# HG changeset patch
# User devteam
# Date 1444755233 14400
# Node ID 5a5f92086188f8cfbcbde217607a0fe440ade9d2
# Parent  7095d651c95fdfe2f8330007aec741e27dea625d
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

diff -r 7095d651c95f -r 5a5f92086188 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,70 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.2">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{SAM_def,
+                title={Definition of SAM/BAM format},
+                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+            </citation>
+            <citation type="doi">10.1093/bioinformatics/btp352</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
+            <citation type="doi">10.1093/bioinformatics/btr509</citation>
+            <citation type="bibtex">
+                @misc{Danecek_et_al,
+                Author={Danecek, P., Schiffels, S., Durbin, R.},
+                title={Multiallelic calling model in bcftools (-m)},
+                url = {http://samtools.github.io/bcftools/call-m.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Durbin_VCQC,
+                Author={Durbin, R.},
+                title={Segregation based metric for variant call QC},
+                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Li_SamMath,
+                Author={Li, H.},
+                title={Mathematical Notes on SAMtools Algorithms},
+                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{SamTools_github,
+                title={SAMTools GitHub page},
+                url = {https://github.com/samtools/samtools},}
+            </citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error" />
+        </stdio>
+    </xml>
+    <token name="@no-chrom-options@">
+-----
+
+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
+
+If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
+
+1. Click on the **pencil** icon adjacent to the dataset in the history
+2. A new menu will appear in the center pane of the interface
+3. Click **Datatype** tab
+4. Set **New Type** to **BAM**
+5. Click **Save**
+
+The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
+
+    </token>
+
+</macros>
diff -r 7095d651c95f -r 5a5f92086188 sam_to_bam.py
--- a/sam_to_bam.py	Thu Mar 27 14:04:25 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,197 +0,0 @@
-#!/usr/bin/env python
-"""
-Converts SAM data to sorted BAM data.
-usage: sam_to_bam.py [options]
-   --input1: SAM file to be converted
-   --dbkey: dbkey value
-   --ref_file: Reference file if choosing from history
-   --output1: output dataset in bam format
-   --index_dir: GALAXY_DATA_INDEX_DIR
-"""
-
-import optparse, os, sys, subprocess, tempfile, shutil, gzip
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.cookbook import doc_optparse
-from galaxy import util
-
-def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
-
-def check_seq_file( dbkey, cached_seqs_pointer_file ):
-    seq_path = ''
-    for line in open( cached_seqs_pointer_file ):
-        line = line.rstrip( '\r\n' )
-        if line and not line.startswith( '#' ) and line.startswith( 'index' ):
-            fields = line.split( '\t' )
-            if len( fields ) < 3:
-                continue
-            if fields[1] == dbkey:
-                seq_path = fields[2].strip()
-                break
-    return seq_path
-
-def __main__():
-    #Parse Command Line
-    parser = optparse.OptionParser()
-    parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
-    parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' )
-    parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
-    parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
-    parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
-    ( options, args ) = parser.parse_args()
-
-    # output version # of tool
-    try:
-        tmp = tempfile.NamedTemporaryFile().name
-        tmp_stdout = open( tmp, 'wb' )
-        proc = subprocess.Popen( args='samtools 2>&1', 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( 'Samtools %s\n' % stdout )
-        else:
-            raise Exception
-    except:
-        sys.stdout.write( 'Could not determine Samtools version\n' )
-
-    cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir
-    if not os.path.exists( cached_seqs_pointer_file ):
-        stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file )
-    # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa,
-    # and the equCab2.fa file will contain fasta sequences.
-    seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
-    tmp_dir = tempfile.mkdtemp( dir='.' )
-    if not options.ref_file or options.ref_file == 'None':
-        # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
-        # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in
-        # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai
-        fai_index_file_base = seq_path
-        fai_index_file_path = '%s.fai' % seq_path 
-        if not os.path.exists( fai_index_file_path ):
-            #clean up temp files
-            if os.path.exists( tmp_dir ):
-                shutil.rmtree( tmp_dir )
-            stop_err( 'No sequences are available for build (%s), request them by reporting this error.' % options.dbkey )
-    else:
-        try:
-            # Create indexes for history reference ( e.g., ~/database/files/000/dataset_1.dat ) using samtools faidx, which will:
-            # - index reference sequence in the FASTA format or extract subsequence from indexed reference sequence
-            # - if no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk
-            # - if regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format
-            # - the input file can be compressed in the RAZF format.
-            # IMPORTANT NOTE: a real weakness here is that we are creating indexes for the history dataset
-            # every time we run this tool.  It would be nice if we could somehow keep track of user's specific
-            # index files so they could be re-used.
-            fai_index_file_base = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-            # At this point, fai_index_file_path will look something like /tmp/dataset_13.dat
-            os.symlink( options.ref_file, fai_index_file_base )
-            fai_index_file_path = '%s.fai' % fai_index_file_base
-            command = 'samtools faidx %s' % fai_index_file_base
-            tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-            tmp_stderr = open( tmp, 'wb' )
-            proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
-            returncode = proc.wait()
-            tmp_stderr.close()
-            # get stderr, allowing for case where it's very large
-            tmp_stderr = open( tmp, 'rb' )
-            stderr = ''
-            buffsize = 1048576
-            try:
-                while True:
-                    stderr += tmp_stderr.read( buffsize )
-                    if not stderr or len( stderr ) % buffsize != 0:
-                        break
-            except OverflowError:
-                pass
-            tmp_stderr.close()
-            if returncode != 0:
-                raise Exception, stderr 
-            if os.path.getsize( fai_index_file_path ) == 0:
-                raise Exception, 'Index file empty, there may be an error with your reference file or settings.'
-        except Exception, e:
-            #clean up temp files
-            if os.path.exists( tmp_dir ):
-                shutil.rmtree( tmp_dir )
-            stop_err( 'Error creating indexes from reference (%s), %s' % ( options.ref_file, str( e ) ) )
-    try:
-        # Extract all alignments from the input SAM file to BAM format ( since no region is specified, all the alignments will be extracted ).
-        tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
-        tmp_aligns_file_name = tmp_aligns_file.name
-        tmp_aligns_file.close()
-        command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 )
-        tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-        tmp_stderr = open( tmp, 'wb' )
-        proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
-        returncode = proc.wait()
-        tmp_stderr.close()
-        # get stderr, allowing for case where it's very large
-        tmp_stderr = open( tmp, 'rb' )
-        stderr = ''
-        buffsize = 1048576
-        try:
-            while True:
-                stderr += tmp_stderr.read( buffsize )
-                if not stderr or len( stderr ) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-        tmp_stderr.close()
-        if returncode != 0:
-            raise Exception, stderr
-    except Exception, e:
-        #clean up temp files
-        if os.path.exists( tmp_dir ):
-            shutil.rmtree( tmp_dir )
-        stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
-    try:
-        # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
-        # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
-        # into memory ( controlled by option -m ).
-        tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
-        tmp_sorted_aligns_file_name = tmp_sorted_aligns_file.name
-        tmp_sorted_aligns_file.close()
-        command = 'samtools sort %s %s' % ( tmp_aligns_file_name, tmp_sorted_aligns_file_name )
-        tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-        tmp_stderr = open( tmp, 'wb' )
-        proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
-        returncode = proc.wait()
-        tmp_stderr.close()
-        # get stderr, allowing for case where it's very large
-        tmp_stderr = open( tmp, 'rb' )
-        stderr = ''
-        buffsize = 1048576
-        try:
-            while True:
-                stderr += tmp_stderr.read( buffsize )
-                if not stderr or len( stderr ) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-        tmp_stderr.close()
-        if returncode != 0:
-            raise Exception, stderr
-    except Exception, e:
-        #clean up temp files
-        if os.path.exists( tmp_dir ):
-            shutil.rmtree( tmp_dir )
-        stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) )
-    # Move tmp_aligns_file_name to our output dataset location
-    sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name
-    shutil.move( sorted_bam_file, options.output1 )
-    #clean up temp files
-    if os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
-    # check that there are results in the output file
-    if os.path.getsize( options.output1 ) > 0:
-        sys.stdout.write( 'SAM file converted to BAM' )
-    else:
-        stop_err( 'Error creating sorted version of BAM file.' )
-
-if __name__=="__main__": __main__()
diff -r 7095d651c95f -r 5a5f92086188 sam_to_bam.xml
--- a/sam_to_bam.xml	Thu Mar 27 14:04:25 2014 -0400
+++ b/sam_to_bam.xml	Tue Oct 13 12:53:53 2015 -0400
@@ -1,97 +1,89 @@
-<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3">
-  <description>converts SAM format to BAM format</description>
-  <requirements>
-    <requirement type="package" version="0.1.19">samtools</requirement>
-  </requirements>
-  <command interpreter="python">
-    sam_to_bam.py
-      --input1=$source.input1
-      #if $source.index_source == "history":
-        --dbkey=${ref_file.metadata.dbkey} 
-        --ref_file=$source.ref_file
-      #else
-        --dbkey=${input1.metadata.dbkey} 
-      #end if
-      --output1=$output1
-      --index_dir=${GALAXY_DATA_INDEX_DIR}
-  </command>
-  <inputs>
-    <conditional name="source">
-      <param name="index_source" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
-      <when value="cached">
-        <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert">
-           <validator type="unspecified_build" />
-           <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
-        </param>
-      </when>
-      <when value="history">
-        <param name="input1" type="data" format="sam" label="Convert SAM file" />
-        <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
-      </when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM">
-      <actions>
-        <conditional name="source.index_source">
-          <when value="cached">
-            <action type="metadata" name="dbkey">
-              <option type="from_param" name="source.input1" param_attribute="dbkey" />
-            </action>
-          </when>
-          <when value="history">
-            <action type="metadata" name="dbkey">
-              <option type="from_param" name="source.ref_file" param_attribute="dbkey" />
-            </action>
-          </when>
+<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1">
+  <description>convert SAM to BAM</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <expand macro="version_command"></expand>
+  <command>
+    <![CDATA[
+        #if $source.index_source == "history":
+          ln -s $source.ref_file input.fa &&
+          samtools faidx input.fa &&
+        #else
+          ln -s ${source.index.fields.path} input.fa &&
+          ln -s ${source.index.fields.path}.fai input.fa.fai &&
+        #end if
+        samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="source">
+            <param label="Choose the source for the reference genome" name="index_source" type="select">
+                <option value="cached">Use a built-in genome</option>
+                <option value="history">Use a genome from the history</option>
+            </param>
+            <when value="cached">
+                <param format="sam" label="SAM file to convert" metadata_name="dbkey" name="input1" type="data">
+                    <validator type="unspecified_build" />
+                    <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
+                </param>
+                <param label="Using reference genome" name="index" type="select">
+                    <options from_data_table="fasta_indexes">
+                        <filter column="1" key="dbkey" ref="input1" type="data_meta" />
+                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param format="sam" label="SAM file to convert" name="input1" type="data" />
+                <param format="fasta" label="Using reference file" metadata_name="dbkey" name="ref_file" type="data" />
+            </when>
         </conditional>
-      </actions>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <!--
-      Sam-to-Bam command:
-      cp test-data/chr_m.fasta .
-      samtools faidx chr_m.fasta
-      samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
-      samtools sort unsorted.bam sam_to_bam_out1
-      chr_m.fasta is the reference file (chrM from equCab2)
-      -->
-      <param name="index_source" value="history" /> 
-      <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
-      <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
-      <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" />
-    </test>
-    <test>
-      <!--
-      Sam-to-Bam command:
-      samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
-      samtools sort unsorted.bam sam_to_bam_out2
-      chr_m.fasta is the reference file and the index chr_m.fasta.fai 
-      these should be in the same directory, and chrM is from equCab2
-      -->
-      <param name="index_source" value="cached" />
-      <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
-      <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
-    </test>
-  </tests>
-  <help>
-
+    </inputs>
+    <outputs>
+        <data format="bam" label="${tool.name} on ${on_string}: converted BAM" name="output1">
+            <actions>
+                <conditional name="source.index_source">
+                    <when value="cached">
+                        <action name="dbkey" type="metadata">
+                            <option name="source.input1" param_attribute="dbkey" type="from_param" />
+                        </action>
+                    </when>
+                    <when value="history">
+                        <action name="dbkey" type="metadata">
+                            <option name="source.ref_file" param_attribute="dbkey" type="from_param" />
+                        </action>
+                    </when>
+                </conditional>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="index_source" value="history" />
+            <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />
+            <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
+            <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />
+        </test>
+        <test>
+            <param name="index_source" value="history" />
+            <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
+            <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
+            <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
 **What it does**
 
-This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.
+Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands::
 
-.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
-
-------
+  samtools sort -O bam -o sorted_input.bam [INPUT SAM] 
+  samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam
 
-**Citation**
-
-For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
-
+]]>
   </help>
+  <expand macro="citations"></expand>
 </tool>
diff -r 7095d651c95f -r 5a5f92086188 test-data/cached_locally/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/all_fasta.loc	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,1 @@
+chrM	chr_m	Horse (Equus caballus): equCab2 chrM	${__HERE__}/chrM.fasta
diff -r 7095d651c95f -r 5a5f92086188 test-data/cached_locally/chr_m.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/chr_m.fasta	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,335 @@
+>chrM
+GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA
+GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT
+TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT
+CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA
+AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG
+ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG
+GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA
+ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA
+AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA
+AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA
+TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA
+AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT
+GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC
+CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT
+CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA
+AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT
+TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC
+TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT
+GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT
+CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA
+CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG
+TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA
+TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC
+TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG
+AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG
+ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT
+AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC
+CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT
+ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG
+AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA
+ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA
+AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA
+ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG
+TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA
+ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG
+TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA
+CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA
+TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA
+AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT
+ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC
+AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca
+taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt
+tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg
+cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG
+ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT
+TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC
+CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA
+TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG
+CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG
+TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT
+CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT
+CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT
+AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA
+AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg
+tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt
+caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT
+GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT
+CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG
+GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA
+CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT
+AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC
+CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC
+CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA
+CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG
+TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC
+ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC
+ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA
+ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA
+TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA
+ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG
+GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC
+ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA
+CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC
+TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA
+CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT
+ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact
+acaggaattgaacctgctcctgagaattcaaaatcctccgtgctaccgaa
+ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT
+ACCCCGAAAATGTTGGATTACACCCTTCCCGTACTAATAAATCCCCTTAT
+CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA
+TAAGCTCACACTGACTAATAATCTGAATCGGATTTGAAATAAATCTACTA
+GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC
+CTCCACCAAATATTTTCTAACCCAAGCCACCGCATCAATACTCCTCATAA
+TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA
+GTCTTCAACCCCACAGCGTCCATCATTATAACTTCAGCTCTCGCCATAAA
+ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA
+TCTCATTAACATCAGGTCTCATCCTACTTACATGACAAAAACTAGCCCCA
+ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT
+AACTATAGCCGTACTGTCAATCCTAGTAGGAGGCTGAGGCGGTCTCAACC
+AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA
+TGAATAACAGCTGTCCTAGTATATAACCCAACACTAACAATACTAAACAT
+ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA
+GCTCCTCTACTACAACACTATCACTCTCCCACACATGAAACAAAATACCT
+CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC
+CCCACTATCAGGATTCATACCCAAATGAATAATCATTCAAGAGCTCACCA
+AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC
+AACCTCTACTTCTACATACGACTAACCTATTCCACCTCACTGACCATATT
+CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA
+TTACTCTCTTACCCCCGTTAATTGTTATATCCTCCCTACTCCTCCCCCTA
+ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC
+CAAGAGCCTTCAAAGCTCTAAGCAAGTGAATCCACTTAATTCCTGCATAC
+TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT
+TTTATTAAGCTAAGCCCTTACTAGATTGGTGGGCTACCATCCCACGAAAT
+TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC
+CGCCGCCTAGAAAAAAAGGCGGGAGAAGCCCCGGCAGAAATTGAAGCTGC
+TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG
+AAGAGGATTCCAACCCCTGTCTTTAGATTTACAGTCTAATGCTTACTCAG
+CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA
+GACATCGGCACTCTGTACCTCCTATTCGGCGCTTGAGCTGGAATAGTAGG
+AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC
+TACTAGGAGATGATCAGATCTACAATGTCATTGTAACCGCCCATGCATTC
+GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA
+CTGATTAGTCCCCCTGATAATTGGAGCACCTGATATAGCTTTCCCCCGAA
+TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC
+GCTTCCTCAATAATTGAAGCAGGTGCCGGAACAGGCTGAACCGTATATCC
+TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA
+TTTTCTCTCTCCACCTAGCTGGGGTGTCCTCGATTTTAGGTGCCATCAAC
+TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA
+AACCCCCCTATTCGTTTGATCTGTCCTTATTACGGCAGTACTCCTTCTCC
+TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT
+AACCTGAACACTACTTTCTTCGACCCCGCAGGAGGAGGGGATCCAATCCT
+TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA
+TCCTACCAGGCTTCGGTATAATCTCACACATCGTCACATACTACTCAGGT
+AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT
+TGGCTTTCTAGGCTTCATCGTATGGGCTCACCACATGTTTACAGTAGGGA
+TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT
+ATCCCTACTGGTGTAAAAGTATTCAGCTGACTAGCCACCCTGCACGGAGG
+AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT
+TATTCACAGTAGGAGGTCTAACAGGAATCGTCCTAGCTAACTCATCCCTA
+GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT
+CCTGTCTATAGGAGCAGTCTTCGCCATTATGGGGGGATTTGTACACTGAT
+TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC
+TTTACAATTATATTCGTAGGGGTAAATATAACCTTCTTCCCACAACATTT
+CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT
+ATACAACATGAAATACCATCTCATCCATAGGATCTTTTATCTCACTTACA
+GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG
+AGAAGTGTCTACAGTAGAATTAACCTCAACTAATCTGGAATGACTACACG
+GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA
+AAAtaagaaaggaaggaatcgaaccccctctaactggtttcaagccaata
+tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC
+ATGACTTTGTCAAAGTTAAATTATAGGTTAAACCCCTATATACCTCTATG
+GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA
+AGAACTCCTACACTTCCACGACCACACACTAATAATCGTATTCCTAATTA
+GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC
+CATACCAGCACCATAGATGCTCAAGAAGTAGAGACAATTTGAACGATTTT
+ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT
+ATATAATAGATGAAATCAATAATCCGTCCCTCACAGTCAAAACAATAGGC
+CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT
+TGACTCCTACATGATCCCCACATCAGACCTAAAACCAGGAGAATTACGTC
+TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA
+ATGCTAATTTCATCCGAAGACGTCCTACACTCATGAGCTGTGCCCTCCCT
+AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG
+TGGCCTCTCGACCAGGACTTTACTACGGTCAATGCTCAGAGATCTGCGGA
+TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA
+CTTCGAAGAATGATCTGCATCAATATTATAAAGTCACTAAGAAGCTATTA
+TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT
+GATATGCCACAGTTGGATACATCAACATGATTTATTAATATCGTCTCAAT
+AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT
+ATCCGACACACCCAGAAGTAAAGACAACCAAAATAACAAAACACTCTGCC
+CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA
+ACAATAGTAGGCCTCCCTATTGTAATTCTGATCATCATATTTCCCAGCAT
+CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC
+AACAATGGCTAGTCCAACTTACATCAAAACAAATAATAGCTATCCATAAC
+AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT
+TGGCTCAACAAACTTATTAGGCCTACTACCTCACTCATTTACACCAACAA
+CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA
+GTATTCATAGGCTTTCGTCACAAAACAAAAGCAGCCCTAGCCCACTTTCT
+ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA
+CTATCAGCCTATTTATTCAACCTGTAGCCCTAGCCGTGCGGCTAACCGCT
+AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT
+AGCCCTCATAAGCATCAGCCCCTCAACAGCCCTTATTACGTTTATCATCC
+TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC
+GTATTCACTCTCCTGGTAAGCCTTTACTTACACGACAACACCTAATGACC
+CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC
+AGGAGCCCTATCAGCCCTCCTGATAACATCAGGACTAGCCATGTGATTTC
+ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT
+ACCATATATCAATGATGACGAGACATCATCCGAGAAAGCACATTCCAAGG
+CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT
+TTATTATCTCAGAAGTCTTCTTCTTCTCTGGCTTCTTCTGAGCCTTTTAC
+CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC
+AGGTATCCACCCCTTAAACCCCCTAGAAGTCCCCTTACTCAACACCTCAG
+TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA
+GAAGGAAACCGTAAAAATATGCTCCAAGGCCTATTCATCACAATTTCACT
+AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT
+TTACTATTTCAGATGGAGTATACGGATCAACATTTTTCGTAGCAACAGGG
+TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT
+CCTACGCCAACTAAAATTCCACTTTACATCCAGCCACCACTTCGGATTCG
+AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG
+TACGTCTCTATTTATTGATGAGGATCCTATTCTTTTAGTATTGACCAGTA
+CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA
+AACCTCATACTGACACTCCTCACTAACACATTACTAGCCTCGCTACTCGT
+ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA
+GCCCATATGAATGCGGATTTGACCCTATAGGGTCAGCACGCCTCCCCTTC
+TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA
+AATTGCCCTCCTATTACCCCTTCCATGAGCATCCCAAACAACTAACCTAA
+ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC
+CTAGCCTACGAATGAACCCAAAAAGGACTAGAATGAACTGAGTATGGTAA
+TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT
+TCATAATTACCAACATGTCACTAGTCCATATTAATATCTTCCTAGCATTC
+ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC
+ACTCCTATGCCTAGAAGGAATAATACTATCACTATTCGTCATAGCAACCA
+TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC
+TTACTAGTATTTGCTGCCTGCGAACGAGCTCTAGGATTATCCCTACTAGT
+CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC
+TCCAATGCTAAAAATTATCATTCCCACAATCATACTTATGCCCCTTACAT
+GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA
+TTAATCAGCCTTATCAGCCTATCCCTCCTAAACCAACCTAGCAACAATAG
+CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC
+TGGTGTTGACAACATGACTACTGCCACTAATACTCATAGCCAGCCAACAC
+CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT
+AACCATACTTCAAACTTTCCTAATCATGACTTTTACCGCCACAGAACTAA
+TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC
+ATCACCCGCTGAGGCAACCAAACAGAACGCCTGAACGCAGGCCTCTACTT
+CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT
+CTATCCAAAACCTAACAGGCTCACTAAACTTCCTATTAATTCAATACTGA
+AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG
+TATAATAGCATTCATAGTCAAAATACCGGTATATGGTCTTCACCTCTGAC
+TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA
+GCCATTCTACTAAAACTAGGAGGCTACGGAATACTACGAATTACAACAAT
+ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC
+TGTGAGGAATAATCATAACTAGTTCCATCTGCTTGCGACAAACCGATCTA
+AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT
+AGCCGTCCTCATCCAAACACCATGAAGTTATATAGGAGCTACAGCCCTAA
+TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA
+AATTACGAACGTACCCATAGCCGAACTATAATCCTAGCCCGCGGGCTTCA
+AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA
+ACCTGGCCCTCCCTCCCAGCATTAACCTAATTGGAGAGCTATTCGTAGTA
+ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA
+TATCACCATCACCGCCCTCTACTCCCTATACATACTAATCACAACACAAC
+GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA
+GAAAACGCACTCATGGCCCTCCACATGACTCCCCTACTACTCCTATCACT
+TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA
+AAACACTAGATTGTGGATCTAGAAACAGAAACTTAATATTTCTTATTTAC
+CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA
+TGGCTCTCTCAAACTTTTAAAGGATAGGAGCTATCCGTTGGTCTTAGGAA
+CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC
+CTCATACTAGTTTCACTATTAGTACTAACCCTCCCAATCATATTATCAAT
+CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA
+TCTCATATGCCTTCATTACTAGCCTAATTCCCACTATAATATTTATTCAC
+TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC
+CCTCAAACTATCCCTAAGCTTCAAACTAGATTACTTCTCAATAATTTTCG
+TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA
+TACATGCACTCAGATCCTTACATTACTCGATTTTTTAAATACTTACTTAC
+ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC
+TGTTCATCGGATGGGAGGGAGTAGGCATCATGTCATTCTTACTAATCGGA
+TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT
+TTATAACCGCATCGGGGATATCGGCTTCATCATGGCCATAGCCTGATTCC
+TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC
+AACCTTACCAACCTCCCGCTCCTAGGCCTCCTCCTAGCCGCAACTGGCAA
+ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC
+CTACACCAGTCTCAGCCCTACTCCACTCCAGCACAATAGTTGTAGCAGGC
+GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT
+CCAGTCACTTACCCTATGCCTAGGAGCCATCACCACACTATTCACAGCAA
+TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC
+TCCAGCCAACTAGGCCTGATAATCGTAACCATCGGTATCAATCAACCCTA
+CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT
+TTATATGTTCCGGATCCATTATCCACAGCCTAAATGACGAGCAAGATATC
+CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT
+AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT
+ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC
+TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG
+TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC
+TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC
+CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA
+CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG
+CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG
+ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC
+CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG
+CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC
+TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC
+CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT
+CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG
+TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA
+ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC
+CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA
+CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT
+AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC
+AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG
+TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC
+ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC
+CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG
+AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA
+ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT
+GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC
+GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA
+CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG
+AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT
+ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA
+GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC
+AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG
+GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC
+ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT
+ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT
+ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC
+AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT
+CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT
+CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC
+CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT
+CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA
+ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA
+TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT
+AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC
+CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC
+CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT
+CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT
+CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC
+ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT
+ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC
+TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC
+TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT
+CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC
+CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG
+TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA
+GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC
+AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC
+GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG
+CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT
+TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA
+ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA
+CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT
+CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA
+CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA
+GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac
+ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct
+gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt
+gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc
+acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac
+ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA
+CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT
+GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT
+AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA
+GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT
+TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC
+TTCTTCCCCC
diff -r 7095d651c95f -r 5a5f92086188 test-data/cached_locally/chr_m.fasta.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/chr_m.fasta.fai	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,1 @@
+chrM	16660	6	50	51
diff -r 7095d651c95f -r 5a5f92086188 test-data/cached_locally/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/fasta_indexes.loc	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,1 @@
+chrM	chr_m	Horse (Equus caballus): equCab2 chrM	${__HERE__}/chrM.fasta
diff -r 7095d651c95f -r 5a5f92086188 test-data/chr_m.fasta.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr_m.fasta.fai	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,1 @@
+chrM	16660	6	50	51
diff -r 7095d651c95f -r 5a5f92086188 test-data/sam_to_bam_noheader_in2.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_to_bam_noheader_in2.sam	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1513:715	16	chrM	9563	25	36M	*	0	0	CTGACTACCACAACTAAACATCTATGCNNAAAAAAC	I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1698:516	16	chrM	2735	25	36M	*	0	0	TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC	I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1491:637	16	chrM	10864	25	36M	*	0	0	TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC	DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1711:249	16	chrM	10617	25	36M	*	0	0	ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1634:211	0	chrM	9350	25	36M	*	0	0	GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1218:141	16	chrM	14062	25	36M	*	0	0	ACAAAACTAACAACAAAAATAACACTCNNAATAAAC	I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1398:854	16	chrM	3921	25	36M	*	0	0	CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC	IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1310:991	16	chrM	10002	25	36M	*	0	0	CTCCTATGCCTAGAAGGAATAATACTANNACTATTC	I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1716:413	0	chrM	6040	25	36M	*	0	0	GATCCAANNCTTTATCAACACCTATTCTGATTCTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1630:59	16	chrM	12387	25	36M	*	0	0	TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC	FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
diff -r 7095d651c95f -r 5a5f92086188 test-data/sam_to_bam_out3.bam
Binary file test-data/sam_to_bam_out3.bam has changed
diff -r 7095d651c95f -r 5a5f92086188 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 7095d651c95f -r 5a5f92086188 tool-data/sam_fa_indices.loc.sample
--- a/tool-data/sam_fa_indices.loc.sample	Thu Mar 27 14:04:25 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a sam_fa_indices.loc file 
-#similar to this one (store it in this directory) that points to 
-#the directories in which those files are stored. The sam_fa_indices.loc 
-#file has this format (white space characters are TAB characters):
-#
-#index	<seq>	<location>
-#
-#So, for example, if you had hg18 indexed stored in 
-#/depot/data2/galaxy/sam/, 
-#then the sam_fa_indices.loc entry would look like this:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#
-#and your /depot/data2/galaxy/sam/ directory
-#would contain hg18.fa and hg18.fa.fai files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
-#
-#Your sam_fa_indices.loc file should include an entry per line for 
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#index	hg19	/depot/data2/galaxy/sam/hg19.fa
diff -r 7095d651c95f -r 5a5f92086188 tool-data/tool_data_table_conf.xml.sample
--- a/tool-data/tool_data_table_conf.xml.sample	Thu Mar 27 14:04:25 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<!-- 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>
-    <!-- Location of SAMTools indexes and other files -->
-    <table name="sam_fa_indexes" comment_char="#">
-        <columns>line_type, value, path</columns>
-        <file path="tool-data/sam_fa_indices.loc" />
-    </table>
-</tables>
\ No newline at end of file
diff -r 7095d651c95f -r 5a5f92086188 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,7 @@
+<!-- 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>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 7095d651c95f -r 5a5f92086188 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Oct 13 12:53:53 2015 -0400
@@ -0,0 +1,10 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/fasta_indexes.loc" />
+    </table>
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" />
+    </table>
+</tables>
\ No newline at end of file
diff -r 7095d651c95f -r 5a5f92086188 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Mar 27 14:04:25 2014 -0400
+++ b/tool_dependencies.xml	Tue Oct 13 12:53:53 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="192f00129358" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>