265	255	36M	*	0	0	GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1670	255	36M	*	0	0	GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	636	255	36M	*	0	0	GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1139	255	34M2H	*	0	0	GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1719	255	36M	*	0	0	GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	598	255	35M1H	*	0	0	GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	379	255	36M	*	0	0	GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2160	255	36M	*	0	0	GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	772	255	36M	*	0	0	GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1224	255	36M	*	0	0	GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	204	255	35M1H	*	0	0	GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1193	255	36M	*	0	0	GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	789	255	35M1H	*	0	0	GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	305	255	36M	*	0	0	GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	220	255	36M	*	0	0	GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1266	255	35M1H	*	0	0	GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2148	255	36M	*	0	0	GCGTACTTATTCGCCACCATGATTATTACCAGTGTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	571	255	35M1H	*	0	0	GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	242	255	36M	*	0	0	GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	338	255	36M	*	0	0	GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1112	255	36M	*	0	0	GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1529	255	36M	*	0	0	GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	156	255	36M	*	0	0	GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	227	255	36M	*	0	0	TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	582	255	34M2H	*	0	0	TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1514	255	36M	*	0	0	GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2071	255	36M	*	0	0	GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1626	255	36M	*	0	0	GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1982	255	36M	*	0	0	GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1521	255	35M1H	*	0	0	TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2099	255	36M	*	0	0	GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1252	255	36M	*	0	0	GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	289	255	36M	*	0	0	TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1203	255	36M	*	0	0	TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	624	255	36M	*	0	0	GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1214	255	36M	*	0	0	GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	558	255	36M	*	0	0	GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2254	255	35M1H	*	0	0	GACCACTCGCGATTCAATCATGACTTCGTGATAAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	646	255	35M1H	*	0	0	TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1045	255	35M1H	*	0	0	TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1588	255	36M	*	0	0	GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	339	255	36M	*	0	0	TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1946	255	36M	*	0	0	GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	727	255	36M	*	0	0	GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	485	255	36M	*	0	0	TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	910	255	36M	*	0	0	TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1379	255	36M	*	0	0	GGTTATTTGAATATCTATAACAACTATTTTAAATCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2225	255	36M	*	0	0	TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2059	255	36M	*	0	0	TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	388	255	36M	*	0	0	TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	154	255	36M	*	0	0	TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	411	255	35M1H	*	0	0	TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	521	255	35M1H	*	0	0	TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	195	255	35M1H	*	0	0	TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2239	255	36M	*	0	0	TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1313	255	36M	*	0	0	GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1249	255	36M	*	0	0	TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	614	255	35M1H	*	0	0	TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	206	255	36M	*	0	0	TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1702	255	36M	*	0	0	TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	900	255	36M	*	0	0	TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	989	255	36M	*	0	0	TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1207	255	36M	*	0	0	TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2116	255	36M	*	0	0	TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2212	255	35M1H	*	0	0	TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1707	255	36M	*	0	0	TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1180	255	34M2H	*	0	0	TATTGACTCTACTGTAGACATTTTTACTTTTTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1012	255	36M	*	0	0	TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	161	255	36M	*	0	0	GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1587	255	36M	*	0	0	TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	441	255	36M	*	0	0	ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	231	255	36M	*	0	0	TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	638	255	35M1H	*	0	0	TTATTATGTTCATCCCGTCAACATTCAAACTGCCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	584	255	36M	*	0	0	TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1728	255	36M	*	0	0	TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1954	255	36M	*	0	0	TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	962	255	36M	*	0	0	TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2004	255	36M	*	0	0	TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2154	255	36M	*	0	0	TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1093	255	35M1H	*	0	0	TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1522	255	36M	*	0	0	TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	409	255	36M	*	0	0	AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	527	255	35M1H	*	0	0	TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	2100	255	36M	*	0	0	AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1002	255	36M	*	0	0	TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	349	255	36M	*	0	0	TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	320	255	34M2H	*	0	0	TTGACATTTTAAAAGAGCGTGGATTACTATCTGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX1	1180	255	34M2H	*	0	0	TATTGACTCTACTGTAGACATTTTTACTTTTTAT	*
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:phiX2	LN:3076
+HWI-EAS91_1_306UPAAXX	0	phiX2	2253	255	36M	*	0	0	GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	358	255	36M	*	0	0	GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1938	255	36M	*	0	0	GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	553	255	36M	*	0	0	GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	247	255	36M	*	0	0	GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	201	255	34M2H	*	0	0	GTCAACGTTATATTTTGATAGTTTGACGGTTAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2842	255	36M	*	0	0	GGATGAAAATGCTCACAATGACAAATCTGTCCACGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2574	255	36M	*	0	0	GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2742	255	36M	*	0	0	GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2599	255	36M	*	0	0	GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	553	255	36M	*	0	0	GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1863	255	36M	*	0	0	GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	903	255	36M	*	0	0	GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1110	255	36M	*	0	0	GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2161	255	36M	*	0	0	GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2789	255	36M	*	0	0	GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1944	255	36M	*	0	0	GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1098	255	36M	*	0	0	GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2250	255	36M	*	0	0	GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2229	255	36M	*	0	0	GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1398	255	36M	*	0	0	GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1016	255	36M	*	0	0	GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1866	255	36M	*	0	0	GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1194	255	36M	*	0	0	GTATATGCACAAAATGAGATGCTTGCTTATCAACAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1262	255	36M	*	0	0	GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1944	255	36M	*	0	0	GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	440	255	35M1H	*	0	0	GTTATTATACCGTCAAGGACTGTGTGACTATTGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2795	255	36M	*	0	0	GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2241	255	36M	*	0	0	GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1695	255	36M	*	0	0	GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	169	255	36M	*	0	0	GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2962	255	36M	*	0	0	GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2581	255	36M	*	0	0	GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1309	255	36M	*	0	0	GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2145	255	36M	*	0	0	GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	654	255	35M1H	*	0	0	GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1716	255	36M	*	0	0	GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	311	255	36M	*	0	0	GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	439	255	36M	*	0	0	GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2877	255	36M	*	0	0	GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1886	255	36M	*	0	0	GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2530	255	36M	*	0	0	GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2555	255	36M	*	0	0	GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	428	255	36M	*	0	0	GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	783	255	36M	*	0	0	GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	841	255	36M	*	0	0	GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2482	255	36M	*	0	0	GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1539	255	36M	*	0	0	GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	705	255	36M	*	0	0	GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2094	255	36M	*	0	0	GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2852	255	36M	*	0	0	GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	951	255	36M	*	0	0	GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1149	255	36M	*	0	0	GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1389	255	36M	*	0	0	GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	331	255	36M	*	0	0	GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	756	255	35M1H	*	0	0	GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2118	255	36M	*	0	0	GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	884	255	36M	*	0	0	GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	379	255	36M	*	0	0	GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2881	255	35M1H	*	0	0	GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	660	255	36M	*	0	0	GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2841	255	36M	*	0	0	GGGATGAAAATGCTCACAATGACAAATCTGTCCACG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1662	255	33M3H	*	0	0	GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2723	255	36M	*	0	0	GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	267	255	36M	*	0	0	GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	711	255	36M	*	0	0	GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	126	255	36M	*	0	0	TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	400	255	36M	*	0	0	GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1918	255	35M1H	*	0	0	TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2296	255	34M2H	*	0	0	GATTAGAGGCGTTTTATGATAATCCCAATGCTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	940	255	36M	*	0	0	GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1826	255	34M2H	*	0	0	GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2104	255	36M	*	0	0	TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1893	255	36M	*	0	0	GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1997	255	35M1H	*	0	0	TATTAATAACACTATAGACCACCGCCCCGAAGGGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	379	255	36M	*	0	0	GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2606	255	36M	*	0	0	GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1518	255	36M	*	0	0	GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2380	255	36M	*	0	0	GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2362	255	36M	*	0	0	TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2767	255	36M	*	0	0	GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1972	255	36M	*	0	0	GCTACAATGTGCTCCCCCAACTTGATATTAATAACA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	646	255	36M	*	0	0	TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	169	255	36M	*	0	0	GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	691	255	36M	*	0	0	GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2357	255	35M1H	*	0	0	TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2601	255	35M1H	*	0	0	TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2627	255	36M	*	0	0	TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2635	255	36M	*	0	0	TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	352	255	36M	*	0	0	TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1003	255	36M	*	0	0	TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	858	255	36M	*	0	0	GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	428	255	33M3H	*	0	0	GCCATGATGGTGGTTATTATACCGTCAAGGACT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1789	255	36M	*	0	0	TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	264	255	36M	*	0	0	TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	143	255	36M	*	0	0	TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2869	255	36M	*	0	0	TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1468	255	34M2H	*	0	0	TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2327	255	36M	*	0	0	TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1001	255	36M	*	0	0	GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	444	255	36M	*	0	0	TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1907	255	36M	*	0	0	TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2309	255	35M1H	*	0	0	TTATGATAATCCCAATGCTTTGCGTGACTATTTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	420	255	35M1H	*	0	0	GAATGGTCGCCATGATGGTGGTTATTATACCGTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1950	255	36M	*	0	0	TTAATGGATGAATTGGCACAATGCTACAATGTGCTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1864	255	36M	*	0	0	TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	11	255	35M1H	*	0	0	TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1778	255	35M1H	*	0	0	TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1524	255	35M1H	*	0	0	GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1402	255	36M	*	0	0	TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2866	255	36M	*	0	0	ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1507	255	35M1H	*	0	0	ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	533	255	35M1H	*	0	0	TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2064	255	36M	*	0	0	GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2124	255	36M	*	0	0	TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2130	255	36M	*	0	0	TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1610	255	36M	*	0	0	GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	857	255	36M	*	0	0	TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2268	255	36M	*	0	0	TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1925	255	35M1H	*	0	0	TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1022	255	36M	*	0	0	TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1822	255	36M	*	0	0	TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2465	255	36M	*	0	0	TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1882	255	36M	*	0	0	ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1669	255	36M	*	0	0	TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1380	255	36M	*	0	0	AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	547	255	35M1H	*	0	0	TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2348	255	35M1H	*	0	0	TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	132	255	36M	*	0	0	TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	569	255	36M	*	0	0	ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	198	255	35M1H	*	0	0	ATCGTCAACGTTATATTTTGATAGTTTGACGTTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	345	255	33M3H	*	0	0	TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1085	255	36M	*	0	0	TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1470	255	36M	*	0	0	TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1672	255	36M	*	0	0	TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	126	255	36M	*	0	0	TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2645	255	36M	*	0	0	TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1552	255	36M	*	0	0	ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	968	255	36M	*	0	0	TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	2298	255	36M	*	0	0	TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	1498	255	35M1H	*	0	0	GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	540	255	36M	*	0	0	TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT	*
+HWI-EAS91_1_306UPAAXX	0	phiX2	446	255	36M	*	0	0	ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC	*
diff -r 000000000000 -r 0bd6b2cb3b2a lastz/test-data/phiX_split.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/test-data/phiX_split.fasta	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,79 @@
+>phiX1
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+>phiX2
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r 000000000000 -r 0bd6b2cb3b2a lastz/tool-data/lastz_seqs.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/tool-data/lastz_seqs.loc.sample	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,30 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of 2bit genome files for use with Lastz. You will
+#need to supply these files and then create a lastz_seqs.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The lastz_seqs.loc
+#file has this format (white space characters are TAB characters):
+#
+#<unique_build_id>	<display_name>		<file_path>
+#
+#So, for example, if your lastz_seqs.loc began like this:
+#
+#hg18	Human (Homo sapiens): hg18		/depot/data2/galaxy/twobit/hg18.2bit
+#hg19	Human (Homo sapiens): hg19		/depot/data2/galaxy/twobit/hg19.2bit
+#mm9	Mouse (Mus musculus): mm9		/depot/data2/galaxy/twobit/mm9.2bit
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 greg    universe 830134 2005-09-13 10:12 hg18.2bit
+#-rw-r--r--  1 greg    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 greg    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+#Your lastz_seqs.loc file should include an entry per line for 
+#each file you have stored that you want to be available. Note that 
+#your files should all have the extension '2bit'.
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. 
+#
diff -r 000000000000 -r 0bd6b2cb3b2a lastz/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/tool_data_table_conf.xml.sample	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of 2bit sequence files for use in Lastz -->
+    <table name="lastz_seqs" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/lastz_seqs.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 0bd6b2cb3b2a lastz/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz/tool_dependencies.xml	Fri Feb 07 15:27:29 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="lastz" version="1.03.52">
+        <repository changeset_revision="03a5b2d4c273" name="package_lastz_1_03_52" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>