# HG changeset patch
# User iuc
# Date 1729518975 0
# Node ID ca2b512e8d7cbe8e998dc69276db5eab361b4111
# Parent  6322be79bd8ea762d273673320455d72d601ca52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7

diff -r 6322be79bd8e -r ca2b512e8d7c gbk2fa.py
--- a/gbk2fa.py	Sat Sep 28 16:27:56 2024 +0000
+++ b/gbk2fa.py	Mon Oct 21 13:56:15 2024 +0000
@@ -6,6 +6,9 @@
 
 
 def get_opener(gbk_filename):
+    """Determines the appropriate opener for a given file, supporting
+    bzip2, gzip, or standard open.
+    """
     try:
         bz2.open(gbk_filename).read(1)
         return bz2.open
@@ -18,30 +21,38 @@
         return open
 
 
-parser = argparse.ArgumentParser()
-parser.add_argument(
-    "genbank_file",
-    help="GenBank input file. Can be compressed with gzip or bzip2"
-)
-parser.add_argument(
-    "fasta_file", help="FASTA output datset"
-)
-parser.add_argument(
-    "--remove_version", action="store_true",
-    help="Remove version number from NCBI form formatted accession numbers. "
-         "For example, this would convert 'B000657.2' to 'B000657'"
-)
-args = parser.parse_args()
+def main():
+    parser = argparse.ArgumentParser(
+        description="Convert GenBank files to FASTA format. "
+                    "Supports gzip and bzip2 compressed files."
+    )
+    parser.add_argument(
+        "genbank_file",
+        help="GenBank input file. Can be compressed with gzip or bzip2"
+    )
+    parser.add_argument(
+        "fasta_file",
+        help="FASTA output dataset"
+    )
+    parser.add_argument(
+        "--remove_version", action="store_true",
+        help="Remove version number from NCBI formatted accession numbers. "
+             "For example, this converts 'B000657.2' to 'B000657'."
+    )
+    args = parser.parse_args()
+
+    gbk_open = get_opener(args.genbank_file)
+    with gbk_open(args.genbank_file, 'rt') as input_handle, \
+            open(args.fasta_file, 'w') as output_handle:
+        for seq_record in SeqIO.parse(input_handle, 'genbank'):
+            if args.remove_version:
+                seq_id = seq_record.id.split('.')[0]
+            else:
+                seq_id = seq_record.id
+            print(f'Writing FASTA record: {seq_id}')
+            output_handle.write(f'>{seq_id}\n')
+            output_handle.write(f'{seq_record.seq}\n')
 
 
-gbk_open = get_opener(args.genbank_file)
-with gbk_open(args.genbank_file, 'rt') as input_handle, \
-     open(args.fasta_file, 'w') as output_handle:
-    for seq_record in SeqIO.parse(input_handle, 'genbank'):
-        if args.remove_version:
-            seq_id = seq_record.id.split('.')[0]
-        else:
-            seq_id = seq_record.id
-        print('Writing FASTA record: {}'.format(seq_id))
-        print('>' + seq_id, file=output_handle)
-        print(seq_record.seq, file=output_handle)
+if __name__ == "__main__":
+    main()
diff -r 6322be79bd8e -r ca2b512e8d7c snpEff.xml
--- a/snpEff.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpEff.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2">
+<tool id="snpEff" name="SnpEff eff:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
     <description> annotate variants</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -13,7 +13,7 @@
             ln -s '${intervals}' intervals.bed &&
         #end if 
         snpEff @JAVA_OPTIONS@ eff
-        -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
+        -i $inputFormat -o ${outputFormat} -upDownStreamLen $udLength
         #if $spliceSiteSize and str($spliceSiteSize) != '':
           -spliceSiteSize "$spliceSiteSize"
         #end if
@@ -53,9 +53,6 @@
         #if $csvStats:
             -csvStats '$csvFile'
         #end if
-        #if str($offset) != 'default':
-          ${offset}
-        #end if
         #if str($chr).strip() != '':
           -chr '$chr'
         #end if
@@ -103,35 +100,21 @@
             mkdir '$statsFile.files_path' &&
             mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
         #end if
-        #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
-          &&
-          ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
-          sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
-        #end if
     ]]></command>
     <inputs>
         <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
-
-        <param name="inputFormat" type="select" label="Input format">
+        <param argument="-i" name="inputFormat" type="select" label="Input format" help="Specify the format of input dataset(s)">
             <option value="vcf" selected="true">VCF</option>
-            <option value="bed">BED (Deprecated)</option>
+            <option value="bed">BED</option>
         </param>
-
-        <conditional name="outputConditional">
-            <param name="outputFormat" type="select" label="Output format">
-                <option value="vcf" selected="true">VCF (only if input is VCF)</option>
-                <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
-                <option value="bed">BED</option>
-                <option value="bedAnn">BED annotations</option>
-            </param>
-            <when value="vcf" />
-            <when value="gatk">
-                <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
-            </when>
-            <when value="bed" />
-            <when value="bedAnn" />
-        </conditional>
-        <param name="csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report, useful for downstream analysis (-csvStats)" />
+        <param argument="-o" name="outputFormat" type="select" label="Output format" help="Specify output format">
+            <option value="vcf" selected="true">VCF (only if input is VCF)</option>
+            <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
+            <option value="bed">BED</option>
+            <option value="bedAnn">BED annotations</option>
+        </param>
+        <param argument="-csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report?" help="Useful for downstream analyses and report generation" />
+        <param argument="-noStats" name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats?" help="Generates an HTML summary of results"/>
         <conditional name="snpDb">
             <param name="genomeSrc" type="select" label="Genome source">
                 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
@@ -171,8 +154,7 @@
                 </section>
             </when>
             <when value="named">
-                <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)">
-                    <help>@SNPEFF_DATABASE_URL@</help>
+                <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)" help="A list of databases can be obtained with 'snpEff download' tool">
                     <validator type="empty_field" message="A genome version name is required" />
                 </param>
             </when>
@@ -209,18 +191,16 @@
             </param>
             </when>
         </conditional>
-
         <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length">
-            <option value="0">No upstream / downstream intervals (0 bases)</option>
+            <option value="0" selected="true">No upstream / downstream intervals (0 bases)</option>
             <option value="200">200 bases</option>
             <option value="500">500 bases</option>
             <option value="1000">1000 bases</option>
             <option value="2000">2000 bases</option>
-            <option value="5000" selected="true">5000 bases</option>
+            <option value="5000">5000 bases</option>
             <option value="10000">10000 bases</option>
             <option value="20000">20000 bases</option>
         </param>
-
         <param name="spliceSiteSize" argument="-ss" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases">
             <option value="1">1 base</option>
             <option value="2" selected="true">2 bases</option>
@@ -232,7 +212,6 @@
             <option value="8">8 bases</option>
             <option value="9">9 bases</option>
         </param>
-
         <conditional name="spliceRegion">
             <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
                 <option value="no">Use Defaults</option>
@@ -245,7 +224,6 @@
                 <param argument="-spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases" />
             </when>
         </conditional>
-
         <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
             <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
             <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option>
@@ -334,12 +312,6 @@
                 </param>
             </when>
         </conditional>
-
-        <param name="offset" type="select" display="radio" label="Chromosomal position">
-            <option value="default" selected="true">Use default (based on input type)</option>
-            <option value="-0">Force zero-based positions (both input and output)</option>
-            <option value="-1">Force one-based positions (both input and output)</option>
-        </param>
         <param argument="-chr" type="text" label="Text to prepend to chromosome name">
             <help>
                By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
@@ -347,7 +319,6 @@
             </help>
             <validator type="regex" message="No whitespace allowed">^\S*$</validator>
         </param>
-        <param name="generate_stats" argument="-noStats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats" />
         <param argument="-noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" />
     </inputs>
     <outputs>
@@ -375,8 +346,8 @@
             <param name="generate_stats" value="true"/>
             <output name="snpeff_output">
                 <assert_contents>
-                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
-                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
+                    <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
+                    <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
                 </assert_contents>
             </output>
             <output name="statsFile">
@@ -398,13 +369,13 @@
             <param name="csvStats" value="true"/>
             <output name="snpeff_output">
                 <assert_contents>
-                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
-                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
+                    <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
+                    <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
                 </assert_contents>
             </output>
             <output name="csvFile">
                 <assert_contents>
-                    <has_n_lines n="185"/>
+                    <has_n_lines n="134"/>
                     <has_n_columns n="1" sep=","/>
                 </assert_contents>
             </output>
diff -r 6322be79bd8e -r ca2b512e8d7c snpEff_create_db.xml
--- a/snpEff_create_db.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpEff_create_db.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,11 +1,11 @@
-<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy6" profile="22.01">
+<tool id="snpEff_build_gb" name="SnpEff build:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
     <description> database from Genbank or GFF record</description>
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
     <requirements>
         <expand macro="requirement" />
-        <requirement type="package" version="1.79">biopython</requirement>
+        <requirement type="package" version="1.84">biopython</requirement>
     </requirements>
     <expand macro="stdio" />
     <expand macro="version_command" />
@@ -36,7 +36,7 @@
             ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.${input_type.input_type_selector}' &&
         #end if
 
-        snpEff @JAVA_OPTIONS@ build -v
+        snpEff @JAVA_OPTIONS@ build -noCheckCds -noCheckProtein -v
         -configOption '${genome_version}'.genome='${genome_version}'
         -configOption '${genome_version}'.codonTable='${codon_table}'
         #if str($input_type.input_type_selector) == "gb":
@@ -186,7 +186,7 @@
     <help><![CDATA[
 **What it does**
 
-This tool uses `"snpEff build -genbank"` or `"snpEff build -gff3"` commands to create a snpEff database.
+This tool uses `snpEff build` to create a snpEff database.
 
 ------
 
@@ -201,7 +201,7 @@
 
  .. class:: warningmark
 
- SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use GFF route described below.
+ SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use the GFF route described below.
 
 -------
 
diff -r 6322be79bd8e -r ca2b512e8d7c snpEff_databases.xml
--- a/snpEff_databases.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpEff_databases.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff_databases" name="SnpEff databases:" version="@WRAPPER_VERSION@.galaxy2">
+<tool id="snpEff_databases" name="SnpEff databases:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
     <description> list available databases</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -19,6 +19,10 @@
              | grep -v '${exclude_pattern}'
         #end if
 
+        #if str($include_download_path) == "no":
+            | cut -f 1,2,3,4
+        #end if
+
         > '${snpeff_dbs}'
     ]]></command>
     <inputs>
@@ -38,7 +42,10 @@
                 </valid>
             </sanitizer>
         </param>
-
+        <param name="include_download_path" type="select" display="radio" label="Include download paths?" help="When snpEff dumps the list of available databases, it includes their download paths. These are not needed in the Galaxy context.">
+            <option value="yes">Yes</option>
+            <option value="no" selected="true">No</option>
+        </param>
     </inputs>
     <outputs>
         <data name="snpeff_dbs" format="tabular" label="${tool.name} @SNPEFF_VERSION@ available databases" />
@@ -63,12 +70,16 @@
     <help><![CDATA[
 **What it does**
 
-This tool downloads the master list of snpEff databases from @SNPEFF_DATABASE_URL@. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse* the it will produce a tabular dataset with the following content::
+This tool downloads the master list of snpEff databases from a remote SnpEff repository. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse*, it will produce a tabular dataset with the following content::
 
-    mm10  Mouse  http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm10.zip
-    mm9   Mouse  http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_mm9.zip
+    mm10  Mouse
+    mm39  Mouse
+    mm9   Mouse
 
-This means that there two available snpEff databases for mouse genome versions mm9 and mm10. In order to download these databases you should use identifier from the first column (e.g., mm9 or mm10 in this case).
+This means that there are three available snpEff databases for mouse genome. If you want to use mm39 in you analysis:
+
+ - set **Genome source** option of **SnpEff eff** Galaxy tool to *Download on demand*
+ - enter 'mm39' into **Snpff Genome Version Name** text box
 
 -------
 
@@ -83,6 +94,7 @@
 
 @SNPEFF_IN_GALAXY_INFO@
 @EXTERNAL_DOCUMENTATION@
+
     ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 6322be79bd8e -r ca2b512e8d7c snpEff_download.xml
--- a/snpEff_download.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpEff_download.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff_download" name="SnpEff download:" version="@WRAPPER_VERSION@.galaxy2">
+<tool id="snpEff_download" name="SnpEff download:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
     <description> download a pre-built database</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -42,7 +42,7 @@
     <help><![CDATA[
 **What it does**
 
-This tool downloads a specified database from @SNPEFF_DATABASE_URL@. It deposits it into the history.
+This tool downloads a specified database from a remote SnpEff repository. It deposits it into the history.
 
 -------
 
diff -r 6322be79bd8e -r ca2b512e8d7c snpEff_macros.xml
--- a/snpEff_macros.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpEff_macros.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <xml name="requirement">
-        <requirement type="package" version="4.3.1t">snpeff</requirement>
+        <requirement type="package" version="5.2">snpeff</requirement>
         <yield/>
     </xml>
   <xml name="stdio">
@@ -14,9 +14,8 @@
 snpEff -version
     ]]></version_command>
   </xml>
-  <token name="@WRAPPER_VERSION@">4.3+T</token>
-  <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
-  <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
+  <token name="@WRAPPER_VERSION@">0</token>
+  <token name="@SNPEFF_VERSION@">5.2</token>
   <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
   <xml name="ref_select">
     <conditional name="reference_source">
@@ -59,7 +58,7 @@
 
 **Download pre-built databases**
 
-SnpEff project generates large numbers of pre-build databases. These are available at @SNPEFF_DATABASE_URL@ and can downloaded. Follow these steps:
+SnpEff project generates large numbers of pre-build databases. To obtain and use them follow these steps:
 
   #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need.
   #. Use **SnpEff download** tool to download the database.
diff -r 6322be79bd8e -r ca2b512e8d7c snpeff_get_chr_names.xml
--- a/snpeff_get_chr_names.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpeff_get_chr_names.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@WRAPPER_VERSION@.galaxy2">
+<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
     <description>list chromosome names/lengths</description>
     <macros>
         <import>snpEff_macros.xml</import>
diff -r 6322be79bd8e -r ca2b512e8d7c test-data/input.vcf
--- a/test-data/input.vcf	Sat Sep 28 16:27:56 2024 +0000
+++ b/test-data/input.vcf	Mon Oct 21 13:56:15 2024 +0000
@@ -2,59 +2,9 @@
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##contig=<ID="KJ660346",length=18959>
 ##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.2
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	EBOV_2014_EM095	EBOV_2014_G3676	EBOV_2014_G3680	EBOV_2014_G3686	EBOV_2014_G3687	EBOV_2014_G3683	EBOV_2014_EM096	EBOV_2014_EM098	EBOV_2014_EM104	EBOV_2014_EM106	EBOV_2014_EM112	EBOV_2014_EM113	EBOV_2014_EM124	EBOV_2014_G3677	EBOV_2014_G3682	EBOV_2014_G3707	EBOV_2014_G3713	EBOV_2014_G3724	EBOV_2014_G3734	EBOV_2014_G3735	EBOV_2014_G3750	EBOV_2014_G3758	EBOV_2014_G3764	EBOV_2014_G3769	EBOV_2014_G3782	EBOV_2014_G3786	EBOV_2014_G3788	EBOV_2014_G3796	EBOV_2014_G3798	EBOV_2014_G3799	EBOV_2014_G3800	EBOV_2014_G3805	EBOV_2014_G3807	EBOV_2014_G3810	EBOV_2014_G3820	EBOV_2014_G3838	EBOV_2014_G3840	EBOV_2014_G3841	EBOV_2014_G3848	EBOV_2014_NM042	EBOV_2014_G3850	EBOV_2014_EM110	EBOV_2014_EM111	EBOV_2014_EM119	EBOV_2014_G3729	EBOV_2014_G3765	EBOV_2014_G3770	EBOV_2014_G3789	EBOV_2014_G3825	EBOV_2014_G3845	EBOV_2014_G3851	EBOV_2014_G3857	EBOV_2014_EM115	EBOV_2014_EM120	EBOV_2014_G3752	EBOV_2014_G3795	EBOV_2014_G3808	EBOV_2014_G3823	EBOV_2014_EM121	EBOV_2014_G3771	EBOV_2014_G3816	EBOV_2014_G3829	EBOV_2014_G3846	EBOV_2014_G3856	EBOV_2014_G3826	EBOV_2014_G3827	EBOV_2014_G3809	EBOV_2014_G3814	EBOV_2014_G3821	EBOV_2014_G3822	EBOV_2014_G3679	EBOV_2014_G3819	EBOV_2014_G3817	EBOV_2014_G3834	EBOV_2014_G3818	EBOV_2014_G3787	EBOV_2014_G3831	EBOV_2014_G3670	EBOV_2014_KJ660346	EBOV_2014_KJ660347	EBOV_2014_KJ660348
-KJ660346	572	.	A	G	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-KJ660346	800	.	C	T	.	.	.	GT	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0
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-KJ660346	13923	.	T	C	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
-KJ660346	14019	.	T	C	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
-KJ660346	14232	.	C	T	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-KJ660346	15599	.	G	A	.	.	.	GT	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-KJ660346	15660	.	C	T	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-KJ660346	15963	.	G	A	.	.	.	GT	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0
-KJ660346	16054	.	T	A	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0
-KJ660346	16455	.	T	C	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
-KJ660346	16750	.	T	C	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-KJ660346	17142	.	T	C	.	.	.	GT	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0
-KJ660346	17985	.	T	C	.	.	.	GT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-KJ660346	18412	.	T	C	.	.	.	GT	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
-KJ660346	18895	.	C	T	.	.	.	GT	0	0	0	0	0	0	0	.	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	0	0	0	0	0	0	0	0	.	0	0	0	0	.	0	.	0	0	0	.	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	0	0	0	0	0	0	0	0	0	0	0	1	1	1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	EBOV_2014_EM095	EBOV_2014_G3676
+KJ660346.1	572	.	A	G	.	.	.	GT	0	0
+KJ660346.1	800	.	C	T	.	.	.	GT	0	0
+KJ660346.1	1024	.	A	C	.	.	.	GT	0	0
+KJ660346.1	1288	.	A	T	.	.	.	GT	0	0
+KJ660346.1	1492	.	A	G	.	.	.	GT	0	0