# HG changeset patch
# User iuc
# Date 1690817003 0
# Node ID 9f166012940332881ddb352a0268a6b3fa7817ca
# Parent  373c1735d31f8b44b576202a764a1c7ef2b501af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6

diff -r 373c1735d31f -r 9f1660129403 cooc_mutbamscan.xml
--- a/cooc_mutbamscan.xml	Thu Aug 11 13:50:37 2022 +0000
+++ b/cooc_mutbamscan.xml	Mon Jul 31 15:23:23 2023 +0000
@@ -1,96 +1,150 @@
 <tool id="cooc_mutbamscan" name="Cojac: mutbamscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
       profile="@PROFILE@">
     <description>
-        scan an alignment file for mutation co-occurrences
+        scans an alignment file for mutation co-occurrences
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="biotools"/>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="0.1.0">viramp-hub</requirement>
+    </expand>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
-ln -s '$bed_file' 'bed_file' &&
-@VOCDIR_COMMAND@
-#import re
-#set identifier = re.sub('[^\s\w\-\\.]', '_', str($bam_file.element_identifier))
-ln -s '$bam_file' ${identifier}.bam &&
-ln -s '${bam_file.metadata.bam_index}' ${identifier}.bai &&
-cooc-mutbamscan
-    -a '${identifier}.bam'
-    -b 'bed_file'
-    -m '$vocdir'
-    -y cooc.yaml
-    -j cooc.json
-    #if $amplicons_file.choice == 'build'
-        -A amplicons.yaml
+## arrange BAM inputs and index files into a V-pipe-style folder structure
+## that cojac understands
+sh arrange_samples.sh &&
+
+#if $spec_layout.mode == 'separate':
+  #set $voc_config = $spec_layout.voc_source
+  @VOCDIR_COMMAND@
+  ## prepare amplicon information
+  #if $spec_layout.amplicon_definitions.choice == 'insert_scheme':
+    ln -s '$spec_layout.amplicon_definitions.insert_bed' bed_cojac.bed &&
+  #else if $spec_layout.amplicon_definitions.choice == 'primer_scheme':
+    scheme-convert '$spec_layout.amplicon_definitions.primer_bed' -t bed -b cojac -o bed_cojac.bed &&
+  #else:
+    scheme-convert '$spec_layout.amplicon_definitions.primer_bed' -t bed -b cojac -a '$spec_layout.amplicon_definitions.amplicon_info' -o bed_cojac.bed &&
+  #end if
+#end if
+
+## run cojac
+cojac cooc-mutbamscan
+    ## use a sample list file to tell cojac to look for the inputs in the
+    ## V-pipe-style folder stucture we've created earlier.
+    -s samples_list.tsv
+    -p inputs
+    -b bed_cojac.bed
+    #if $spec_layout.mode == 'separate':
+      -m voc/
+      -A amplicons.yaml
+      --cooc $spec_layout.cooc
     #else
-        -Q '$amplicons_file.in_amp'
+      -Q '$spec_layout.in_amp'
+    #end if
+    #if 'yaml' in $out_opts.output_formats:
+      -y cooc.yaml
+    #end if
+    #if 'json' in $out_opts.output_formats:
+      -j cooc.json
+    #end if
+    #if 'tabular' in $out_opts.output_formats:
+      -t cooc.tsv
     #end if
-    -t cooc.tsv
-    --cooc $cooc
     ]]></command>
+    <configfiles>
+        <configfile filename="arrange_samples.sh"><![CDATA[#for $dataset in $mapped_input:
+  #set $sample_id = $dataset.element_identifier.replace("'", '_').replace('/', '_')
+mkdir -p 'inputs/$sample_id/1/alignments/' &&
+ln -s '$dataset' 'inputs/$sample_id/1/alignments/REF_aln.bam' &&
+ln -s '$dataset.metadata.bam_index' 'inputs/$sample_id/1/alignments/REF_aln.bam.bai' &&
+#end for
+#set $num_samples = len($mapped_input)
+echo "Gathered $num_samples sample and index files for cojac to discover from a samples list."
+        ]]></configfile>
+        <configfile filename="samples_list.tsv"><![CDATA[#for $dataset in $mapped_input:
+  #set $line = '\t'.join([$dataset.element_identifier.replace("'", '_').replace('/', '_'), '1', str($dataset)])
+$line
+#end for]]></configfile>
+    </configfiles>
     <inputs>
-        <expand macro="vocdir_input"/>
-        <param name="bed_file" type="data" format="bed"
-               label="BED file defining the amplicons"/>
-        <param name="bam_file" type="data" format="bam,cram,sam"
-               label="Alignment BAM/CRAM/SAM file"/>
-        <param argument="--cooc" type="integer" min="1" value="2"
-               label="Minimum number of cooccurence mutations on the same amplicon"/>
-        <conditional name="amplicons_file">
-            <param name="choice" type="select" label="Source of amplicons YAML file">
-                <option value="build">Build from BED + set of YAMLs for variants of concern</option>
-                <option value="custom">From history</option>
+        <param name="mapped_input" type="data" format="bam" multiple="true" label="Aligned reads input to analyze"/>
+        <conditional name="spec_layout">
+            <param name="mode" type="select" label="How would you like to provide amplicon and lineage information?">
+                <option value="separate">Separately</option>
+                <option value="combined">Combined</option>
             </param>
-            <when value="build"/>
-            <when value="custom">
-                <param name="in_amp" type="data" format="yaml"
-                       label="YAML file to query amplicons"/>
+            <when value="separate">
+                <expand macro="vocdir_input"/>
+                <conditional name="amplicon_definitions">
+                    <param name="choice" type="select" label="Format of amplicon definitions">
+                        <option value="insert_scheme">Amplicon insert scheme (Cojac-native format)</option>
+                        <option value="primer_scheme">Primer scheme (with autodetection of grouping into amplicons</option>
+                        <option value="primer_scheme_plus">Primer scheme and explicit amplicon grouping information</option>
+                    </param>
+                    <when value="insert_scheme">
+                        <param name="insert_bed" type="data" format="bed" label="Amplicon insert scheme" help="BED dataset providing the positions of the amplicon inserts (i.e. excluding the primer sequences) on the reference sequence."/>
+                    </when>
+	                <when value="primer_scheme">
+		                <param name="primer_bed" type="data" format="bed" label="Primer scheme" help="The tool will attempt to autodetect the relationship between primers and amplicons based on the primer names."/>
+                    </when>
+                    <when value="primer_scheme_plus">
+                        <param name="primer_bed" type="data" format="bed" label="Primer scheme" />
+                        <param name="amplicon_info" type="data" format="tabular" label="Primers to amplicons assignments" help ="This input should have one line of tab-separated primer names (as they appear in the primer scheme) per amplicon."/>
+                    </when>
+                </conditional>
+                <param argument="--cooc" type="integer" min="1" value="2" label="Minimum number of mutations required to co-occur on an amplicon"/>
+                <param name="output_cojac_ampl" type="boolean" checked="true" label="Produce combined per-amplicon lineage definition output" help="The tool can generate a YAML-formatted report of expected co-occurrences of mutations per amplicon and lineage. This output combines amplicon scheme and lineage definitions and can be used for rerunning the tool with identical configuration in 'Combined' mode. It is also a recommended input to the cojac pubmut tool so leave this option checked if you are intending to use this downstream tool."/>
+            </when>
+            <when value="combined">
+                <param name="in_amp" type="data" format="yaml" label="Combined per-amplicon lineage definitions"
+                help="YAML-formatted report of expected co-occurrences of mutations per amplicon and lineage generated by a previous run of the tool."/>
             </when>
         </conditional>
-        <param name="output_files" type="select" display="checkboxes"
-               multiple="true" label="Output files">
-            <option value="yaml" selected="true">YAML</option>
-            <option value="json">JSON</option>
-            <option value="tabular">tabular</option>
-        </param>
+        <section name="out_opts" title="Output options" expanded="true">
+            <param name="output_formats" type="select" display="checkboxes" multiple="true" label="Produce output in these formats"
+            help="Please note that only yaml- and json-formatted results can be processed with the downstream pubmut and tabmut tools.">
+                <option value="yaml">YAML</option>
+                <option value="json" selected="true">JSON</option>
+                <option value="tabular">tabular</option>
+            </param>
+        </section>
     </inputs>
     <outputs>
-        <data name="cooc_yaml" format="yaml"
-              label="${tool.name} on ${on_string}: Mutation cooccurrence (yaml)"
-              from_work_dir="cooc.yaml">
-            <filter>'yaml' in output_files</filter>
+        <data name="cooc_yaml" format="yaml" from_work_dir="cooc.yaml" label="${tool.name} on ${on_string}: Mutation co-occurrence (yaml)">
+            <filter>'yaml' in out_opts['output_formats']</filter>
         </data>
-        <data name="cooc_json" format="json"
-              label="${tool.name} on ${on_string}: Mutation cooccurrence (json)"
-              from_work_dir="cooc.json">
-            <filter>'json' in output_files</filter>
+        <data name="cooc_json" format="json" from_work_dir="cooc.json" label="${tool.name} on ${on_string}: Mutation co-occurrence (json)">
+            <filter>'json' in out_opts['output_formats']</filter>
         </data>
-        <data name="cooc_tsv" format="tabular"
-              label="${tool.name} on ${on_string}: Mutation cooccurrence (tabular)"
-              from_work_dir="cooc.tsv">
-            <filter>'tabular' in output_files</filter>
+        <data name="cooc_tsv" format="tabular" from_work_dir="cooc.tsv" label="${tool.name} on ${on_string}: Mutation co-occurrence (tabular)">
+            <filter>'tabular' in out_opts['output_formats']</filter>
         </data>
-        <data name="amplicons" format="yaml"
-              label="${tool.name} on ${on_string}: Amplicons (yaml)"
-              from_work_dir="amplicons.yaml">
-            <filter>amplicons_file['choice'] == 'build'</filter>
+        <data name="amplicons" format="yaml" from_work_dir="amplicons.yaml" label="${tool.name} on ${on_string}: Combined per-amplicon lineage definitions">
+            <filter>spec_layout['mode'] == 'separate' and spec_layout['output_cojac_ampl']</filter>
         </data>
     </outputs>
     <tests>
         <!-- Test 1: build yaml for amplicons from bed and voc/ -->
         <test expect_num_outputs="4">
-            <conditional name="vocdir_option">
-                <param name="choice" value="custom"/>
-                <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
+            <param name="mapped_input" value="tbam11.bam"/>
+            <conditional name="spec_layout">
+                <conditional name="voc_source">
+                    <param name="choice" value="custom"/>
+                    <param name="collection">
+                        <collection type="list">
+                            <element name="BA.1" ftype="yaml" value="omicron_ba1_mutations.yaml" />
+                        </collection>
+                    </param>
+                </conditional>
+                <conditional name="amplicon_definitions">
+                    <param name="insert_bed" value="nCoV-2019.insert.V3.bed" ftype="bed"/>
+                </conditional>
             </conditional>
-            <param name="bam_file" value="tbam11.bam"/>
-            <param name="bed_file" value="nCoV-2019.insert.V3.bed"/>
-            <conditional name="amplicons_file">
-                <param name="choice" value="build"/>
-            </conditional>
-            <param name="output_files" value="yaml,json,tabular"/>
+            <section name="out_opts">
+                <param name="output_formats" value="yaml,json,tabular"/>
+            </section>
             <output name="cooc_yaml" ftype="yaml">
                 <assert_contents>
                     <has_text text="76_om1"/>
@@ -116,18 +170,75 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- Test 2: supply yaml for amplicons and voc/ from cache -->
+        <!-- Test 2: configure via cojac yaml -->
         <test expect_num_outputs="2">
-            <conditional name="vocdir_option">
-                <param name="choice" value="cache"/>
-            </conditional>
-            <param name="bam_file" value="tbam11.bam"/>
-            <param name="bed_file" value="nCoV-2019.insert.V3.bed"/>
-            <conditional name="amplicons_file">
-                <param name="choice" value="custom"/>
+            <param name="mapped_input" value="tbam11.bam"/>
+            <conditional name="spec_layout">
+                <param name="mode" value="combined"/>
                 <param name="in_amp" value="amplicons111.yaml"/>
             </conditional>
-            <param name="output_files" value="yaml,tabular"/>
+            <section name="out_opts">
+                <param name="output_formats" value="yaml,tabular"/>
+            </section>
+            <output name="cooc_yaml" ftype="yaml">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+            <output name="cooc_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 3: use computed cojac format amplicon definitions from 2 files -->
+        <test expect_num_outputs="2">
+            <param name="mapped_input" value="tbam11.bam"/>
+            <conditional name="spec_layout">
+                <conditional name="voc_source">
+                    <param name="choice" value="builtin"/>
+                </conditional>
+                <conditional name="amplicon_definitions">
+                    <param name="choice" value="primer_scheme_plus"/>
+                    <param name="primer_bed" value="primers.bed" ftype="bed"/>
+                    <param name="amplicon_info" value="ampl_info.tsv"/>
+                </conditional>
+                <param name="output_cojac_ampl" value="false"/>
+            </conditional>
+            <section name="out_opts">
+                <param name="output_formats" value="yaml,tabular"/>
+            </section>
+            <output name="cooc_yaml" ftype="yaml">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+            <output name="cooc_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 4: test primer scheme as input -->
+        <test expect_num_outputs="2">
+            <param name="mapped_input" value="tbam11.bam"/>
+            <conditional name="spec_layout">
+                <conditional name="voc_source">
+                    <param name="choice" value="builtin"/>
+                </conditional>
+                <conditional name="amplicon_definitions">
+                    <param name="choice" value="primer_scheme"/>
+                    <param name="primer_bed" value="primers.bed" ftype="bed"/>
+                </conditional>
+                <param name="output_cojac_ampl" value="false"/>
+            </conditional>
+            <section name="out_opts">
+                <param name="output_formats" value="yaml,tabular"/>
+            </section>
             <output name="cooc_yaml" ftype="yaml">
                 <assert_contents>
                     <has_text text="76_om1"/>
@@ -145,11 +256,11 @@
     <help><![CDATA[
 @HELP_HEADER@
 
-Information about **cooc-mutbamscan** method
-============================================
+Information about **cojac cooc-mutbamscan**
+===========================================
 
-The method scans an alignment BAM/CRAM/SAM file for mutation co-occurrences and output a JSON or YAML file.
-
+The tool scans an alignment BAM/CRAM/SAM file for mutation co-occurrences.
+It can report its findings in json, yaml and/or tabular format.
     ]]></help>
     <expand macro="citations"/>
 </tool>
diff -r 373c1735d31f -r 9f1660129403 macros.xml
--- a/macros.xml	Thu Aug 11 13:50:37 2022 +0000
+++ b/macros.xml	Mon Jul 31 15:23:23 2023 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.2</token>
+    <token name="@TOOL_VERSION@">0.9</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -18,34 +18,28 @@
         <version_command>echo @TOOL_VERSION@</version_command>
     </xml>
     <xml name="vocdir_input">
-        <conditional name="vocdir_option">
+        <conditional name="voc_source">
             <param name="choice" type="select"
-                   label="Source of YAML files with definition of the variant of concerns"
-                   help="Cojac ships with a directory with variant definitions yaml files (https://github.com/cbg-ethz/cojac/tree/master/voc), which the tool can access internally. You can also download the latest version of the yaml files from https://github.com/phe-genomics/variant_definitions and use it as a custom yamls defining the variant of concerns.">
-                <option value="cache">Definitions shipped with the tool (can be outdated)</option>
-                <option value="custom">From history</option>
+                   label="Source of lineage definitions"
+                   help="Cojac detects lineage evidence based on lineage mutation patterns deined in tool-specific yaml format. You can choose between the (possibly outdated) definitions shipped with the tool or definitions provided as a collection of yaml datasets in your history. See the tool help below for more details.">
+                <option value="builtin">Lineage definitions shipped with the tool</option>
+                <option value="custom">YAML dataset collection in history</option>
             </param>
-            <when value="cache"/>
+            <when value="builtin"/>
             <when value="custom">
-                <param name="voc_file" type="data" format="yaml" multiple="true"
-                       label="YAML defining the variant of concern"/>
+                <param name="collection" type="data_collection" collection_type="list" format="yaml" label="Collection of lineage definitions" />
             </when>
         </conditional>
     </xml>
     <token name="@VOCDIR_COMMAND@"><![CDATA[
-#if $vocdir_option.choice == 'custom'
-    #set vocdir = 'voc/'
-    #set file_paths1 = []
+#if $voc_config.choice == 'custom'
     mkdir -p voc &&
-    #for $input_file in $voc_file
-        #set $file_path = $vocdir + $input_file.element_identifier
-        ln -s '$input_file' '$file_path' &&
-        $file_paths1.append($file_path)
+    #for $input_file in $voc_config.collection
+        ln -s '$input_file' 'voc/$input_file.element_identifier' &&
     #end for
 #else
-    DB_PATH="\$(dirname "\$(dirname "\$(which cooc-mutbamscan)")")/share/cojac" &&
-    ln -s "\$DB_PATH" db &&
-    #set $vocdir = 'db/voc'
+    DB_PATH="\$(dirname "\$(dirname "\$(which cojac)")")/share/cojac/voc" &&
+    ln -s "\$DB_PATH" voc &&
 #end if
 ]]></token>
     <token name="@HELP_HEADER@"><![CDATA[
@@ -59,4 +53,4 @@
             <citation type="doi">10.1101/2021.01.08.21249379</citation>
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r 373c1735d31f -r 9f1660129403 test-data/ampl_info.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ampl_info.tsv	Mon Jul 31 15:23:23 2023 +0000
@@ -0,0 +1,99 @@
+SARS-CoV-2_1_LEFT	SARS-CoV-2_1_RIGHT
+SARS-CoV-2_2_LEFT	SARS-CoV-2_2_RIGHT
+SARS-CoV-2_3_LEFT	SARS-CoV-2_3_RIGHT
+SARS-CoV-2_4_LEFT	SARS-CoV-2_4_RIGHT
+SARS-CoV-2_5_LEFT	SARS-CoV-2_5_RIGHT
+SARS-CoV-2_6_LEFT	SARS-CoV-2_6_RIGHT
+SARS-CoV-2_7_LEFT	SARS-CoV-2_7_RIGHT
+SARS-CoV-2_8_LEFT	SARS-CoV-2_8_RIGHT
+SARS-CoV-2_9_LEFT	SARS-CoV-2_9_RIGHT
+SARS-CoV-2_10_LEFT	SARS-CoV-2_10_RIGHT
+SARS-CoV-2_11_LEFT	SARS-CoV-2_11_RIGHT
+SARS-CoV-2_12_LEFT	SARS-CoV-2_12_RIGHT
+SARS-CoV-2_13_LEFT	SARS-CoV-2_13_RIGHT
+SARS-CoV-2_14_LEFT	SARS-CoV-2_14_RIGHT
+SARS-CoV-2_15_LEFT	SARS-CoV-2_15_RIGHT
+SARS-CoV-2_16_LEFT	SARS-CoV-2_16_RIGHT
+SARS-CoV-2_17_LEFT	SARS-CoV-2_17_RIGHT
+SARS-CoV-2_18_LEFT	SARS-CoV-2_18_RIGHT
+SARS-CoV-2_19_LEFT	SARS-CoV-2_19_RIGHT
+SARS-CoV-2_20_LEFT	SARS-CoV-2_20_RIGHT
+SARS-CoV-2_21_LEFT	SARS-CoV-2_21_RIGHT
+SARS-CoV-2_22_LEFT	SARS-CoV-2_22_RIGHT
+SARS-CoV-2_23_LEFT	SARS-CoV-2_23_RIGHT
+SARS-CoV-2_24_LEFT	SARS-CoV-2_24_RIGHT
+SARS-CoV-2_25_LEFT	SARS-CoV-2_25_RIGHT
+SARS-CoV-2_26_LEFT	SARS-CoV-2_26_RIGHT
+SARS-CoV-2_27_LEFT	SARS-CoV-2_27_RIGHT
+SARS-CoV-2_28_LEFT	SARS-CoV-2_28_RIGHT
+SARS-CoV-2_29_LEFT	SARS-CoV-2_29_RIGHT
+SARS-CoV-2_30_LEFT	SARS-CoV-2_30_RIGHT
+SARS-CoV-2_31_LEFT	SARS-CoV-2_31_RIGHT
+SARS-CoV-2_32_LEFT	SARS-CoV-2_32_RIGHT
+SARS-CoV-2_33_LEFT	SARS-CoV-2_33_RIGHT
+SARS-CoV-2_34_LEFT	SARS-CoV-2_34_RIGHT
+SARS-CoV-2_35_LEFT	SARS-CoV-2_35_RIGHT
+SARS-CoV-2_36_LEFT	SARS-CoV-2_36_RIGHT
+SARS-CoV-2_37_LEFT	SARS-CoV-2_37_RIGHT
+SARS-CoV-2_38_LEFT	SARS-CoV-2_38_RIGHT
+SARS-CoV-2_39_LEFT	SARS-CoV-2_39_RIGHT
+SARS-CoV-2_40_LEFT	SARS-CoV-2_40_RIGHT
+SARS-CoV-2_41_LEFT	SARS-CoV-2_41_RIGHT
+SARS-CoV-2_42_LEFT	SARS-CoV-2_42_RIGHT
+SARS-CoV-2_43_LEFT	SARS-CoV-2_43_RIGHT
+SARS-CoV-2_44_LEFT	SARS-CoV-2_44_RIGHT
+SARS-CoV-2_45_LEFT	SARS-CoV-2_45_RIGHT
+SARS-CoV-2_46_LEFT	SARS-CoV-2_46_RIGHT
+SARS-CoV-2_47_LEFT	SARS-CoV-2_47_RIGHT
+SARS-CoV-2_48_LEFT	SARS-CoV-2_48_RIGHT
+SARS-CoV-2_49_LEFT	SARS-CoV-2_49_RIGHT
+SARS-CoV-2_50_LEFT	SARS-CoV-2_50_RIGHT
+SARS-CoV-2_51_LEFT	SARS-CoV-2_51_RIGHT
+SARS-CoV-2_52_LEFT	SARS-CoV-2_52_RIGHT
+SARS-CoV-2_53_LEFT	SARS-CoV-2_53_RIGHT
+SARS-CoV-2_54_LEFT	SARS-CoV-2_54_RIGHT
+SARS-CoV-2_55_LEFT	SARS-CoV-2_55_RIGHT
+SARS-CoV-2_56_LEFT	SARS-CoV-2_56_RIGHT
+SARS-CoV-2_57_LEFT	SARS-CoV-2_57_RIGHT
+SARS-CoV-2_58_LEFT	SARS-CoV-2_58_RIGHT
+SARS-CoV-2_59_LEFT	SARS-CoV-2_59_RIGHT
+SARS-CoV-2_60_LEFT	SARS-CoV-2_60_RIGHT
+SARS-CoV-2_61_LEFT	SARS-CoV-2_61_RIGHT
+SARS-CoV-2_62_LEFT	SARS-CoV-2_62_RIGHT
+SARS-CoV-2_63_LEFT	SARS-CoV-2_63_RIGHT
+SARS-CoV-2_64_LEFT	SARS-CoV-2_64_RIGHT
+SARS-CoV-2_65_LEFT	SARS-CoV-2_65_RIGHT
+SARS-CoV-2_66_LEFT	SARS-CoV-2_66_RIGHT
+SARS-CoV-2_67_LEFT	SARS-CoV-2_67_RIGHT
+SARS-CoV-2_68_LEFT	SARS-CoV-2_68_RIGHT
+SARS-CoV-2_69_LEFT	SARS-CoV-2_69_RIGHT
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diff -r 373c1735d31f -r 9f1660129403 test-data/bed_cojac.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_cojac.bed	Mon Jul 31 15:23:23 2023 +0000
@@ -0,0 +1,99 @@
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diff -r 373c1735d31f -r 9f1660129403 test-data/primers.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers.bed	Mon Jul 31 15:23:23 2023 +0000
@@ -0,0 +1,198 @@
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