Repository 'ivar_filtervariants'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants

Changeset 0:c88553ec696e (2020-03-30)
Next changeset 1:2b95d5c04908 (2020-04-04)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
added:
ivar_filtervariants.xml
macros.xml
test-data/covid19/ARTIC-V1.bed
test-data/covid19/NC_045512.fa
test-data/covid19/NC_045512.fa.amb
test-data/covid19/NC_045512.fa.ann
test-data/covid19/NC_045512.fa.bwt
test-data/covid19/NC_045512.fa.fai
test-data/covid19/NC_045512.fa.pac
test-data/covid19/NC_045512.fa.sa
test-data/covid19/PC00101P_sub.fa
test-data/covid19/PC00101P_sub.qual.txt
test-data/covid19/PC00101P_sub.sorted.bam
test-data/covid19/PC00101P_sub.sorted.bam.bai
test-data/covid19/PC00101P_sub.trimmed.bam
test-data/covid19/PC00101P_sub.trimmed.sorted.bam
test-data/covid19/PC00101P_sub.trimmed.sorted.bam.bai
test-data/covid19/PC00101P_variants.tsv
test-data/covid19/nCoV-2019.scheme.bed
test-data/covid19/primers_consensus.tsv
test-data/covid19/zika_primers.bam
test-data/covid19/zika_primers.bed
test-data/covid19/zika_primers.fa
test-data/covid19/zika_primers_consensus.bam
test-data/covid19/zika_primers_consensus.bed
test-data/zika/Z52.consensus.fa
test-data/zika/Z52.consensus.fa.fai
test-data/zika/Z52.consensus.qual.txt
test-data/zika/Z52.masked.sorted.depth
test-data/zika/Z52.merged.bam
test-data/zika/Z52.sorted.depth
test-data/zika/Z52.trimmed.sorted.depth
test-data/zika/Z52.tsv
test-data/zika/Z52_a.masked.bam
test-data/zika/Z52_a.masked.sorted.bam
test-data/zika/Z52_a.sorted.bam
test-data/zika/Z52_a.sorted.bam.bai
test-data/zika/Z52_a.trimmed.bam
test-data/zika/Z52_a.trimmed.sorted.bam
test-data/zika/Z52_a.trimmed.sorted.bam.bai
test-data/zika/Z52_a.tsv
test-data/zika/Z52_b.masked.bam
test-data/zika/Z52_b.masked.sorted.bam
test-data/zika/Z52_b.sorted.bam
test-data/zika/Z52_b.sorted.bam.bai
test-data/zika/Z52_b.trimmed.bam
test-data/zika/Z52_b.trimmed.sorted.bam
test-data/zika/Z52_b.trimmed.sorted.bam.bai
test-data/zika/Z52_b.tsv
test-data/zika/db/PRV.fa
test-data/zika/db/PRV.fa.amb
test-data/zika/db/PRV.fa.ann
test-data/zika/db/PRV.fa.bwt
test-data/zika/db/PRV.fa.fai
test-data/zika/db/PRV.fa.pac
test-data/zika/db/PRV.fa.sa
test-data/zika/db/Z52.consensus.amb
test-data/zika/db/Z52.consensus.ann
test-data/zika/db/Z52.consensus.bwt
test-data/zika/db/Z52.consensus.pac
test-data/zika/db/Z52.consensus.sa
test-data/zika/db/pair_information.tsv
test-data/zika/db/zika_primers.bam
test-data/zika/db/zika_primers.bed
test-data/zika/db/zika_primers.fa
test-data/zika/db/zika_primers_consensus.bam
test-data/zika/db/zika_primers_consensus.bed
test-data/zika/primer_mismatchers_indices.txt
test-data/zika/primers_Z52_consensus.tsv
b
diff -r 000000000000 -r c88553ec696e ivar_filtervariants.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ivar_filtervariants.xml Mon Mar 30 07:18:00 2020 -0400
[
@@ -0,0 +1,45 @@
+<tool id="ivar_filtervariants" name="ivar filtervariants" version="@VERSION@+galaxy0">
+    <description>Filter variants across replicates or multiple samples aligned using the same reference</description>
+        <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        #for $counter, $input in enumerate($inputs):
+            ln -s '$input' ./var_${counter}.tsv &&
+        #end for
+        ivar filtervariants 
+        -p filtered.tsv
+        #for $counter, $input in enumerate($inputs)
+            ./var_${counter}.tsv
+        #end for
+    ]]></command>
+    <inputs>
+        <param name="inputs" type="data" format="tabular" multiple="true" label="Variant tsv files for each replicate"/>
+    </inputs>
+    <outputs>
+        <data name="output_filtered" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="filtered.tsv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="zika/Z52_a.tsv,zika/Z52_b.tsv" ftype="tabular"/>
+            <output name="output_filtered" file="zika/Z52.tsv" ftype="tabular" lines_diff="10"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        iVar can be used to get an intersection of variants(in .tsv files) called
+        from any number of replicates or from different samples using the same
+        reference sequence. This intersection will filter out any iSNVs that do not
+        occur in a minimum fraction of the files supplied. This parameter can be
+        changed using the -t flag which range from 0 to 1 (default). Fields that are
+        different across replicates(fields apart from REGION, POS, REF, ALT,
+        REF_CODON, REF_AA, ALT_CODON, ALT_AA) will have the filename added as a
+        suffix. If there are a large number of files to be filtered, the -f flag can
+        be used to supply a text file with one sample/replicate variant .tsv file
+        per line.
+        
+        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
+    ]]></help>
+<expand macro="citations" />
+</tool>
b
diff -r 000000000000 -r c88553ec696e macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,18 @@
+<macros>
+  <token name="@VERSION@">1.0.1</token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@VERSION@">ivar</requirement>
+      <requirement type="package" version="1.9">samtools</requirement>
+      <yield />
+    </requirements>
+  </xml>
+  <xml name="version_command">
+    <version_command>ivar version | grep version</version_command>
+  </xml>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">10.1186/s13059-018-1618-7</citation>
+    </citations>
+  </xml>
+</macros>
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/ARTIC-V1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/ARTIC-V1.bed Mon Mar 30 07:18:00 2020 -0400
b
b'@@ -0,0 +1,196 @@\n+MN908947.3\t30\t54\tnCoV-2019_1_LEFT\t60\t+\n+MN908947.3\t385\t410\tnCoV-2019_1_RIGHT\t60\t-\n+MN908947.3\t320\t342\tnCoV-2019_2_LEFT\t60\t+\n+MN908947.3\t704\t726\tnCoV-2019_2_RIGHT\t60\t-\n+MN908947.3\t642\t664\tnCoV-2019_3_LEFT\t60\t+\n+MN908947.3\t1004\t1028\tnCoV-2019_3_RIGHT\t60\t-\n+MN908947.3\t943\t965\tnCoV-2019_4_LEFT\t60\t+\n+MN908947.3\t1312\t1337\tnCoV-2019_4_RIGHT\t60\t-\n+MN908947.3\t1242\t1264\tnCoV-2019_5_LEFT\t60\t+\n+MN908947.3\t1623\t1651\tnCoV-2019_5_RIGHT\t60\t-\n+MN908947.3\t1573\t1595\tnCoV-2019_6_LEFT\t60\t+\n+MN908947.3\t1942\t1964\tnCoV-2019_6_RIGHT\t60\t-\n+MN908947.3\t1875\t1897\tnCoV-2019_7_LEFT\t60\t+\n+MN908947.3\t2247\t2269\tnCoV-2019_7_RIGHT\t60\t-\n+MN908947.3\t2181\t2205\tnCoV-2019_8_LEFT\t60\t+\n+MN908947.3\t2568\t2592\tnCoV-2019_8_RIGHT\t60\t-\n+MN908947.3\t2505\t2529\tnCoV-2019_9_LEFT\t60\t+\n+MN908947.3\t2882\t2904\tnCoV-2019_9_RIGHT\t60\t-\n+MN908947.3\t2826\t2850\tnCoV-2019_10_LEFT\t60\t+\n+MN908947.3\t3183\t3210\tnCoV-2019_10_RIGHT\t60\t-\n+MN908947.3\t3144\t3166\tnCoV-2019_11_LEFT\t60\t+\n+MN908947.3\t3507\t3531\tnCoV-2019_11_RIGHT\t60\t-\n+MN908947.3\t3460\t3482\tnCoV-2019_12_LEFT\t60\t+\n+MN908947.3\t3826\t3853\tnCoV-2019_12_RIGHT\t60\t-\n+MN908947.3\t3771\t3795\tnCoV-2019_13_LEFT\t60\t+\n+MN908947.3\t4142\t4164\tnCoV-2019_13_RIGHT\t60\t-\n+MN908947.3\t4054\t4077\tnCoV-2019_14_LEFT\t60\t+\n+MN908947.3\t4428\t4450\tnCoV-2019_14_RIGHT\t60\t-\n+MN908947.3\t4294\t4321\tnCoV-2019_15_LEFT\t60\t+\n+MN908947.3\t4674\t4696\tnCoV-2019_15_RIGHT\t60\t-\n+MN908947.3\t4636\t4658\tnCoV-2019_16_LEFT\t60\t+\n+MN908947.3\t4995\t5017\tnCoV-2019_16_RIGHT\t60\t-\n+MN908947.3\t4939\t4966\tnCoV-2019_17_LEFT\t60\t+\n+MN908947.3\t5296\t5321\tnCoV-2019_17_RIGHT\t60\t-\n+MN908947.3\t5230\t5259\tnCoV-2019_18_LEFT\t60\t+\n+MN908947.3\t5620\t5644\tnCoV-2019_18_RIGHT\t60\t-\n+MN908947.3\t5563\t5586\tnCoV-2019_19_LEFT\t60\t+\n+MN908947.3\t5932\t5957\tnCoV-2019_19_RIGHT\t60\t-\n+MN908947.3\t5867\t5894\tnCoV-2019_20_LEFT\t60\t+\n+MN908947.3\t6247\t6272\tnCoV-2019_20_RIGHT\t60\t-\n+MN908947.3\t6167\t6196\tnCoV-2019_21_LEFT\t60\t+\n+MN908947.3\t6528\t6550\tnCoV-2019_21_RIGHT\t60\t-\n+MN908947.3\t6466\t6495\tnCoV-2019_22_LEFT\t60\t+\n+MN908947.3\t6846\t6873\tnCoV-2019_22_RIGHT\t60\t-\n+MN908947.3\t6718\t6745\tnCoV-2019_23_LEFT\t60\t+\n+MN908947.3\t7092\t7117\tnCoV-2019_23_RIGHT\t60\t-\n+MN908947.3\t7035\t7058\tnCoV-2019_24_LEFT\t60\t+\n+MN908947.3\t7389\t7415\tnCoV-2019_24_RIGHT\t60\t-\n+MN908947.3\t7305\t7332\tnCoV-2019_25_LEFT\t60\t+\n+MN908947.3\t7671\t7694\tnCoV-2019_25_RIGHT\t60\t-\n+MN908947.3\t7626\t7651\tnCoV-2019_26_LEFT\t60\t+\n+MN908947.3\t7997\t8019\tnCoV-2019_26_RIGHT\t60\t-\n+MN908947.3\t7943\t7968\tnCoV-2019_27_LEFT\t60\t+\n+MN908947.3\t8319\t8341\tnCoV-2019_27_RIGHT\t60\t-\n+MN908947.3\t8249\t8275\tnCoV-2019_28_LEFT\t60\t+\n+MN908947.3\t8635\t8661\tnCoV-2019_28_RIGHT\t60\t-\n+MN908947.3\t8595\t8619\tnCoV-2019_29_LEFT\t60\t+\n+MN908947.3\t8954\t8983\tnCoV-2019_29_RIGHT\t60\t-\n+MN908947.3\t8888\t8913\tnCoV-2019_30_LEFT\t60\t+\n+MN908947.3\t9245\t9271\tnCoV-2019_30_RIGHT\t60\t-\n+MN908947.3\t9204\t9226\tnCoV-2019_31_LEFT\t60\t+\n+MN908947.3\t9557\t9585\tnCoV-2019_31_RIGHT\t60\t-\n+MN908947.3\t9477\t9502\tnCoV-2019_32_LEFT\t60\t+\n+MN908947.3\t9834\t9858\tnCoV-2019_32_RIGHT\t60\t-\n+MN908947.3\t9784\t9806\tnCoV-2019_33_LEFT\t60\t+\n+MN908947.3\t10146\t10171\tnCoV-2019_33_RIGHT\t60\t-\n+MN908947.3\t10076\t10099\tnCoV-2019_34_LEFT\t60\t+\n+MN908947.3\t10437\t10459\tnCoV-2019_34_RIGHT\t60\t-\n+MN908947.3\t10362\t10384\tnCoV-2019_35_LEFT\t60\t+\n+MN908947.3\t10737\t10763\tnCoV-2019_35_RIGHT\t60\t-\n+MN908947.3\t10666\t10688\tnCoV-2019_36_LEFT\t60\t+\n+MN908947.3\t11048\t11074\tnCoV-2019_36_RIGHT\t60\t-\n+MN908947.3\t10999\t11022\tnCoV-2019_37_LEFT\t60\t+\n+MN908947.3\t11372\t11394\tnCoV-2019_37_RIGHT\t60\t-\n+MN908947.3\t11306\t11331\tnCoV-2019_38_LEFT\t60\t+\n+MN908947.3\t11668\t11693\tnCoV-2019_38_RIGHT\t60\t-\n+MN908947.3\t11555\t11584\tnCoV-2019_39_LEFT\t60\t+\n+MN908947.3\t11927\t11949\tnCoV-2019_39_RIGHT\t60\t-\n+MN908947.3\t11863\t11889\tnCoV-2019_40_LEFT\t60\t+\n+MN908947.3\t12234\t12256\tnCoV-2019_40_RIGHT\t60\t-\n+MN908947.3\t12110\t12133\tnCoV-2019_41_LEFT\t60\t+\n+MN908947.3\t12465\t12490\tnCoV-2019_41_RIGHT\t60\t-\n+MN908947.3\t12417\t12439\tnCoV-2019_42_LEFT\t60\t+\n+MN908947.3\t12779\t12802\tnCoV-2019_42_RIGHT\t60\t-\n+MN908947.3\t12710\t12732\tnCoV-2019_43_LEFT\t60\t+\n+MN908947.3\t13074\t13096\tnCoV-2019_43_RIGHT\t60\t-\n+MN908947.3\t13005\t13027\tnCoV-2019_44_LEFT\t60\t+\n+MN908947.3'..b'GHT\t60\t-\n+MN908947.3\t17065\t17087\tnCoV-2019_57_LEFT\t60\t+\n+MN908947.3\t17430\t17452\tnCoV-2019_57_RIGHT\t60\t-\n+MN908947.3\t17381\t17406\tnCoV-2019_58_LEFT\t60\t+\n+MN908947.3\t17738\t17761\tnCoV-2019_58_RIGHT\t60\t-\n+MN908947.3\t17674\t17697\tnCoV-2019_59_LEFT\t60\t+\n+MN908947.3\t18036\t18062\tnCoV-2019_59_RIGHT\t60\t-\n+MN908947.3\t17966\t17993\tnCoV-2019_60_LEFT\t60\t+\n+MN908947.3\t18324\t18348\tnCoV-2019_60_RIGHT\t60\t-\n+MN908947.3\t18253\t18275\tnCoV-2019_61_LEFT\t60\t+\n+MN908947.3\t18650\t18672\tnCoV-2019_61_RIGHT\t60\t-\n+MN908947.3\t18596\t18618\tnCoV-2019_62_LEFT\t60\t+\n+MN908947.3\t18957\t18979\tnCoV-2019_62_RIGHT\t60\t-\n+MN908947.3\t18896\t18918\tnCoV-2019_63_LEFT\t60\t+\n+MN908947.3\t19275\t19297\tnCoV-2019_63_RIGHT\t60\t-\n+MN908947.3\t19204\t19232\tnCoV-2019_64_LEFT\t60\t+\n+MN908947.3\t19591\t19616\tnCoV-2019_64_RIGHT\t60\t-\n+MN908947.3\t19548\t19570\tnCoV-2019_65_LEFT\t60\t+\n+MN908947.3\t19911\t19939\tnCoV-2019_65_RIGHT\t60\t-\n+MN908947.3\t19844\t19866\tnCoV-2019_66_LEFT\t60\t+\n+MN908947.3\t20231\t20255\tnCoV-2019_66_RIGHT\t60\t-\n+MN908947.3\t20172\t20200\tnCoV-2019_67_LEFT\t60\t+\n+MN908947.3\t20542\t20572\tnCoV-2019_67_RIGHT\t60\t-\n+MN908947.3\t20472\t20496\tnCoV-2019_68_LEFT\t60\t+\n+MN908947.3\t20867\t20890\tnCoV-2019_68_RIGHT\t60\t-\n+MN908947.3\t20786\t20813\tnCoV-2019_69_LEFT\t60\t+\n+MN908947.3\t21146\t21169\tnCoV-2019_69_RIGHT\t60\t-\n+MN908947.3\t21075\t21104\tnCoV-2019_70_LEFT\t60\t+\n+MN908947.3\t21427\t21455\tnCoV-2019_70_RIGHT\t60\t-\n+MN908947.3\t21357\t21386\tnCoV-2019_71_LEFT\t60\t+\n+MN908947.3\t21716\t21743\tnCoV-2019_71_RIGHT\t60\t-\n+MN908947.3\t21658\t21682\tnCoV-2019_72_LEFT\t60\t+\n+MN908947.3\t22013\t22038\tnCoV-2019_72_RIGHT\t60\t-\n+MN908947.3\t21961\t21990\tnCoV-2019_73_LEFT\t60\t+\n+MN908947.3\t22324\t22346\tnCoV-2019_73_RIGHT\t60\t-\n+MN908947.3\t22262\t22290\tnCoV-2019_74_LEFT\t60\t+\n+MN908947.3\t22626\t22650\tnCoV-2019_74_RIGHT\t60\t-\n+MN908947.3\t22516\t22542\tnCoV-2019_75_LEFT\t60\t+\n+MN908947.3\t22877\t22903\tnCoV-2019_75_RIGHT\t60\t-\n+MN908947.3\t22797\t22819\tnCoV-2019_76_LEFT\t60\t+\n+MN908947.3\t23192\t23214\tnCoV-2019_76_RIGHT\t60\t-\n+MN908947.3\t23122\t23144\tnCoV-2019_77_LEFT\t60\t+\n+MN908947.3\t23500\t23522\tnCoV-2019_77_RIGHT\t60\t-\n+MN908947.3\t23443\t23466\tnCoV-2019_78_LEFT\t60\t+\n+MN908947.3\t23822\t23847\tnCoV-2019_78_RIGHT\t60\t-\n+MN908947.3\t23789\t23812\tnCoV-2019_79_LEFT\t60\t+\n+MN908947.3\t24145\t24169\tnCoV-2019_79_RIGHT\t60\t-\n+MN908947.3\t24078\t24100\tnCoV-2019_80_LEFT\t60\t+\n+MN908947.3\t24443\t24467\tnCoV-2019_80_RIGHT\t60\t-\n+MN908947.3\t24391\t24416\tnCoV-2019_81_LEFT\t60\t+\n+MN908947.3\t24765\t24789\tnCoV-2019_81_RIGHT\t60\t-\n+MN908947.3\t24696\t24721\tnCoV-2019_82_LEFT\t60\t+\n+MN908947.3\t25052\t25076\tnCoV-2019_82_RIGHT\t60\t-\n+MN908947.3\t24978\t25003\tnCoV-2019_83_LEFT\t60\t+\n+MN908947.3\t25347\t25369\tnCoV-2019_83_RIGHT\t60\t-\n+MN908947.3\t25279\t25301\tnCoV-2019_84_LEFT\t60\t+\n+MN908947.3\t25646\t25673\tnCoV-2019_84_RIGHT\t60\t-\n+MN908947.3\t25601\t25623\tnCoV-2019_85_LEFT\t60\t+\n+MN908947.3\t25969\t25994\tnCoV-2019_85_RIGHT\t60\t-\n+MN908947.3\t25902\t25924\tnCoV-2019_86_LEFT\t60\t+\n+MN908947.3\t26290\t26315\tnCoV-2019_86_RIGHT\t60\t-\n+MN908947.3\t26197\t26219\tnCoV-2019_87_LEFT\t60\t+\n+MN908947.3\t26566\t26590\tnCoV-2019_87_RIGHT\t60\t-\n+MN908947.3\t26520\t26542\tnCoV-2019_88_LEFT\t60\t+\n+MN908947.3\t26890\t26913\tnCoV-2019_88_RIGHT\t60\t-\n+MN908947.3\t26835\t26857\tnCoV-2019_89_LEFT\t60\t+\n+MN908947.3\t27202\t27227\tnCoV-2019_89_RIGHT\t60\t-\n+MN908947.3\t27141\t27164\tnCoV-2019_90_LEFT\t60\t+\n+MN908947.3\t27511\t27533\tnCoV-2019_90_RIGHT\t60\t-\n+MN908947.3\t27446\t27471\tnCoV-2019_91_LEFT\t60\t+\n+MN908947.3\t27825\t27854\tnCoV-2019_91_RIGHT\t60\t-\n+MN908947.3\t27784\t27808\tnCoV-2019_92_LEFT\t60\t+\n+MN908947.3\t28145\t28172\tnCoV-2019_92_RIGHT\t60\t-\n+MN908947.3\t28081\t28104\tnCoV-2019_93_LEFT\t60\t+\n+MN908947.3\t28442\t28464\tnCoV-2019_93_RIGHT\t60\t-\n+MN908947.3\t28394\t28416\tnCoV-2019_94_LEFT\t60\t+\n+MN908947.3\t28756\t28779\tnCoV-2019_94_RIGHT\t60\t-\n+MN908947.3\t28677\t28699\tnCoV-2019_95_LEFT\t60\t+\n+MN908947.3\t29041\t29063\tnCoV-2019_95_RIGHT\t60\t-\n+MN908947.3\t28985\t29007\tnCoV-2019_96_LEFT\t60\t+\n+MN908947.3\t29356\t29378\tnCoV-2019_96_RIGHT\t60\t-\n+MN908947.3\t29288\t29316\tnCoV-2019_97_LEFT\t60\t+\n+MN908947.3\t29665\t29693\tnCoV-2019_97_RIGHT\t60\t-\n+MN908947.3\t29486\t29510\tnCoV-2019_98_LEFT\t60\t+\n+MN908947.3\t29836\t29866\tnCoV-2019_98_RIGHT\t60\t-\n'
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/NC_045512.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/NC_045512.fa Mon Mar 30 07:18:00 2020 -0400
b
b'@@ -0,0 +1,430 @@\n+>NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome\n+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA\n+CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC\n+TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG\n+TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC\n+CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC\n+GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG\n+CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT\n+GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC\n+GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT\n+TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA\n+GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG\n+TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG\n+CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG\n+TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG\n+CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA\n+ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA\n+CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC\n+CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA\n+GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT\n+ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG\n+GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG\n+CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA\n+CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA\n+ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA\n+GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT\n+TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG\n+GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG\n+TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC\n+GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG\n+ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG\n+GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT\n+AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA\n+TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT\n+AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA\n+GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC\n+TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT\n+AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA\n+GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT\n+ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA\n+GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT\n+GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA\n+ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC\n+ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA\n+TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG\n+AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT\n+TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA\n+CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC\n+AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT\n+AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA\n+GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA\n+CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG\n+TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT\n+GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT\n+TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCA'..b'GACTATTACCAGCTGTACTCA\n+ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC\n+CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT\n+TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC\n+TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT\n+TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT\n+GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT\n+CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA\n+TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC\n+CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA\n+AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT\n+AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC\n+ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC\n+TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT\n+GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA\n+GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG\n+ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG\n+CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC\n+TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA\n+AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC\n+CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA\n+GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA\n+TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT\n+TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT\n+GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT\n+ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG\n+CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA\n+GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG\n+TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC\n+GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA\n+TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT\n+GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA\n+AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG\n+ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG\n+TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT\n+GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC\n+CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG\n+TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT\n+GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA\n+AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC\n+ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT\n+AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA\n+ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG\n+TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG\n+CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC\n+AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA\n+ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG\n+TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC\n+TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC\n+TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT\n+TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG\n+CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT\n+GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT\n+TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC\n+GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT\n+TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAA\n+\n'
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/NC_045512.fa.amb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/NC_045512.fa.amb Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,1 @@
+29903 1 0
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/NC_045512.fa.ann
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/NC_045512.fa.ann Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,3 @@
+29903 1 11
+0 NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
+0 29903 0
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/NC_045512.fa.bwt
b
Binary file test-data/covid19/NC_045512.fa.bwt has changed
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/NC_045512.fa.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/NC_045512.fa.fai Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,1 @@
+NC_045512.2 29903 97 70 71
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/NC_045512.fa.pac
b
Binary file test-data/covid19/NC_045512.fa.pac has changed
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/NC_045512.fa.sa
b
Binary file test-data/covid19/NC_045512.fa.sa has changed
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/PC00101P_sub.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/PC00101P_sub.fa Mon Mar 30 07:18:00 2020 -0400
b
b'@@ -0,0 +1,2 @@\n+>Consensus_PC00101P_sub_threshold_0.6_quality_20\n+NNNNNNNNNNNNNNNNNCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTTTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAATGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGTGAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTAAACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAA'..b'TAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATNNNNNNNNNNNGAGCCTAAAAANNACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATNTCACATNNNNNNNNNNNNNNNNNNNNNAACATTAGGGAGGACTTGAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n'
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/PC00101P_sub.qual.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/PC00101P_sub.qual.txt Mon Mar 30 07:18:00 2020 -0400
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diff -r 000000000000 -r c88553ec696e test-data/covid19/PC00101P_sub.sorted.bam
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diff -r 000000000000 -r c88553ec696e test-data/covid19/PC00101P_sub.sorted.bam.bai
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diff -r 000000000000 -r c88553ec696e test-data/covid19/PC00101P_sub.trimmed.bam
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diff -r 000000000000 -r c88553ec696e test-data/covid19/PC00101P_variants.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/PC00101P_variants.tsv Mon Mar 30 07:18:00 2020 -0400
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+REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS
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+NC_045512.2 28424 T C 23 0 36 1 0 38 0.0416667 24 0.5 FALSE
+NC_045512.2 29377 T -A 14 13 38 1 0 20 0.0714286 14 0.535714 FALSE
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diff -r 000000000000 -r c88553ec696e test-data/covid19/nCoV-2019.scheme.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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b
diff -r 000000000000 -r c88553ec696e test-data/covid19/primers_consensus.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/primers_consensus.tsv Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,1 @@
+REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/zika_primers.bam
b
Binary file test-data/covid19/zika_primers.bam has changed
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/zika_primers.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/zika_primers.bed Mon Mar 30 07:18:00 2020 -0400
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+NC_045512.2 3144 3153 400_31_out_L 0 +
+NC_045512.2 27186 27199 400_31_out_R 0 +
+NC_045512.2 16494 16503 400_31_out_R 0 -
+NC_045512.2 22565 22576 400_32_out_L 0 -
+NC_045512.2 14948 14958 400_32_out_L 0 -
+NC_045512.2 10089 10101 400_32_out_R 0 +
+NC_045512.2 26251 26261 400_33_out_L* 0 -
+NC_045512.2 9642 9650 400_33_out_L* 0 +
+NC_045512.2 28807 28815 400_33_out_L* 0 +
+NC_045512.2 11383 11394 400_33_out_R* 0 -
+NC_045512.2 8948 8962 400_33_out_R* 0 +
+NC_045512.2 2507 2516 400_34_out_L* 0 +
+NC_045512.2 11229 11239 400_34_out_R* 0 -
+NC_045512.2 3611 3619 400_34_out_R* 0 -
+NC_045512.2 17081 17090 400_35_out_L 1 +
+NC_045512.2 27497 27508 400_35_out_R 0 +
+NC_045512.2 21585 21595 400_35_out_R 0 +
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/zika_primers.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covid19/zika_primers.fa Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,140 @@
+>400_1_out_L
+GACAGTTCGAGTTTGAAGCGAAAG
+>400_1_out_R
+AGTATGCACTCCCACGTCTAGT
+>400_2_out_L
+AAGAAAGATCTGGCTGCCATGC
+>400_2_out_R
+TGATTCCAACCAGGTTTGCGAC
+>400_3_out_L*
+AGATGACGTCGATTGTTGGTGC
+>400_3_out_R*
+TACGGTGACACAACCTCCATGT
+>400_4_out_L
+TCAGGTGCATAGGAGTCAGCAA
+>400_4_out_R
+GGAGCCATGAACTGACAGCATT
+>400_5_out_L
+AGAACGTTAGTGGACAGAGGCT
+>400_5_out_R
+TGTGCGTCCTTGAACTCTACCA
+>400_6_out_L
+TTGATTGTGAACCGAGGACAGG
+>400_6_out_R
+CCATCTGTCCCTGCGTACTGTA
+>400_7_out_L
+TGAAGGGCGTGTCATACTCCTT
+>400_7_out_R
+CGCCTCCAACTGATCCAAAGTC
+>400_8_out_L*
+GGGAGAAGAAGATCACCCACCA
+>400_8_out_R*
+TTGACTGCTGCTGCCAATCTAC
+>400_9_out_L*
+GCCTTAGGGGGAGTGTTGATCT
+>400_9_out_R*
+GAGTGGGCATTCCTTCAGTGTG
+>400_10_out_L
+ACGGTCGTTGTGGGATCTGTAA
+>400_10_out_R
+GTGGGACTTTGGCCATTCACAT
+>400_11_out_L
+CAGCCGTTATTGGAACAGCTGT
+>400_11_out_R
+CCTGGGCCTTATCTCCATTCCA
+>400_12_out_L
+CACTAAGGTCCACGTGGAGGAA
+>400_12_out_R
+TATCAGCGCCAGATGAGCTACA
+>400_13_out_L
+TGGCAGTGCTGGTAGCTATGAT
+>400_13_out_R
+AGAGAGAGGAGCATAAACCCCC
+>400_14_out_L*
+CAATGGTTTTGCTTTGGCCTGG
+>400_14_out_R*
+TTTCCCATGTGATGTCACCTGC
+>400_15_out_L
+CCCTAGCGAAGTACTCACAGCT
+>400_15_out_R
+TACACTCCATCTGTGGTCTCCC
+>400_16_out_L*
+GTGGCATGAACCCAATAGCCAT
+>400_16_out_R*
+GCTCCAATGTCCCCATCCTTTG
+>400_17_out_L**
+GTGGTCCATGGAAGCTAGATGC
+>400_17_out_R**
+CCTCTAAGGGCCTCCTCCATTT
+>400_18_out_L**
+CTGTTGAGTGCTTCGAGCCTTC
+>400_18_out_R**
+TGGTGAGTTGGAGTCCGGAAAT
+>400_19_out_L
+TATGGATGAGGCCCACTTCACA
+>400_19_out_R
+GCCATCAAGTATGACCGGCTTT
+>400_20_out_L*
+GGCTGGAAAACGGGTCATACAG
+>400_20_out_R*
+CCTTTGCTCCGTCCTAAGCTTG
+>400_21_out_L*
+AGAGACTGACGAAGACCATGCA
+>400_21_out_R*
+CTCCAAAAGCCGCTCCTCTTTT
+>400_22_out_L**
+TGGACCAGACACGGAGAGAAAA
+>400_22_out_R**
+ATTCTGGCTGGCTCAATTTCCG
+>400_23_out_L
+CGTCTTGATGAGGAACAAGGGC
+>400_23_out_R
+AAGTGGTCACTGCATGTTGGAC
+>400_24_out_L**
+TAATGGGAAGGAGAGAGGAGGG
+>400_24_out_R**
+TCTCCACTTGGGGGTCAATTGT
+>400_25_out_L**
+CCCTGACCCTAATAGTGGCCAT
+>400_25_out_R**
+CCTTCCATTTCTCTCCCAGGGT
+>400_26_out_L
+ACTGGAACTCCTCTACAGCCAC
+>400_26_out_R
+ACCAGGGCCTCCTTTTGTGTAT
+>400_27_out_L
+AGTGCAAAGCTGAGATGGTTGG
+>400_27_out_R
+ATGTGTAGAGTTGCGGGAGAGT
+>400_28_out_L
+GGTGGGGGATTGGCTTGAAAAA
+>400_28_out_R
+GGGCCTCATAGCTTCCATGGTA
+>400_29_out_L
+AGGATGTGAATCTCGGCTCTGG
+>400_29_out_R
+ATGCTGCATTGCTACGAACCTT
+>400_30_out_L
+AAAAGTGGACACTAGGGTGCCA
+>400_30_out_R
+TAATCCCAGCCCTTCAACACCA
+>400_31_out_L
+ACAAGGGGAATTTGGAAAGGCC
+>400_31_out_R
+CGTAAGTGACAACTTGTCCGCT
+>400_32_out_L
+AAATGGAAAAAGGGCACAGGGC
+>400_32_out_R
+TGTCCCATCCAGTTGAGGGTTT
+>400_33_out_L*
+CAAACGAATGGCAGTCAGTGGA
+>400_33_out_R*
+ATCCACACTCTGTTCCACACCA
+>400_34_out_L*
+ATTTCCACAGAAGGGACCTCCG
+>400_34_out_R*
+TGACTAGCAGGCCTGACAACAT
+>400_35_out_L
+ACCACCTGGGCTGAGAACATTA
+>400_35_out_R
+ACCACTAGTCCCTCTTCTGGAG
b
diff -r 000000000000 -r c88553ec696e test-data/covid19/zika_primers_consensus.bam
b
Binary file test-data/covid19/zika_primers_consensus.bam has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/Z52.consensus.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52.consensus.fa Mon Mar 30 07:18:00 2020 -0400
b
b'@@ -0,0 +1,2 @@\n+>Consensus_Z52.consensus_threshold_0_quality_20\n+CGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATCTGGCTGCCATGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACTAGTGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACAGAAACGATGCTGGGGAGGCCATATCTTTTCCAACCACATTGGGGATGAATAAGTGTTATATACAGATCATGGATCTTGGACACATGTGTGATGCCACCATGAGCTATGAATGCCCTATGCTGGATGAGGGGGTGGAACCAGATGACGTCGATTGTTGGTGCAACACGACGTCAACTTGGGTTGTGTACGGAACCTGCCATCACAAAAAAGGTGAAGCACGGAGATCTAGAAGAGCTGTGACGCTCCCCTCCCATTCCACCAGGAAGCTGCAAACGCGGTCGCAAACCTGGTTGGAATCAAGAGAATACACAAAGCACTTGATTAGAGTCGAAAATTGGATATTCAGGAACCCTGGCTTCGCGTTAGCAGCAGCTGCCATCGCTTGGCTTTTGGGAAGCTCAACGAGCCAAAAAGTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGCATCAGGTGCATAGGAGTCAGCAATAGGGACTTTGTGGAAGGTATGTCAGGTGGGACTTGGGTTGATGTTGTCTTGGAACATGGAGGTTGTGTCACCGTAATGGCACAGGACAAACCGACTGTCGACATAGAGCTGGTTACAACAACAGTCAGCAACATGGCGGAGGTAAGATCCTACTGCTATGAGGCATCAATATCAGACATGGCTTCTGACAGCCGCTGCCCAACACAAGGTGAAGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTGCAAAAGAACGTTAGTGGACAGAGGCTGGGGAAATGGATGTGGACTTTTTGGCAAAGGGAGCCTGGTGACATGCGCTAAGTTTGCATGCTCCAAGAAAATGACCGGGAAGAGCATCCAGCCAGAGAATCTGGAGTACCGGATAATGCTGTCAGTTCATGGCTCCCAGCACAGTGGGATGATCGTTAATGACACAGGACATGAAACTGATGAGAATAGAGCGAAAGTTGAGATAACGCCCAATTCACCGAGAGCCGAAGCCACCCTGGGGGGTTTTGGAAGCCTAGGACTTGATTGTGAACCGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTCACAAGGAGTGGTTCCACGACATTCCATTACCTTGGCACGCTGGGGCAGACACCGGAACTCCACACTGGAACAACAAAGAAGCACTGGTAGAGTTCAAGGACGCACATGCCAAAAGGCAAACTGTCGTGGTTCTAGGGAGTCAAGAAGGAGCAGTTCACACGGCCCTTGCTGGAGCTCTGGAGGCTGAGATGGATGGTGCAAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTGTCATACTCCTTGTGTACTGCAGCGTTCACATTCACCAAGATCCCGGCTGAAACACTGCACGGGACAGTCACAGTGGAGTTACAGTACGCAGGGACAGATGGACCTTGCAAGGTTCCAGCTCAGATGGCGGTGGACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTAATCACTGAAAGCACTGAGAACTCTAAGATGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAGAAGATCACCCACCACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGGCAGTCTTGGGAGACACAGCCTGGGACTTTGGATCAGTTGGAGGCGCTCTCAACTCATTGGGCAAGGGCATCCATCAAATTTTTGGAGCAGCTTTCAAATCATTGTTTGGAGGAATGTCCTGGTTCTCACAAATTCTCATTGGAACGTTGCTGATGTGGTTGGGTCTGAACACAAAGAATGGATCTATTTCCCTTATGTGCTTGGCCTTAGGGGGAGTGTTGATCTTCTTATCCACAGCCGTCTCTGCTGATGTGGGGTGCTCGGTGGACTTCTCAAAGAAGGAGACGAGATGCGGTACAGGGGTGTTCGTCTATAACGACGTTGAAGCCTGGAGGGACAGGTACAAGTACCATCCTGACTCCCCCCGTAGATTGGCAGCAGCAGTCAAGCAAGCCTGGGAAGATGGTATCTGCGGGATCTCCTCTGTTTCAAGAATGGAAAACATCATGTGGAGATCAGTAGAAGGGGAGCTCAACGCAATCCTGGAAGAGAATGGAGTTCAACTGACGGTCGTTGTGGGATCTGTAAAAAACCCCATGTGGAGAGGTCCACAGAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGCTGGAAGGCTTGGGGGAAATCGTATTTCGTCAGAGCAGCAAAGACAAATAACAGCTTTGTCGTGGATGGTGACACACTGAAGGAATGCCCACTCAAACATAGAGCATGGAACAGCTTTCTTGTGGAGGATCATGGGTTCGGGGTATTTCACACTAGTGTCTGGCTCAAGGTTAGAGAAGATTATTCATTAGAGTGTGATCCAGCCGTTATTGGAACAGCTGTTAAGGGAAAGGAGGCTGTACACAGTGATCTAGGCTACTGGATTGAGAGTGAGAAGAATGACACATGGAGGCTGAAGAGGGCCCATCTGATCGAGATGAAAACATGTGAATGGCCAAAGTCCCACACATTGTGGACAGATGGAATAGAAGAGAGTGATCTGATCATACCCAAGTCTTTAGCTGGGCCACTCAGCCATCACAATACCAGAGAGGGCTACAGGACCCAAATGAAAGGGCCATGGCACAGTGAAGAGCTTGAAATTCGGTTTGAGGAATGCCCAGGCACTAAGGTCCACGTGGAGGAAACATGTGGAACAAGAGGACCATCTCTGAGATCAACCACTGCAAGCGGAAGGGTGATCGAGGAATGGTGCTGCAGGGAGTGCACAATGCCCCCACTGTCGTTCCGGGCTAAAGATGGCTGTTGGTATGGAATGGAGATAAGGCCCAGGAAAGAACCAGAAAGCAACTTAGTAAGGTCAATGGTGACTGCAGGATCAACTGATCACATGGACCACTTCTCCCTTGGAGTGCTTGTGATCCTGCTCATGGTGCAGGAAGGGCTGAAGAAGAGAATGACCACAAAGATCATCATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAGGATTTTCAATGAGTGACCTGGCTAAGCTTGCAATTTTGATGGGTGCCACCTTCGCGGAAATGAACACTGGAGGAGATGTAGCTCATCTGGCGCTGATAGCGGCATTCAAAGTCAGACCAGCGTTGCTGGTATCTTTCATCTTCAGAGCTAATTGGACACCCCGTGAAAGCATGCTGCTGGCCTTGGCCTCGTGTCTTTTGCAAACTGCGATCTCCGCCTTGGAAGGCGACCTGATGGTTCTCATCAATGGTTTTGCTTTGGCCTGGTTGGCAATACGAGCGATGGTTGTTCCACGCACTGATAACATCACCTTGGCAATCCTGGCTGCTCTGACACCACTGGCCCGGGGCACACTGCTTGTGGCGTGGAGAGCAGGCCTTGCTACTTGCGGGGGGTTTATGCTCCTCTCTCTGAAGGGAAAAGGCAGTGTGAAGAAGAACTTACCATTTGTCATGGCCCTGGGACTAACCGCTGTGAGGCTGGTCGACCCCATCAACG'..b'GGATGGACGCCAGAGTTTGTTCAGATCATGCGGCCCTGAAGTCATTCAAGGAGTTTGCCGCTGGGAAAAGAGGAGCGGCTTTTGGAGTGATGGAAGCCCTGGGAACACTGCCAGGACACATGACAGAGAGATTCCAGGAAGCCATTGACAACCTCGCTGTGCTCATGCGGGCAGAGACTGGAAGCAGGCCTTACAAAGCCGCGG------------------------------------------------TGGGAACAGTCTCGCTGGGAATCTTCTTCGTCTTGATGAGGAACAAGGGCATAGGGAAGATGGGCTTTGGAATGGTGACTCTTGGGGCCAGCGCATGGCTCATGTGGCTCTCGGAAATTGAGCCAGCCAGAATTGCATGTGTCCTCATTGTTGTGTTCCTATTGCTGGTGGTGCTCATACCTGAGCCAGAAAAGCAAAGATCTCCCCAGGACAACCAAATGGCAATCATCATCATGGTAGCAGTAGGTCTTCTGGGCTTGATTACCGCCAATGAACTCGGATGGTTGGAGAGAACAAAGAGTGACCTAAGCCATCTAATGGGAAGGAGAGAGGAGGGGGCAACCATAGGATTCTCAATGGACATTGACCTGCGGCCAGCCTCAGCTTGGGCCATCTATGCTGCCTTGACAACTTTCATTACCCCAGCCGTCCAACATGCAGTGACCACCTCATACAACAACTACTCCTTAATGGCGATGGCCACGCAAGCTGGAGTGTTGTTTGGCATGGGCAAAGGGATGCCATTCTACGCATGGGACTTTGGAGTCCCGCTGCTAATGATAGGTTGCTACTCACAATTAACACCCCTGACCCTAATAGTGGCCATCATTTTGCTCGTGGCGCACTACATGTACTTGATCCCAGGGCTGCAGGCAGCAGCTGCGCGTGCTGCCCAGAAGAGAACGGCAGCTGGCATCATGAAGAACCCTGTTGTGGATGGAATAGTGGTGACTGACATTGACACAATGACAATTGACCCCCAAGTGGAGAAAAAGATGGGACAGGTGCTACTCATAGCAGTAGCCGTCTCCAGCGCCATACTGTCGCGGACCGCCTGGGGGTGGGGGGAGGCTGGGGCTCTGATCACAGCCGCAACTTCCACTTTGTGGGAAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACTTCACTGTGTAACATTTTTAGGGGAAGTTACTTGGCTGGAGCTTCTCTAATCTACACAGTAACAAGAAACGCTGGCTTGGTCAAGAGACGTGGGGGTGGAACAGGAGAGACCCTGGGAGAGAAATGGAAGGCCCGCTTGAACCAGATGTCGGCCCTGGAGTTCTACTCCTACAAAAAGTCAGGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATGCTGTGTCCCGAGGAAGTGCAAAGCTGAGATGGTTGGTGGAGCGGGGATACCTGCAGCCCTATGGAAAGGTCATTGATCTTGGATGTGGCAGAGGGGGCTGGAGTTACTACGTCGCCACCATCCGCAAAGTTCAAGAAGTGAAAGGATACACAAAAGGAGGCCCTGGTCATGAAGAACCCGTGTTGGTGCAAAGCTATGGGTGGAACATAGTCCGTCTTAAGAGTGGGGTGGACGTCTTTCATATGGCGGCTGAGCCGTGTGACACGTTGCTGTGTGACATAGGTGAGTCATCATCTAGTCCTGAAGTGGAAGAAGCACGGACGCTCAGAGTCCTCTCCATGGTGGGGGATTGGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGATGGAAACCCTGGAGCGACTGCAGCGTAGGTATGGGGGAGGACTGGTCAGAGTGCCACTCTCCCGCAACTCTACACATGAGATGTACTGGGTCTCTGGAGCGAAAAGCAACACCATAAAAAGTGTGTCCACCACGAGCCAGCTCCTCTTGGGGCGCATGGACGGGCCTAGGAGGCCAGTGAAATATGAGGAGGATGTGAATCTCGGCTCTGGCACGCGGGCTGTGGTAAGCTGCGCTGAAGCTCCCAACATGAAGATCATTGGTAACCGCATTGAAAGGATCCGCAGTGAGCACGCGGAAACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCACACAAGGGTCAGCGTCCTCTCTAATAAACGGGGTTGTCAGGCTCCTGTCAAAACCCTGGGATGTGGTGACTGGAGTCACAGGAATAGCCATGACCGACACCACACCGTATGGTCAGCAAAGAGTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGGTCTCTTCCTGGTTGTGGAAAGAGCTAGGCAAACACAAACGGCCACGAGTCTGCACCAAAGAAGAGTTCATCAACAAGGTTCGTAGCAATGCAGCATTAGGGGCAATATTTGAAGAGGAAAAAGAGTGGAAGACTGCAGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGAGAGTGCCAGAGCTGTGTGTACAACATGATGGGAAAAAGAGAAAAGAAACAAGGGGAATTTGGAAAGGCCAAGGGCAGCCGCGCCATCTGGTATATGTGGCTAGGGGCTAGATTTCTAGAGTTCGAAGCCCTTGGATTCTTGAACGAGGATCACTGGATGGGGAGAGAGAACTCAGGAGGTGGTGTTGAAGGGCTGGGATTACAAAGACTCGGATATGTCCTAGAAGAGATGAGTCGTATACCAGGAGGAAGGATGTATGCAGATGACACTGCTGGCTGGGACACCCGCATTAGCAGGTTTGATCTGGAGAATGAAGCTCTAATCACCAACCAAATGGAGAAAGGGCACAGGGCCTTGGCATTGGCCATAATCAAGTACACATACCAAAACAAAGTGGTAAAGGTCCTTAGACCAGCTGAAAAAGGGAAAACAGTTATGGACATTATTTCGAGACAAGACCAAAGGGGGAGCGGACAAGTTGTCACTTACGCTCTTAACACATTTACCAACCTAGTGGTGCAACTCATTCGGAATATGGAGGCTGAGGAAGTTCTAGAGATGCAAGACTTGTGGCTGCTGCGGAGGTCAGAGAAAGTGACCAACTGGTTGCAGAGCAACGGATGGGATAGGCTCAAACGAATGGCAGTCAGTGGAGATGATTGCGTTGTGAAGCCAATTGATGATAGGTTTGCACATGCCCTCAGGTTCTTGAATGATATGGGAAAAGTTAGGAAGGACACACAAGAGTGGAAACCCTCAACTGGATGGGACAACTGGGAAGAAGTTCCGTTTTGCTCCCACCACTTCAACAAGCTCCATCTCAAGGACGGGAGGTCCATTGTGGTTCCCTGCCGCCACCAAGATGAACTGATTGGCCGGGCCCGCGTCTCTCCAGGGGCGGGATGGAGCATCCGGGAGACTGCTTGCCTAGCAAAATCATATGCGCAAATGTGGCAGCTCCTTTATTTCCACAGAAGGGACCTCCGACTGATGGCCAATGCCATTTGTTCATCTGTGCCAGTTGACTGGGTTCCAACTGGGAGAACTACCTGGTCAATCCATGGAAAGGGAGAATGGATGACCACTGAAGACATGCTTGTGGTGTGGAACAGAGTGTGGATTGAGGAGAACGACCACATGGAAGACAAGACCCCAGTTACGAAATGGACAGACATTCCCTATTTGGGAAAAAGGGAAGACTTGTGGTGTGGATCTCTCATAGGGCACAGACCGCGCACCACCTGGGCTGAGAACATTAAAAACACAGTCAACATGGTGCGCAGGATCATAGGTGATGAAGAAAAGTACATGGACTACCTATCCACCCAAGTTCGCTACTTGGGTGAAGAAGGGTCTACACCTGGAGTGCTGTAAGCACCAATCTTA\n'
b
diff -r 000000000000 -r c88553ec696e test-data/zika/Z52.consensus.fa.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52.consensus.fa.fai Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,1 @@
+Consensus_Z52.consensus_threshold_0_quality_20 10139 48 10139 10140
b
diff -r 000000000000 -r c88553ec696e test-data/zika/Z52.consensus.qual.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52.consensus.qual.txt Mon Mar 30 07:18:00 2020 -0400
[
b'@@ -0,0 +1,1 @@\n+8:BBCBCAAAACCBCCA@BBACBCACDACC@@CDBBBCBBCBCCDDBBCCDBBEECDDCBDDEDDCBDDDDEEEEEFFFFEEEECDEDEFFEEDFFEFFFFFFEEDEFFEEEFEDDEEFFEFFEEFFFEFFEFFFFFEEFFFFFEEFFFEFFFEFFFFEFFEFFFFEFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFEEEEEFFFFFEEFEFFEFFFFFFFFEEFFEEEFEFEEEEEFEEEDEEEEEEEDEEEEEEEEEEEEEEDCDEEEDCD=ILPRTSUTTTUVVWVVVUUUWVWVUTUUWVWUUUUUUUTUTUMFEDDEDEEDDCEDEEDEDEEDDDDDEEEEDEEEEEDEEEEEEEEEEEEEEEEEEEEEEEFEEEEEEEEEDEFEEEEEEFEEFFEEFFFEFFFFFFFEFFFFEFFEEFFEFFEFFFFFFFFEFEEFEFFFFEFFEFFFFFEFEFFFFEFFFFEEEEEEEEEFEEFFFEFFFFFFFFFFFEFFFFFEFEEDEEFEEEEDEEDEEEEDEEEEDDEEEEJMOORRSQQQRSRSSRQTSRRTUVXVVUXVXXUTWWXWWYYYXWWWWWVWXUTTUVUUTTSUVTUUUTSSUUUTSRUVTTTTRQEEEEFEDDCCEEDECECDFFFFFEEEFFEFEEEEEFEEEEFEEEFFEFFFFFFFEEEEFFFFEFFFFFFEFFFFFFFFFFFFFFFEFFFFFFFFFFFFEEEFFFFEEFFFFFFFFFFFFFFFFFEFFFFEEFFFFFFFFFFFFFEFFFFFFEEEEFFFFFFEFFFFFEEFEFFFFFFEFFFEFEEEFFFFFEFEEEFEEFFEFFEEFFEFEEEFFFEEEEFFEFEEEEEEEEEEEEEEEDDEEEEEEFEDEEEEEPYYZ[ZZZX[[\\\\[[\\Z[[ZY[Z\\Z[[ZZYZYYZYYW[[[[ZYZ[YVWVWWVXWXWWXWWWWXWPFFEEEFEEEEDDDEFFEFFEEEFEFFEEEEEFFEEFFFEFFFEFEFFEFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFEFFFEEEFFFFFFFFEFFEEFFFFFFFFFFEFFFFEFFFFFFFEEFEFFFFFFEFEEEFEEEEFEEEEEEEEEEEEEEEEEEEEEEEEEDEEEEEEEEEECEEEEDDDDEEDDDDDEEEEDDDDDDDDDDEEEDDDDCDDBCCCCBDCDLMMMMMNMMNMMNMLLLMMNMNNOPPNLLKMLMMIDCBACADCCDDDDDEEEDEEEEEDDDEEEEEDEEEEEEEEEEEDEEEEEFEEEEDEFEEFEFFEEEFFEEEFFEFEFFEEFFFEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFEEEFEFEEEEEEEEEEEEFFFEFEEEEDFDEEDZ^\\_^_`^``^^__`aaa_`_aa_`a`a`_a``a_```^___^]]]]]]]]]\\IHGFFFFFFFFEEEDFFEFFFFFFFFEFFFFFFFFFFEEFFFEEEEEEFFFEFFFFFFEFFEFEEFFFFFFEFFFEEEEFEEEFFEEFFFEFFEFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFEFFEFFFFFFFFFEEEEFFFEEFEEFFFFFFFFFEFEFFEEFFEEFFEEFEEEEEEEEEFEEEEEEFEEEEEFWVXXYXZYZZ[[\\\\\\\\[[]]\\\\]\\[\\\\[]\\^]]^^]^\\\\]]]^]]\\]]]]\\\\[]\\[\\[]\\\\[[\\Z[\\ZZ[[ZZZZZYYYXWWXXWVWWVTTEEEDEEEFEDDEEEEEEFFEEEDEEFEFEFFFEFFEEEEEEEDEEEEFFFFEFFFFFEFFFFFFFEFEFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFEEEFFFEFFFEEFEFEEEFFEFEFFFFEFFFFFEEFFEEEFFFFFEFEFFEEFEEEEEEEFFFFFEEEFFFEEFEFEEEFFFEEFEDEDEEFEFEEEFFEEEEEDCEEFFFRXZYXXXYXXYYXYXVYZYYYYYTDEEDEEEEEEDEEEEDEEDECEEEEEEEEDEDEEEEDEEDEEDCEEEEEEEDEDEEEEEEDEEEEEEEEEEFEFEFEFFEEEFFFEEFFFFEEEFFEEEEEFFEEEDEEEEEEEEEEEEEEEEEEEEEEEEEEFFEEFFEEEEFEEEFEEEEFEEEEEEFEEEEEEEEEEFFEEEEEFEEEFEFEEEEEFFFEEFEEEEEEEEEEEDCDCEDDDEEDDEEDEEDDDDDDEDDDDDDEEDDDCCDEDCCDCDDCDAB@BACCCDDEBCBCCCDIHIJIHIHJIIHHHIJJLMLGAABDCCECCDCDDDBDBCADDBC@DCCCCDEEEECBDCEDEEDEDCCEEDCDCEEEDDDDDEEEEDDDDEEDEDFFEEEEFFEFEFEFEEEEEEEFEFEFEEEEFEEEFEEEEFFFFEEFFFEEEEEEEEEEEEFEDEEEEEEEEEEEEEFDEEEEEEEEEFFFEEEEEFFEFFEEEFFFEEEFFFEEEEEEFEEEEEEEDEEEFEEEEEEEEEEEEEEEEEEDEEEDEE]\\[[[\\ZY[[\\\\]][\\[[\\[Z[[[\\]][[[Z[\\XVXYY[[[WXXZZZZXYXZYXYYYYXXYYXWXWYXVTSSPFFEEFEEEFFEEEEEEEEEEEFFEEEEEEEEEEEEEEFFFFEFFFFFEFFEEFEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEFFEFFFEFFFFFFFFFFFFFFFFFFFFFFFFFEFFFEEEEEFFFFFFEFFEFFEFFFFFFFEFFEEFEFFEEFFFFEEEEEEEEEEEEEEEEEEEEDEEEEEEEEEEEEEEDEEDEEEEDEEEEEEDEDDDDEEEDEDEEDDECCDBCBDDDDDDCEDSQRSTSRQQRRSRQRSQSTSQPSSTTQOLEEDDEDCDDCEDCDBEDDEEEDCDCDEEEDDBEDEEDEEEEEEEEEECEEEEEDEDEEEEECDEEDEEEFFEFEFFEEEFEFFFFEFFFFFFFEFFEEEEFFEFFEEFFEFFEFFFFFFFFFFFFFFFFEEFFFFFFFFFFFFEFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFEFFFEEEFEFFFFFFFFFFFFFFFFFFFFFFEFFGT`a_`aaaaabbbaaabcbbca`bbbbbccccbcbaabaaaaabbb```a\\FFFEEEDEEEEEEEFEFFFFEFFFFFFFFEFFFFFFFFFFFFFFEEFFFFFFFEEFEEEEFFFFEFFFEFFFFFFFFFFFFFFFFFFEFFFFEFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFEFEFFEFEFFFFFFFFEFFFEFEEFEEFEEEFEEEEEFEFFFEEEFFDDDEEFEEEEEEEEEEFFEEFEEDDEEDDDEDDDEEEEENQQQQRSSSSTSTTTSTUUTTUVTTVTTVVVVUVYYWYWXXXVVVVWUSSSSUUTTTTTNEEEEDDDEDDDDDEEEEEDEDEDDEEEEEEEEEEEEEFEEDEEFEFFFFEFFFFFFEFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFEFFEFFEFEFFFFFFFFFFFFFFFFEFFFEFFFCDDEEEFEEFEEEFEFEECDEEFDEEEEEEEEEEEEEEEEEFEEFEFFFFEEFFFFFFFDEEEEEEEEEFEEEFGFGMXVYY[\\ZZZ[ZZYYYZZZZY[TEDEDDEDEDEEDEEDEEEEEEDDEEEEFECFEFEEEEEEEEDEEEEEEEDDE'..b'FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFEFEFFFFFEEDEFFFFFFFEFFFFFEFEFEFFFFFFFFFFEFFFFFFFEFEEFEEFEFDFEEEFEFFFFFFFEEFFFFFFFFEEFFFEFEEFEFEFEFDFFFFFEEEEEFFEEEFFEFEFDCEFEEDDEDEEBD!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!GGFAEC??:GGFF=<C<AFAEGGGEGCCFCEEDCE?AFFAFEEC8?FECEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFEFFEFEFFFEEFFFEFEFFFFFFFFEFFFEFFFFFEFFFFFEFFEFFEFEFFEFFEFFDEEEEEDDECECEEEEEFEDEEEFEEEEEEEEEFFENPQRSUWVVVXWWYYYYZZYYYYZYZXYZXYZYZZ[[[Z[ZZ[Z[\\[ZYZYZ[[[[[ZZ[[[ZZYYYXXXXWXXWWUTVRFEEEFEEEEEEEFEEEFFFFFFEEEEEEEFFEEEEEEFFFFFFFFFFEFEFFFEEFFFEFFFFEFFFFFFEFFFFFFFFFFFFFEFFFFFFFFFFEFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDEEEFEDEEEEEFFEEEEEFEEFDEEEEEEEEEFDFFEEEEFEEEFEDEET\\[ZZ[Z[\\]\\\\\\\\\\]\\\\\\\\\\]]][\\\\\\][]]\\[[\\]\\[\\Z[Z[ZUGGFFEEEEEEDEEECDECEEEEDEEEEEEEEDEFFEFEFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFEFFFFFEEFFEFFFFFFFEFFFEFFFFFFFFFFFFFFF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b
diff -r 000000000000 -r c88553ec696e test-data/zika/Z52.masked.sorted.depth
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52.masked.sorted.depth Mon Mar 30 07:18:00 2020 -0400
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diff -r 000000000000 -r c88553ec696e test-data/zika/Z52.merged.bam
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Binary file test-data/zika/Z52.merged.bam has changed
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diff -r 000000000000 -r c88553ec696e test-data/zika/Z52.sorted.depth
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52.sorted.depth Mon Mar 30 07:18:00 2020 -0400
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b
diff -r 000000000000 -r c88553ec696e test-data/zika/Z52.trimmed.sorted.depth
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52.trimmed.sorted.depth Mon Mar 30 07:18:00 2020 -0400
b
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b
diff -r 000000000000 -r c88553ec696e test-data/zika/Z52.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52.tsv Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,11 @@
+REGION POS REF ALT REF_DP_Z52_a.tsv REF_RV_Z52_a.tsv REF_QUAL_Z52_a.tsv ALT_DP_Z52_a.tsv ALT_RV_Z52_a.tsv ALT_QUAL_Z52_a.tsv ALT_FREQ_Z52_a.tsv TOTAL_DP_Z52_a.tsv PVAL_Z52_a.tsv PASS_Z52_a.tsv REF_DP_Z52_b.tsv REF_RV_Z52_b.tsv REF_QUAL_Z52_b.tsv ALT_DP_Z52_b.tsv ALT_RV_Z52_b.tsv ALT_QUAL_Z52_b.tsv ALT_FREQ_Z52_b.tsv TOTAL_DP_Z52_b.tsv PVAL_Z52_b.tsv PASS_Z52_b.tsv
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+PRV 2922 C T 263 0 36 11 0 36 0.040146 274 0.000431954 TRUE 277 0 36 19 0 34 0.0641892 296 1.46245e-06 TRUE
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diff -r 000000000000 -r c88553ec696e test-data/zika/Z52_a.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52_a.tsv Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,17 @@
+REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS
+PRV 350 A T 101 101 36 5 5 35 0.0471698 106 0.0304989 FALSE
+PRV 722 C +A 280 234 36 9 0 20 0.0319149 282 0.0349042 FALSE
+PRV 1682 C T 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE
+PRV 1965 T G 302 113 37 41 3 35 0.119534 343 2.81419e-14 TRUE
+PRV 2702 A G 31 31 36 1 1 23 0.03125 32 0.507937 FALSE
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diff -r 000000000000 -r c88553ec696e test-data/zika/Z52_b.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52_b.tsv Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,24 @@
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+PRV 3295 A G 1806 1806 36 69 69 34 0.0368 1875 2.28815e-20 TRUE
+PRV 3827 C T 248 0 37 14 0 36 0.0534351 262 5.10688e-05 TRUE
+PRV 5680 C T 38 5 50 7 1 49 0.155556 45 0.00133612 TRUE
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+PRV 8074 C T 18 2 39 1 0 76 0.0526316 19 0.463415 FALSE
+PRV 9713 C T 475 0 37 27 0 36 0.0537849 502 4.66646e-09 TRUE
+PRV 10227 G T 533 528 37 18 18 37 0.0326087 552 2.31457e-06 TRUE
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diff -r 000000000000 -r c88553ec696e test-data/zika/db/PRV.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/PRV.fa Mon Mar 30 07:18:00 2020 -0400
b
b'@@ -0,0 +1,2 @@\n+>PRV\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGCTAGCAACAGTATCAACAGGTTTTATTTTGGATTTGGAAACGAGAGTTTCTGGTCATGAAAAACCCAAAAAAGAAATCCGGAGGATTCCGGATTGTCAATATGCTAAAACGCGGAGTAGCCCGTGTGAGCCCCTTTGGGGGCTTGAAGAGGCTGCCAGCCGGACTTCTGCTGGGTCATGGGCCCATCAGGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATCTGGCTGCCATGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACTAGTGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACAGAAACGATGCTGGGGAGGCCATATCTTTTCCAACCACATTGGGGATGAATAAGTGTTATATACAGATCATGGATCTTGGACACATGTGTGATGCCACCATGAGCTATGAATGCCCTATGCTGGATGAGGGGGTGGAACCAGATGACGTCGATTGTTGGTGCAACACGACGTCAACTTGGGTTGTGTACGGAACCTGCCATCACAAAAAAGGTGAAGCACGGAGATCTAGAAGAGCTGTGACGCTCCCCTCCCATTCCACCAGGAAGCTGCAAACGCGGTCGCAAACCTGGTTGGAATCAAGAGAATACACAAAGCACTTGATTAGAGTCGAAAATTGGATATTCAGGAACCCTGGCTTCGCGTTAGCAGCAGCTGCCATCGCTTGGCTTTTGGGAAGCTCAACGAGCCAAAAAGTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGCATCAGGTGCATAGGAGTCAGCAATAGGGACTTTGTGGAAGGTATGTCAGGTGGGACTTGGGTTGATGTTGTCTTGGAACATGGAGGTTGTGTCACCGTAATGGCACAGGACAAACCGACTGTCGACATAGAGCTGGTTACAACAACAGTCAGCAACATGGCGGAGGTAAGATCCTACTGCTATGAGGCATCAATATCAGACATGGCTTCTGACAGCCGCTGCCCAACACAAGGTGAAGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTGCAAAAGAACGTTAGTGGACAGAGGCTGGGGAAATGGATGTGGACTTTTTGGCAAAGGGAGCCTGGTGACATGCGCTAAGTTTGCATGCTCCAAGAAAATGACCGGGAAGAGCATCCAGCCAGAGAATCTGGAGTACCGGATAATGCTGTCAGTTCATGGCTCCCAGCACAGTGGGATGATCGTTAATGACACAGGACATGAAACTGATGAGAATAGAGCGAAAGTTGAGATAACGCCCAATTCACCGAGAGCCGAAGCCACCCTGGGGGGTTTTGGAAGCCTAGGACTTGATTGTGAACCGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTCACAAGGAGTGGTTCCACGACATTCCATTACCTTGGCACGCTGGGGCAGACACCGGAACTCCACACTGGAACAACAAAGAAGCACTGGTAGAGTTCAAGGACGCACATGCCAAAAGGCAAACTGTCGTGGTTCTAGGGAGTCAAGAAGGAGCAGTTCACACGGCCCTTGCTGGAGCTCTGGAGGCTGAGATGGATGGTGCAAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTGTCATACTCCTTGTGTACTGCAGCGTTCACATTCACCAAGATCCCGGCTGAAACACTGCACGGGACAGTCACAGTGGAGTTACAGTACGCAGGGACAGATGGACCTTGCAAGGTTCCAGCTCAGATGGCGGTGGACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTAATCACTGAAAGCACTGAGAACTCTAAGATGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAGAAGATCACCCACCACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGGCAGTCTTGGGAGACACAGCCTGGGACTTTGGATCAGTTGGAGGCGCTCTCAACTCATTGGGCAAGGGCATCCATCAAATTTTTGGAGCAGCTTTCAAATCATTGTTTGGAGGAATGTCCTGGTTCTCACAAATTCTCATTGGAACGTTGCTGATGTGGTTGGGTCTGAACACAAAGAATGGATCTATTTCCCTTATGTGCTTGGCCTTAGGGGGAGTGTTGATCTTCTTATCCACAGCCGTCTCTGCTGATGTGGGGTGCTCGGTGGACTTCTCAAAGAAGGAGACGAGATGCGGTACAGGGGTGTTCGTCTATAACGACGTTGAAGCCTGGAGGGACAGGTACAAGTACCATCCTGACTCCCCCCGTAGATTGGCAGCAGCAGTCAAGCAAGCCTGGGAAGATGGTATCTGCGGGATCTCCTCTGTTTCAAGAATGGAAAACATCATGTGGAGATCAGTAGAAGGGGAGCTCAACGCAATCCTGGAAGAGAATGGAGTTCAACTGACGGTCGTTGTGGGATCTGTAAAAAACCCCATGTGGAGAGGTCCACAGAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGCTGGAAGGCTTGGGGGAAATCGTATTTCGTCAGAGCAGCAAAGACAAATAACAGCTTTGTCGTGGATGGTGACACACTGAAGGAATGCCCACTCAAACATAGAGCATGGAACAGCTTTCTTGTGGAGGATCATGGGTTCGGGGTATTTCACACTAGTGTCTGGCTCAAGGTTAGAGAAGATTATTCATTAGAGTGTGATCCAGCCGTTATTGGAACAGCTGTTAAGGGAAAGGAGGCTGTACACAGTGATCTAGGCTACTGGATTGAGAGTGAGAAGAATGACACATGGAGGCTGAAGAGGGCCCATCTGATCGAGAYGAAAACATGTGAATGGCCAAAGTCCCACACATTGTGGACAGATGGAATAGAAGAGAGTGATCTGATCATACCCAAGTCTTTAGCTGGGCCACTCAGCCATCACAATACCAGAGAGGGCTACAGGACCCAAATGAAAGGGCCATGGCACAGTGAAGAGCTTGAAATTCGGTTTGAGGAATGCCCAGGCACTAAGGTCCACGTGGAGGAAACATGTGGAACAAGAGGACCATCTCTGAGATCAACCACTGCAAGCGGAAGGGTGATCGAGGAATGGTGCTGCAGGGAGTGCACAATGCCCCCACTGTCGTTCCGGGCTAAAGATGGCTGTTGGTATGGAATGGAGATAAGGCCCAGGAAAGAACCAGAAAGCAACTTAGTAAGGTCAATGGTGACTGCAGGATCAACTGATCACATGGACCACTTCTCCCTTGGAGTGCTTGTGATCCTGCTCATGGTGCAGGAAGGGCTGAAGAAGAGAATGACCACAAAGATCATCATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAGGATTTTCAATGAGTGACCTGGCTAAGCTTGCAATTTTGATGGGTGCCACCTTCGCGGAAATGAACACTGGAGGAGATGTAGCTCATCTGGCGCTGATAGCGGCATTCAAAGTCAGACCAGCGTTGCTGGTATCTTTCATCTTCAGAGCTAATTGGACACCCCGTGAAAGCATGCTGCTGGCCTTGGCCTCGTGTCTTTTGCAAACTGCGATCTCCGCCTTGGAAGGCGACCTGATGGTTCTCATCAATGGTTTTGCTTTGGCCTGGTTGGCAATACGAGCGATGGTTGT'..b'CTGGTGGTGCTCATACCTGAGCCAGAAAAGCAAAGATCTCCCCAGGACAACCAAATGGCAATCATCATCATGGTAGCAGTAGGTCTTCTGGGCTTGATTACCGCCAATGAACTCGGATGGTTGGAGAGAACAAAGAGTGACCTAAGCCATCTAATGGGAAGGAGAGAGGAGGGGGCAACCATAGGATTCTCAATGGACATTGACCTGCGGCCAGCCTCAGCTTGGGCCATCTATGCTGCCTTGACAACTTTCATTACCCCAGCCGTCCAACATGCAGTGACCACCTCATACAACAACTACTCCTTAATGGCGATGGCCACGCAAGCTGGAGTGTTGTTTGGCATGGGCAAAGGGATGCCATTCTACGCATGGGACTTTGGAGTCCCGCTGCTAATGATAGGTTGCTACTCACAATTAACACCCCTGACCCTAATAGTGGCCATCATTTTGCTCGTGGCGCACTACATGTACTTGATCCCAGGGCTGCAGGCAGCAGCTGCGCGTGCTGCCCAGAAGAGAACGGCAGCTGGCATCATGAAGAACCCTGTTGTGGATGGAATAGTGGTGACTGACATTGACACAATGACAATTGACCCCCAAGTGGAGAAAAAGATGGGACAGGTGCTACTCATAGCAGTAGCCGTCTCCAGCGCCATACTGTCGCGGACCGCCTGGGGGTGGGGGGAGGCTGGGGCTCTGATCACAGCCGCAACTTCCACTTTGTGGGAAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACTTCACTGTGTAACATTTTTAGGGGAAGTTACTTGGCTGGAGCTTCTCTAATCTACACAGTAACAAGAAACGCTGGCTTGGTCAAGAGACGTGGGGGTGGAACAGGAGAGACCCTGGGAGAGAAATGGAAGGCCCGCTTGAACCAGATGTCGGCCCTGGAGTTCTACTCCTACAAAAAGTCAGGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATGCTGTGTCCCGAGGAAGTGCAAAGCTGAGATGGTTGGTGGAGCGGGGATACCTGCAGCCCTATGGAAAGGTCATTGATCTTGGATGTGGCAGAGGGGGCTGGAGTTACTACGTCGCCACCATCCGCAAAGTTCAAGAAGTGAAAGGATACACAAAAGGAGGCCCTGGTCATGAAGAACCCGTGTTGGTGCAAAGCTATGGGTGGAACATAGTCCGTCTTAAGAGTGGGGTGGACGTCTTTCATATGGCGGCTGAGCCGTGTGACACGTTGCTGTGTGACATAGGTGAGTCATCATCTAGTCCTGAAGTGGAAGAAGCACGGACGCTCAGAGTCCTCTCCATGGTGGGGGATTGGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGATGGAAACCCTGGAGCGACTGCAGCGTAGGTATGGGGGAGGACTGGTCAGAGTGCCACTCTCCCGCAACTCTACACATGAGATGTACTGGGTCTCTGGAGCGAAAAGCAACACCATAAAAAGTGTGTCCACCACGAGCCAGCTCCTCTTGGGGCGCATGGACGGGCCTAGGAGGCCAGTGAAATATGAGGAGGATGTGAATCTCGGCTCTGGCACGCGGGCTGTGGTAAGCTGCGCTGAAGCTCCCAACATGAAGATCATTGGTAACCGCATTGAAAGGATCCGCAGTGAGCACGCGGAAACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCACACAAGGGTCAGCGTCCTCTCTAATAAACGGGGTTGTCAGGCTCCTGTCAAAACCCTGGGATGTGGTGACTGGAGTCACAGGAATAGCCATGACCGACACCACACCGTATGGTCAGCAAAGAGTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGGTCTCTTCCTGGTTGTGGAAAGAGCTAGGCAAACACAAACGGCCACGAGTCTGCACCAAAGAAGAGTTCATCAACAAGGTTCGTAGCAATGCAGCATTAGGGGCAATATTTGAAGAGGAAAAAGAGTGGAAGACTGCAGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGAGAGTGCCAGAGCTGTGTGTACAACATGATGGGAAAAAGAGAAAAGAAACAAGGGGAATTTGGAAAGGCCAAGGGCAGCCGCGCCATCTGGTATATGTGGCTAGGGGCTAGATTTCTAGAGTTCGAAGCCCTTGGATTCTTGAACGAGGATCACTGGATGGGGAGAGAGAACTCAGGAGGTGGTGTTGAAGGGCTGGGATTACAAAGACTCGGATATGTCCTAGAAGAGATGAGTCGTATACCAGGAGGAAGGATGTATGCAGATGACACTGCTGGCTGGGACACCCGCATTAGCAGGTTTGATCTGGAGAATGAAGCTCTAATCACCAACCAAATGGAGAAAGGGCACAGGGCCTTGGCATTGGCCATAATCAAGTACACATACCAAAACAAAGTGGTAAAGGTCCTTAGACCAGCTGAAAAAGGGAAAACAGTTATGGACATTATTTCGAGACAAGACCAAAGGGGGAGCGGACAAGTTGTCACTTACGCTCTTAACACATTTACCAACCTAGTGGTGCAACTCATTCGGAATATGGAGGCTGAGGAAGTTCTAGAGATGCAAGACTTGTGGCTGCTGCGGAGGTCAGAGAAAGTGACCAACTGGTTGCAGAGCAACGGATGGGATAGGCTCAAACGAATGGCAGTCAGTGGAGATGATTGCGTTGTGAAGCCAATTGATGATAGGTTTGCACATGCCCTCAGGTTCTTGAATGATATGGGAAAAGTTAGGAAGGACACACAAGAGTGGAAACCCTCAACTGGATGGGACAACTGGGAAGAAGTTCCGTTTTGCTCCCACCACTTCAACAAGCTCCATCTCAAGGACGGGAGGTCCATTGTGGTTCCCTGCCGCCACCAAGATGAACTGATTGGCCGGGCCCGCGTCTCTCCAGGGGCGGGATGGAGCATCCGGGAGACTGCTTGCCTAGCAAAATCATATGCGCAAATGTGGCAGCTCCTTTATTTCCACAGAAGGGACCTCCGACTGATGGCCAATGCCATTTGTTCATCTGTGCCAGTTGACTGGGTTCCAACTGGGAGAACTACCTGGTCAATCCATGGAAAGGGAGAATGGATGACCACTGAAGACATGCTTGTGGTGTGGAACAGAGTGTGGATTGAGGAGAACGACCACATGGAAGACAAGACCCCAGTTACGAAATGGACAGACATTCCCTATTTGGGAAAAAGGGAAGACTTGTGGTGTGGATCTCTCATAGGGCACAGACCGCGCACCACCTGGGCTGAGAACATTAAAAACACAGTCAACATGGTGCGCAGGATCATAGGTGATGAAGAAAAGTACATGGACTACCTATCCACCCAAGTTCGCTACTTGGGTGAAGAAGGGTCTACACCTGGAGTGCTGTAAGCACCAATCTTAATGTTGTCAGGCCTGCTAGTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n'
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/PRV.fa.amb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/PRV.fa.amb Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,5 @@
+10807 1 4
+0 49 N
+3147 1 Y
+6597 48 N
+10413 394 N
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/PRV.fa.ann
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/PRV.fa.ann Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,3 @@
+10807 1 11
+0 PRV (null)
+0 10807 4
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/PRV.fa.bwt
b
Binary file test-data/zika/db/PRV.fa.bwt has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/PRV.fa.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/PRV.fa.fai Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,1 @@
+PRV 10807 5 10807 10808
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/PRV.fa.pac
b
Binary file test-data/zika/db/PRV.fa.pac has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/PRV.fa.sa
b
Binary file test-data/zika/db/PRV.fa.sa has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/Z52.consensus.amb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/Z52.consensus.amb Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,2 @@
+10139 1 1
+6345 48 -
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/Z52.consensus.ann
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/Z52.consensus.ann Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,3 @@
+10139 1 11
+0 Consensus_Z52.consensus_threshold_0_quality_20 (null)
+0 10139 1
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/Z52.consensus.bwt
b
Binary file test-data/zika/db/Z52.consensus.bwt has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/Z52.consensus.pac
b
Binary file test-data/zika/db/Z52.consensus.pac has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/Z52.consensus.sa
b
Binary file test-data/zika/db/Z52.consensus.sa has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/pair_information.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/pair_information.tsv Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,35 @@
+400_1_out_L 400_1_out_R
+400_2_out_L 400_2_out_R
+400_3_out_L* 400_3_out_R*
+400_4_out_L 400_4_out_R
+400_5_out_L 400_5_out_R
+400_6_out_L 400_6_out_R
+400_7_out_L 400_7_out_R
+400_8_out_L* 400_8_out_R*
+400_9_out_L* 400_9_out_R*
+400_10_out_L 400_10_out_R
+400_11_out_L 400_11_out_R
+400_12_out_L 400_12_out_R
+400_13_out_L 400_13_out_R
+400_14_out_L* 400_14_out_R*
+400_15_out_L 400_15_out_R
+400_16_out_L* 400_16_out_R*
+400_17_out_L** 400_17_out_R**
+400_18_out_L** 400_18_out_R**
+400_19_out_L 400_19_out_R
+400_20_out_L* 400_20_out_R*
+400_21_out_L* 400_21_out_R*
+400_22_out_L** 400_22_out_R**
+400_23_out_L 400_23_out_R
+400_24_out_L** 400_24_out_R**
+400_25_out_L** 400_25_out_R**
+400_26_out_L 400_26_out_R
+400_27_out_L 400_27_out_R
+400_28_out_L 400_28_out_R
+400_29_out_L 400_29_out_R
+400_30_out_L 400_30_out_R
+400_31_out_L 400_31_out_R
+400_32_out_L 400_32_out_R
+400_33_out_L* 400_33_out_R*
+400_34_out_L* 400_34_out_R*
+400_35_out_L 400_35_out_R
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/zika_primers.bam
b
Binary file test-data/zika/db/zika_primers.bam has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/zika_primers.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/zika_primers.bed Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,68 @@
+PRV 482 504 400_1_out_R 60 -
+PRV 359 381 400_2_out_L 60 +
+PRV 796 818 400_2_out_R 60 -
+PRV 658 680 400_3_out_L* 60 +
+PRV 1054 1076 400_3_out_R* 60 -
+PRV 978 1000 400_4_out_L 60 +
+PRV 1393 1415 400_4_out_R 60 -
+PRV 1256 1278 400_5_out_L 60 +
+PRV 1701 1723 400_5_out_R 60 -
+PRV 1539 1561 400_6_out_L 60 +
+PRV 1965 1987 400_6_out_R 60 -
+PRV 1875 1897 400_7_out_L 60 +
+PRV 2264 2286 400_7_out_R 60 -
+PRV 2151 2173 400_8_out_L* 60 +
+PRV 2607 2629 400_8_out_R* 60 -
+PRV 2444 2466 400_9_out_L* 60 +
+PRV 2902 2924 400_9_out_R* 60 -
+PRV 2747 2769 400_10_out_L 60 +
+PRV 3154 3176 400_10_out_R 60 -
+PRV 3030 3052 400_11_out_L 60 +
+PRV 3481 3503 400_11_out_R 60 -
+PRV 3334 3356 400_12_out_L 60 +
+PRV 3763 3785 400_12_out_R 60 -
+PRV 3657 3679 400_13_out_L 60 +
+PRV 4077 4099 400_13_out_R 60 -
+PRV 3931 3953 400_14_out_L* 60 +
+PRV 4388 4410 400_14_out_R* 60 -
+PRV 4231 4253 400_15_out_L 60 +
+PRV 4659 4681 400_15_out_R 60 -
+PRV 4542 4564 400_16_out_L* 60 +
+PRV 4965 4987 400_16_out_R* 60 -
+PRV 4851 4873 400_17_out_L** 60 +
+PRV 5304 5326 400_17_out_R** 60 -
+PRV 5136 5158 400_18_out_L** 60 +
+PRV 5587 5609 400_18_out_R** 60 -
+PRV 5461 5483 400_19_out_L 60 +
+PRV 5902 5924 400_19_out_R 60 -
+PRV 5746 5768 400_20_out_L* 60 +
+PRV 6178 6200 400_20_out_R* 60 -
+PRV 6046 6068 400_21_out_L* 60 +
+PRV 6458 6480 400_21_out_R* 60 -
+PRV 6353 6375 400_22_out_L** 60 +
+PRV 6756 6778 400_22_out_R** 60 -
+PRV 6673 6695 400_23_out_L 60 +
+PRV 7073 7095 400_23_out_R 60 -
+PRV 6960 6982 400_24_out_L** 60 +
+PRV 7394 7416 400_24_out_R** 60 -
+PRV 7230 7252 400_25_out_L** 60 +
+PRV 7685 7707 400_25_out_R** 60 -
+PRV 7554 7576 400_26_out_L 60 +
+PRV 7972 7994 400_26_out_R 60 -
+PRV 7841 7863 400_27_out_L 60 +
+PRV 8296 8318 400_27_out_R 60 -
+PRV 8167 8189 400_28_out_L 60 +
+PRV 8582 8604 400_28_out_R 60 -
+PRV 8430 8452 400_29_out_L 60 +
+PRV 8873 8895 400_29_out_R 60 -
+PRV 8740 8762 400_30_out_L 60 +
+PRV 9184 9206 400_30_out_R 60 -
+PRV 9052 9074 400_31_out_L 60 +
+PRV 9473 9495 400_31_out_R 60 -
+PRV 9336 9358 400_32_out_L 30 +
+PRV 9755 9777 400_32_out_R 60 -
+PRV 9637 9659 400_33_out_L* 60 +
+PRV 10104 10126 400_33_out_R* 60 -
+PRV 9969 9991 400_34_out_L* 60 +
+PRV 10391 10413 400_34_out_R* 60 -
+PRV 10241 10263 400_35_out_L 60 +
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/zika_primers.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/zika_primers.fa Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,140 @@
+>400_1_out_L
+GACAGTTCGAGTTTGAAGCGAAAG
+>400_1_out_R
+AGTATGCACTCCCACGTCTAGT
+>400_2_out_L
+AAGAAAGATCTGGCTGCCATGC
+>400_2_out_R
+TGATTCCAACCAGGTTTGCGAC
+>400_3_out_L*
+AGATGACGTCGATTGTTGGTGC
+>400_3_out_R*
+TACGGTGACACAACCTCCATGT
+>400_4_out_L
+TCAGGTGCATAGGAGTCAGCAA
+>400_4_out_R
+GGAGCCATGAACTGACAGCATT
+>400_5_out_L
+AGAACGTTAGTGGACAGAGGCT
+>400_5_out_R
+TGTGCGTCCTTGAACTCTACCA
+>400_6_out_L
+TTGATTGTGAACCGAGGACAGG
+>400_6_out_R
+CCATCTGTCCCTGCGTACTGTA
+>400_7_out_L
+TGAAGGGCGTGTCATACTCCTT
+>400_7_out_R
+CGCCTCCAACTGATCCAAAGTC
+>400_8_out_L*
+GGGAGAAGAAGATCACCCACCA
+>400_8_out_R*
+TTGACTGCTGCTGCCAATCTAC
+>400_9_out_L*
+GCCTTAGGGGGAGTGTTGATCT
+>400_9_out_R*
+GAGTGGGCATTCCTTCAGTGTG
+>400_10_out_L
+ACGGTCGTTGTGGGATCTGTAA
+>400_10_out_R
+GTGGGACTTTGGCCATTCACAT
+>400_11_out_L
+CAGCCGTTATTGGAACAGCTGT
+>400_11_out_R
+CCTGGGCCTTATCTCCATTCCA
+>400_12_out_L
+CACTAAGGTCCACGTGGAGGAA
+>400_12_out_R
+TATCAGCGCCAGATGAGCTACA
+>400_13_out_L
+TGGCAGTGCTGGTAGCTATGAT
+>400_13_out_R
+AGAGAGAGGAGCATAAACCCCC
+>400_14_out_L*
+CAATGGTTTTGCTTTGGCCTGG
+>400_14_out_R*
+TTTCCCATGTGATGTCACCTGC
+>400_15_out_L
+CCCTAGCGAAGTACTCACAGCT
+>400_15_out_R
+TACACTCCATCTGTGGTCTCCC
+>400_16_out_L*
+GTGGCATGAACCCAATAGCCAT
+>400_16_out_R*
+GCTCCAATGTCCCCATCCTTTG
+>400_17_out_L**
+GTGGTCCATGGAAGCTAGATGC
+>400_17_out_R**
+CCTCTAAGGGCCTCCTCCATTT
+>400_18_out_L**
+CTGTTGAGTGCTTCGAGCCTTC
+>400_18_out_R**
+TGGTGAGTTGGAGTCCGGAAAT
+>400_19_out_L
+TATGGATGAGGCCCACTTCACA
+>400_19_out_R
+GCCATCAAGTATGACCGGCTTT
+>400_20_out_L*
+GGCTGGAAAACGGGTCATACAG
+>400_20_out_R*
+CCTTTGCTCCGTCCTAAGCTTG
+>400_21_out_L*
+AGAGACTGACGAAGACCATGCA
+>400_21_out_R*
+CTCCAAAAGCCGCTCCTCTTTT
+>400_22_out_L**
+TGGACCAGACACGGAGAGAAAA
+>400_22_out_R**
+ATTCTGGCTGGCTCAATTTCCG
+>400_23_out_L
+CGTCTTGATGAGGAACAAGGGC
+>400_23_out_R
+AAGTGGTCACTGCATGTTGGAC
+>400_24_out_L**
+TAATGGGAAGGAGAGAGGAGGG
+>400_24_out_R**
+TCTCCACTTGGGGGTCAATTGT
+>400_25_out_L**
+CCCTGACCCTAATAGTGGCCAT
+>400_25_out_R**
+CCTTCCATTTCTCTCCCAGGGT
+>400_26_out_L
+ACTGGAACTCCTCTACAGCCAC
+>400_26_out_R
+ACCAGGGCCTCCTTTTGTGTAT
+>400_27_out_L
+AGTGCAAAGCTGAGATGGTTGG
+>400_27_out_R
+ATGTGTAGAGTTGCGGGAGAGT
+>400_28_out_L
+GGTGGGGGATTGGCTTGAAAAA
+>400_28_out_R
+GGGCCTCATAGCTTCCATGGTA
+>400_29_out_L
+AGGATGTGAATCTCGGCTCTGG
+>400_29_out_R
+ATGCTGCATTGCTACGAACCTT
+>400_30_out_L
+AAAAGTGGACACTAGGGTGCCA
+>400_30_out_R
+TAATCCCAGCCCTTCAACACCA
+>400_31_out_L
+ACAAGGGGAATTTGGAAAGGCC
+>400_31_out_R
+CGTAAGTGACAACTTGTCCGCT
+>400_32_out_L
+AAATGGAAAAAGGGCACAGGGC
+>400_32_out_R
+TGTCCCATCCAGTTGAGGGTTT
+>400_33_out_L*
+CAAACGAATGGCAGTCAGTGGA
+>400_33_out_R*
+ATCCACACTCTGTTCCACACCA
+>400_34_out_L*
+ATTTCCACAGAAGGGACCTCCG
+>400_34_out_R*
+TGACTAGCAGGCCTGACAACAT
+>400_35_out_L
+ACCACCTGGGCTGAGAACATTA
+>400_35_out_R
+ACCACTAGTCCCTCTTCTGGAG
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/zika_primers_consensus.bam
b
Binary file test-data/zika/db/zika_primers_consensus.bam has changed
b
diff -r 000000000000 -r c88553ec696e test-data/zika/db/zika_primers_consensus.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/zika_primers_consensus.bed Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,67 @@
+Consensus_Z52.consensus_threshold_0_quality_20 107 129 400_2_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 230 252 400_1_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 406 428 400_3_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 544 566 400_2_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 726 748 400_4_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 802 824 400_3_out_R* 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 1004 1026 400_5_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 1141 1163 400_4_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 1287 1309 400_6_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 1449 1471 400_5_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 1623 1645 400_7_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 1713 1735 400_6_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 1899 1921 400_8_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 2012 2034 400_7_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 2192 2214 400_9_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 2355 2377 400_8_out_R* 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 2495 2517 400_10_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 2650 2672 400_9_out_R* 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 2778 2800 400_11_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 2902 2924 400_10_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 3082 3104 400_12_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 3229 3251 400_11_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 3405 3427 400_13_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 3511 3533 400_12_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 3679 3701 400_14_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 3825 3847 400_13_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 3979 4001 400_15_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 4136 4158 400_14_out_R* 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 4290 4312 400_16_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 4407 4429 400_15_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 4599 4621 400_17_out_L** 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 4713 4735 400_16_out_R* 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 4884 4906 400_18_out_L** 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 5052 5074 400_17_out_R** 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 5209 5231 400_19_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 5335 5357 400_18_out_R** 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 5494 5516 400_20_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 5650 5672 400_19_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 5794 5816 400_21_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 5926 5948 400_20_out_R* 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 6101 6123 400_22_out_L** 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 6206 6228 400_21_out_R* 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 6421 6443 400_23_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 6504 6526 400_22_out_R** 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 6708 6730 400_24_out_L** 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 6821 6843 400_23_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 6978 7000 400_25_out_L** 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 7142 7164 400_24_out_R** 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 7302 7324 400_26_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 7433 7455 400_25_out_R** 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 7589 7611 400_27_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 7720 7742 400_26_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 7915 7937 400_28_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 8044 8066 400_27_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 8178 8200 400_29_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 8330 8352 400_28_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 8488 8510 400_30_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 8621 8643 400_29_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 8800 8822 400_31_out_L 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 8932 8954 400_30_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 9084 9106 400_32_out_L 30 +
+Consensus_Z52.consensus_threshold_0_quality_20 9221 9243 400_31_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 9385 9407 400_33_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 9503 9525 400_32_out_R 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 9717 9739 400_34_out_L* 60 +
+Consensus_Z52.consensus_threshold_0_quality_20 9852 9874 400_33_out_R* 60 -
+Consensus_Z52.consensus_threshold_0_quality_20 9989 10011 400_35_out_L 60 +
b
diff -r 000000000000 -r c88553ec696e test-data/zika/primer_mismatchers_indices.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/primer_mismatchers_indices.txt Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,1 @@
+400_18_out_L** 400_18_out_R** 400_23_out_R 400_23_out_L 400_32_out_L 400_32_out_R
\ No newline at end of file
b
diff -r 000000000000 -r c88553ec696e test-data/zika/primers_Z52_consensus.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/primers_Z52_consensus.tsv Mon Mar 30 07:18:00 2020 -0400
b
@@ -0,0 +1,4 @@
+REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS
+Consensus_Z52.consensus_threshold_0_quality_20 4904 C T 0 0 0 1 0 93 1 1 1 FALSE
+Consensus_Z52.consensus_threshold_0_quality_20 6842 C T 0 0 0 1 1 93 1 1 1 FALSE
+Consensus_Z52.consensus_threshold_0_quality_20 9092 G A 0 0 0 1 0 93 1 1 1 FALSE