Repository 'poppunk'
hg clone https://toolshed.g2.bx.psu.edu/repos/johnlees/poppunk

Changeset 2:1d7ba8646dd1 (2019-05-16)
Previous changeset 1:88ea7ea4b3d2 (2019-05-15) Next changeset 3:a3613553c65f (2019-05-16)
Commit message:
planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
added:
LICENSE
README.rst
tools/PopPUNK/poppunk_cluster.xml
tools/PopPUNK/test-data/12673_8_24.contigs_velvet.fa
tools/PopPUNK/test-data/12673_8_34.contigs_velvet.fa
tools/PopPUNK/test-data/12673_8_43.contigs_velvet.fa
tools/PopPUNK/test-data/12754_4_71.contigs_velvet.fa
tools/PopPUNK/test-data/12754_4_77.contigs_velvet.fa
tools/PopPUNK/test-data/clusters.csv
tools/PopPUNK/test-data/distances.png
tools/PopPUNK/test-data/gmm_contours.pdf
tools/PopPUNK/test-data/gmm_fit.png
tools/PopPUNK/test-data/refs.txt
removed:
clusters.csv
poppunk_cluster.xml
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diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Thu May 16 11:08:09 2019 -0400
[
b'@@ -0,0 +1,201 @@\n+                                 Apache License\n+                           Version 2.0, January 2004\n+                        http://www.apache.org/licenses/\n+\n+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n+\n+   1. Definitions.\n+\n+      "License" shall mean the terms and conditions for use, reproduction,\n+      and distribution as defined by Sections 1 through 9 of this document.\n+\n+      "Licensor" shall mean the copyright owner or entity authorized by\n+      the copyright owner that is granting the License.\n+\n+      "Legal Entity" shall mean the union of the acting entity and all\n+      other entities that control, are controlled by, or are under common\n+      control with that entity. For the purposes of this definition,\n+      "control" means (i) the power, direct or indirect, to cause the\n+      direction or management of such entity, whether by contract or\n+      otherwise, or (ii) ownership of fifty percent (50%) or more of the\n+      outstanding shares, or (iii) beneficial ownership of such entity.\n+\n+      "You" (or "Your") shall mean an individual or Legal Entity\n+      exercising permissions granted by this License.\n+\n+      "Source" form shall mean the preferred form for making modifications,\n+      including but not limited to software source code, documentation\n+      source, and configuration files.\n+\n+      "Object" form shall mean any form resulting from mechanical\n+      transformation or translation of a Source form, including but\n+      not limited to compiled object code, generated documentation,\n+      and conversions to other media types.\n+\n+      "Work" shall mean the work of authorship, whether in Source or\n+      Object form, made available under the License, as indicated by a\n+      copyright notice that is included in or attached to the work\n+      (an example is provided in the Appendix below).\n+\n+      "Derivative Works" shall mean any work, whether in Source or Object\n+      form, that is based on (or derived from) the Work and for which the\n+      editorial revisions, annotations, elaborations, or other modifications\n+      represent, as a whole, an original work of authorship. For the purposes\n+      of this License, Derivative Works shall not include works that remain\n+      separable from, or merely link (or bind by name) to the interfaces of,\n+      the Work and Derivative Works thereof.\n+\n+      "Contribution" shall mean any work of authorship, including\n+      the original version of the Work and any modifications or additions\n+      to that Work or Derivative Works thereof, that is intentionally\n+      submitted to Licensor for inclusion in the Work by the copyright owner\n+      or by an individual or Legal Entity authorized to submit on behalf of\n+      the copyright owner. For the purposes of this definition, "submitted"\n+      means any form of electronic, verbal, or written communication sent\n+      to the Licensor or its representatives, including but not limited to\n+      communication on electronic mailing lists, source code control systems,\n+      and issue tracking systems that are managed by, or on behalf of, the\n+      Licensor for the purpose of discussing and improving the Work, but\n+      excluding communication that is conspicuously marked or otherwise\n+      designated in writing by the copyright owner as "Not a Contribution."\n+\n+      "Contributor" shall mean Licensor and any individual or Legal Entity\n+      on behalf of whom a Contribution has been received by Licensor and\n+      subsequently incorporated within the Work.\n+\n+   2. Grant of Copyright License. Subject to the terms and conditions of\n+      this License, each Contributor hereby grants to You a perpetual,\n+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n+      copyright license to reproduce, prepare Derivative Works of,\n+      publicly display, publicly perform, sublicense, and distribute the\n+      Work and such Derivative Works in Source or Objec'..b'r shall be under the terms and conditions of\n+      this License, without any additional terms or conditions.\n+      Notwithstanding the above, nothing herein shall supersede or modify\n+      the terms of any separate license agreement you may have executed\n+      with Licensor regarding such Contributions.\n+\n+   6. Trademarks. This License does not grant permission to use the trade\n+      names, trademarks, service marks, or product names of the Licensor,\n+      except as required for reasonable and customary use in describing the\n+      origin of the Work and reproducing the content of the NOTICE file.\n+\n+   7. Disclaimer of Warranty. Unless required by applicable law or\n+      agreed to in writing, Licensor provides the Work (and each\n+      Contributor provides its Contributions) on an "AS IS" BASIS,\n+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or\n+      implied, inclu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diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu May 16 11:08:09 2019 -0400
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@@ -0,0 +1,2 @@
+# PopPUNK_galaxy
+Galaxy tool for PopPUNK
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 clusters.csv
--- a/clusters.csv Wed May 15 14:58:24 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,6 +0,0 @@
-Taxon,Cluster
-12754_4_77.contigs_velvet.fa,1
-12673_8_34.contigs_velvet.fa,1
-12673_8_43.contigs_velvet.fa,1
-12673_8_24.contigs_velvet.fa,1
-12754_4_71.contigs_velvet.fa,2
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 poppunk_cluster.xml
--- a/poppunk_cluster.xml Wed May 15 14:58:24 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,284 +0,0 @@\n-<tool id="poppunk_cluster" name="PopPUNK (cluster)" version="1.1.6">\n-   <description>Cluster bacterial genomes</description>\n-\n-   <requirements>\n-        <requirement type="package" version="1.1.6">poppunk</requirement>\n-     </requirements>\n-\n-    <version_command><![CDATA[\n-poppunk --version\n-    ]]></version_command>\n-\n-    <command detect_errors="exit_code"><![CDATA[\n-       ##Set up input files\n-       ##echo "$input_assemblies" | tr \',\' \'\\n\' > r_files.txt\n-       #for $input in $input_assemblies\n-       ln -s $input $input.element_identifier && echo $input.element_identifier >> r_files.txt; \n-       #end for\n-\n-       ## command line 1 (create db)\n-       echo "\n-       poppunk \n-       --create-db \n-       --r-files r_files.txt \n-       --output poppunk_db \n-       --threads \\${GALAXY_SLOTS:-1} \n-       --min-k $min_k \n-       --max-k $max_k \n-       --k-step $k_step \n-       --sketch-size $sketch_size \n-       --max-a-dist $max_a_dist \n-       #if $ignore_length\n-       --ignore_length \n-       #end if\n-       --no-stream \n-       " > poppunk_1.sh\n-\n-       && sh poppunk_1.sh\n-\n-       ## command line 2 (fit model)\n-       && echo "\n-       poppunk \n-       --fit-model \n-       --distances poppunk_db/poppunk_db.dists \n-       --ref-db poppunk_db \n-       --output poppunk_db \n-\n-       ## mode\n-       #if str( $model.model_mode ) == "gmm":\n-       --K ${model.K} \n-       #end if\n-       #if str( $model.model_mode ) == "dbscan":\n-       --dbscan \n-       --D $model.D \n-       --min-cluster-prop $model.min_cluster_prop \n-       #end if\n-\n-       #if not $no_full_db or $refine.refine_model\n-       --full-db \n-       #end if\n-\n-       #if not $refine.refine_model:\n-         #if $external_clusters\n-         --external-clustering $external_clusters\n-         #end if\n-\n-         ## viz\n-         #if $cytoscape:\n-         --cytoscape \n-         #end if\n-         #if $viz.microreact:\n-         --microreact \n-         --rapidnj rapidnj \n-         --perplexity $viz.perplexity \n-         #end if\n-         #if ($cytoscape or $viz.microreact) and $info_csv:\n-         --info-csv $info_csv \n-         #end if\n-       #end if\n-\n-       " > poppunk_2.sh\n-\n-       && sh poppunk_2.sh\n-\n-       ## command line 3 (refine)\n-       #if $refine.refine_model:\n-         && echo "\n-         poppunk \n-         --refine-model \n-         --distances poppunk_db/poppunk_db.dists \n-         --ref-db poppunk_db \n-         --output poppunk_db \n-         --threads \\${GALAXY_SLOTS:-1} \n-         --pos-shift $refine.pos_shift\n-         --neg-shift $refine.neg_shift\n-\n-         #if not $no_full_db\n-         --full-db \n-         #end if\n-\n-         #if $external_clusters\n-         --external-clustering $external_clusters\n-         #end if\n-\n-         ## viz\n-         #if $cytoscape:\n-         --cytoscape \n-         #end if\n-         #if $viz.microreact:\n-         --microreact \n-         --rapidnj rapidnj \n-         --perplexity $viz.perplexity \n-         #end if\n-         #if ($cytoscape or $viz.microreact) and $info_csv:\n-         --info-csv $info_csv \n-         #end if\n-\n-         " > poppunk_3.sh\n-\n-         && sh poppunk_3.sh;\n-       #end if\n-\n-       ]]></command>\n-\n-    <inputs>\n-\n-       <!-- input files -->\n-       <param name="input_assemblies" type="data" format="fasta" multiple="true" label="FASTA datasets (assemblies)">\n-       </param>\n-\n-       <!-- model type -->\n-       <conditional name="model">\n-         <param name="model_mode" type="select" label="Choose a model to use" help="See documentation or description below for advice, if default does not work." display="radio">\n-           <option value="gmm" selected="true">GMM</option>\n-           <option value="dbscan">DBSCAN</option>\n-         </param>\n-         <!-- model options -->\n-         <when value="gmm">\n-           <param name="K" type="integer" value="3" min="2" max="10" label="Number of mixture components">\n-           </param>\n-         </when>\n-         <when '..b'output name="distances" ftype=\'png\' file="distances.png" />\n-          <output name="references" file="refs.txt" />\n-          <output name="gmm_plot" ftype=\'png\' file="gmm_fit.png" />\n-          <output name="gmm_contours" ftype=\'pdf\' file="gmm_contours.pdf" />\n-       </test>\n-    </tests>\n-\n-    <help><![CDATA[\n-**What it does**\n-\n-PopPUNK will calculate core and accessory distance between input assemblies using variable length k-mers. A model will be fitted to all of these distances to determine genetic clusters for all inpits.\n-\n-------\n-\n-**Description**\n-\n-       The most important thing to check is that in the output plot the component (blob) closest to the origin has been correctly identified - this should be checked in the cluster/model plot output. If it has not, you may wish to try another model. Some broad advice:\n-\n-  * DBSCAN is a good default, but may lead to unclassified points (black). If there are a large number of these consider another model.\n-  * GMM will work well with well-separated components and an appropriate choice of K (consider increasing it based on the number of components that can be seen).\n-  * The refine mode should be added in recombining species, which can be seen from the output plots if the coloured components are overlapping, or if there is a blur of points rather than discrete blobs of points..\n-       ]]></help>\n-\n-    <citations>\n-       <citation type=\'bibtex\'>\n-@article{Lees01022019,\n-  author = {Lees, John A. and Harris, Simon R. and Tonkin-Hill, Gerry and Gladstone, Rebecca A. and Lo, Stephanie W. and Weiser, Jeffrey N. and Corander, Jukka and Bentley, Stephen D. and Croucher, Nicholas J.},\n-  title = {Fast and flexible bacterial genomic epidemiology with PopPUNK},\n-  volume = {29},\n-  number = {2},\n-  pages = {304-316},\n-  year = {2019},\n-  doi = {10.1101/gr.241455.118},\n-  abstract ={The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (Population Partitioning Using Nucleotide K-mers), a software implementing scalable and expandable annotation- and alignment-free methods for population analysis and clustering. Variable-length k-mer comparisons are used to distinguish isolates\xe2\x80\x99 divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using data from both simulations and genomic collections representing 10 taxonomically widespread species. Connections between closely related isolates of the same strain are robustly identified, despite interspecies variation in the pairwise distance distributions that reflects species\xe2\x80\x99 diverse evolutionary patterns. PopPUNK can process 103\xe2\x80\x93104 genomes in a single batch, with minimal memory use and runtimes up to 200-fold faster than existing model-based methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to reanalyze all genomes de novo. This facilitates real-time surveillance with consistent cluster naming between studies and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualization and online publication is streamlined through the automatic output of results to multiple platforms. PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.},\n-  URL = {http://genome.cshlp.org/content/29/2/304.abstract},\n-  eprint = {http://genome.cshlp.org/content/29/2/304.full.pdf+html},\n-  journal = {Genome Research}\n-          }</citation>\n-    </citations>\n-</tool>\n'
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/poppunk_cluster.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/poppunk_cluster.xml Thu May 16 11:08:09 2019 -0400
[
b'@@ -0,0 +1,284 @@\n+<tool id="poppunk_cluster" name="PopPUNK (cluster)" version="1.1.6">\n+   <description>Cluster bacterial genomes</description>\n+\n+   <requirements>\n+        <requirement type="package" version="1.1.6">poppunk</requirement>\n+     </requirements>\n+\n+    <version_command><![CDATA[\n+poppunk --version\n+    ]]></version_command>\n+\n+    <command detect_errors="exit_code"><![CDATA[\n+       ##Set up input files\n+       ##echo "$input_assemblies" | tr \',\' \'\\n\' > r_files.txt\n+       #for $input in $input_assemblies\n+       ln -s $input $input.element_identifier && echo $input.element_identifier >> r_files.txt; \n+       #end for\n+\n+       ## command line 1 (create db)\n+       echo "\n+       poppunk \n+       --create-db \n+       --r-files r_files.txt \n+       --output poppunk_db \n+       --threads \\${GALAXY_SLOTS:-1} \n+       --min-k $min_k \n+       --max-k $max_k \n+       --k-step $k_step \n+       --sketch-size $sketch_size \n+       --max-a-dist $max_a_dist \n+       #if $ignore_length\n+       --ignore_length \n+       #end if\n+       --no-stream \n+       " > poppunk_1.sh\n+\n+       && sh poppunk_1.sh\n+\n+       ## command line 2 (fit model)\n+       && echo "\n+       poppunk \n+       --fit-model \n+       --distances poppunk_db/poppunk_db.dists \n+       --ref-db poppunk_db \n+       --output poppunk_db \n+\n+       ## mode\n+       #if str( $model.model_mode ) == "gmm":\n+       --K ${model.K} \n+       #end if\n+       #if str( $model.model_mode ) == "dbscan":\n+       --dbscan \n+       --D $model.D \n+       --min-cluster-prop $model.min_cluster_prop \n+       #end if\n+\n+       #if not $no_full_db or $refine.refine_model\n+       --full-db \n+       #end if\n+\n+       #if not $refine.refine_model:\n+         #if $external_clusters\n+         --external-clustering $external_clusters\n+         #end if\n+\n+         ## viz\n+         #if $cytoscape:\n+         --cytoscape \n+         #end if\n+         #if $viz.microreact:\n+         --microreact \n+         --rapidnj rapidnj \n+         --perplexity $viz.perplexity \n+         #end if\n+         #if ($cytoscape or $viz.microreact) and $info_csv:\n+         --info-csv $info_csv \n+         #end if\n+       #end if\n+\n+       " > poppunk_2.sh\n+\n+       && sh poppunk_2.sh\n+\n+       ## command line 3 (refine)\n+       #if $refine.refine_model:\n+         && echo "\n+         poppunk \n+         --refine-model \n+         --distances poppunk_db/poppunk_db.dists \n+         --ref-db poppunk_db \n+         --output poppunk_db \n+         --threads \\${GALAXY_SLOTS:-1} \n+         --pos-shift $refine.pos_shift\n+         --neg-shift $refine.neg_shift\n+\n+         #if not $no_full_db\n+         --full-db \n+         #end if\n+\n+         #if $external_clusters\n+         --external-clustering $external_clusters\n+         #end if\n+\n+         ## viz\n+         #if $cytoscape:\n+         --cytoscape \n+         #end if\n+         #if $viz.microreact:\n+         --microreact \n+         --rapidnj rapidnj \n+         --perplexity $viz.perplexity \n+         #end if\n+         #if ($cytoscape or $viz.microreact) and $info_csv:\n+         --info-csv $info_csv \n+         #end if\n+\n+         " > poppunk_3.sh\n+\n+         && sh poppunk_3.sh;\n+       #end if\n+\n+       ]]></command>\n+\n+    <inputs>\n+\n+       <!-- input files -->\n+       <param name="input_assemblies" type="data" format="fasta" multiple="true" label="FASTA datasets (assemblies)">\n+       </param>\n+\n+       <!-- model type -->\n+       <conditional name="model">\n+         <param name="model_mode" type="select" label="Choose a model to use" help="See documentation or description below for advice, if default does not work." display="radio">\n+           <option value="gmm" selected="true">GMM</option>\n+           <option value="dbscan">DBSCAN</option>\n+         </param>\n+         <!-- model options -->\n+         <when value="gmm">\n+           <param name="K" type="integer" value="3" min="2" max="10" label="Number of mixture components">\n+           </param>\n+         </when>\n+         <when '..b'output name="distances" ftype=\'png\' file="distances.png" />\n+          <output name="references" file="refs.txt" />\n+          <output name="gmm_plot" ftype=\'png\' file="gmm_fit.png" />\n+          <output name="gmm_contours" ftype=\'pdf\' file="gmm_contours.pdf" />\n+       </test>\n+    </tests>\n+\n+    <help><![CDATA[\n+**What it does**\n+\n+PopPUNK will calculate core and accessory distance between input assemblies using variable length k-mers. A model will be fitted to all of these distances to determine genetic clusters for all inpits.\n+\n+------\n+\n+**Description**\n+\n+       The most important thing to check is that in the output plot the component (blob) closest to the origin has been correctly identified - this should be checked in the cluster/model plot output. If it has not, you may wish to try another model. Some broad advice:\n+\n+  * DBSCAN is a good default, but may lead to unclassified points (black). If there are a large number of these consider another model.\n+  * GMM will work well with well-separated components and an appropriate choice of K (consider increasing it based on the number of components that can be seen).\n+  * The refine mode should be added in recombining species, which can be seen from the output plots if the coloured components are overlapping, or if there is a blur of points rather than discrete blobs of points..\n+       ]]></help>\n+\n+    <citations>\n+       <citation type=\'bibtex\'>\n+@article{Lees01022019,\n+  author = {Lees, John A. and Harris, Simon R. and Tonkin-Hill, Gerry and Gladstone, Rebecca A. and Lo, Stephanie W. and Weiser, Jeffrey N. and Corander, Jukka and Bentley, Stephen D. and Croucher, Nicholas J.},\n+  title = {Fast and flexible bacterial genomic epidemiology with PopPUNK},\n+  volume = {29},\n+  number = {2},\n+  pages = {304-316},\n+  year = {2019},\n+  doi = {10.1101/gr.241455.118},\n+  abstract ={The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (Population Partitioning Using Nucleotide K-mers), a software implementing scalable and expandable annotation- and alignment-free methods for population analysis and clustering. Variable-length k-mer comparisons are used to distinguish isolates\xe2\x80\x99 divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using data from both simulations and genomic collections representing 10 taxonomically widespread species. Connections between closely related isolates of the same strain are robustly identified, despite interspecies variation in the pairwise distance distributions that reflects species\xe2\x80\x99 diverse evolutionary patterns. PopPUNK can process 103\xe2\x80\x93104 genomes in a single batch, with minimal memory use and runtimes up to 200-fold faster than existing model-based methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to reanalyze all genomes de novo. This facilitates real-time surveillance with consistent cluster naming between studies and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualization and online publication is streamlined through the automatic output of results to multiple platforms. PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.},\n+  URL = {http://genome.cshlp.org/content/29/2/304.abstract},\n+  eprint = {http://genome.cshlp.org/content/29/2/304.full.pdf+html},\n+  journal = {Genome Research}\n+          }</citation>\n+    </citations>\n+</tool>\n'
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/12673_8_24.contigs_velvet.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/test-data/12673_8_24.contigs_velvet.fa Thu May 16 11:08:09 2019 -0400
b
b'@@ -0,0 +1,50725 @@\n+>.12673_8_24.1\n+ATTTTAACCCTTGCCCCAGGTTCGGAAATAACAGAAGGCGATGCAGTCATGGCTATTGAA\n+GCACCAGAGAATATCCAGGCAGGAAAATATACAGGGAACGTTGTGTTTTCGATTAAGTAT\n+GAATGATGTAAATTAACCAGACTAGTGATTATGTCACAGTCCTGTGGTTATGAATAAATT\n+GGAGGTTACCTATGAAGAAGAAAAGAGTAGTGATTATATCCTTACTACTATTGTTAGTAA\n+GTGTCATTGGAATCAGTAGTTATTTTCTATTCAAGGATAAAATAAATCTGTTGGATGTAG\n+ACCATTCTGCCGTTGATTGGAACGGAAAAAAACAGAAGGATACAAGTGGAGAAGAAAATA\n+CAATTGCCATTCCAGGGTTTGAAAAAGTAACGTTGTATGCAAATGAAACAACACAAGCAG\n+TGAATTTCCATAATCCGGAAATTAATGATTGTTACTTCAAAATATCGCTTATTCATCCGG\n+ATGGTTCGGTTCTATGGATATCTGATTTAATCGAACCGGGAAAAGGTATGTATTCCATTG\n+AATTAGAAAAAACGTTAGCGGTAGGCGAATATGAAAATGCAGTATTAAAATATGAATGTT\n+TTTCTTTAAACGATCAGTCACCTTTAAACGGGTCTGAAATAAATTTAAAATTAGTTGTCG\n+TCTAGACAAAGGAGGAAATTTTTTATGAATAAATTAGTATTAAGTACGTTAAGTGTAGCA\n+GCAATGGGTATGGTATTTTTTAGCGGAGGGACAGCCTACGCTGCAGATAAAGAAGGTAAT\n+ACAGTAGTGGAATATTCTGTTGAAGGTGATTATACCCTCGTTGTACCAGAAAAAGTAAAT\n+TTATCTAATGATAACGCCACAGAAATGTCTGTGAAAACAATCAATCGTAACTTAGAACCA\n+GGAAAAGAAGTAGAGGTGACATTATCTAGTGGATTATCAGCCGATGGAGAGATTGAATTA\n+CAACGGGTTGGCGCTACTTCGGACGTAATAACTAGTAGTTTTAAAAGTAATAATAGTGTA\n+GTACCCATGGCTAATCCTGTTATCGGAAGCTTTTCAGGTTATGCGATAGAGGAAACAGAA\n+GTAAGTAAAATTCAAATTGGAAACCCTCAAGGAGACAAAAAAGCTGGAGCATATCAAACA\n+ACGTTAACTTTTACAGCTGCTTTTAAATAAGAAATTACGAAAGGAGTTGTGCATTTCTTG\n+AAAAGGAAATTAGTTCTGGCAATGGTACTAATCAGCTTTTGTGGGATGTTCCTCTTATCG\n+CCTGAACGAGTTCAAGCTAGTCAAACAGTGGTTGAGGTGTTCATTTCAGAGGATGATTTG\n+GATGTCAGTGAAGAAAACATACAGGAGATCCCTAAAAAAGAACTGGCAGCCTCTTCAGAT\n+AAGGATAACAAACAACCCATATTACCTAAAGCAGGTGATACAGTAACTAACTATACCTTA\n+TTGGGTTTAGTGCTCGTCCTTATTTGGTTGATAATGCAAAGAAAAAGGAAGAAGAAGGAA\n+TAACCCCCTGTGACATCATCATAATGTAGTAAGTAAAAAGGATATAAAAATTTCTGTGTT\n+AGATAGGAAGTGACAGGTATGGCTCGAATCGAATATGGAGAAGAAATTCAAAAAAGCCTA\n+CTGGTTTTATACTCTAGGGGGTCTACCATAGACTCTATCTGCAAGGAGTATGGTATCCCT\n+CGTTACGAATTTCACAAATGGATGAAGTTACATGATGCCGATAAACTGGAAACCAAAGAG\n+GTGAAGACTTTCCTACAGATAAGAGAATTAAAACAACAAAAAAACAAATTAGAAGAAGAA\n+ATTTTGTTTTTAAATGAAGCAATCAATCTGTTGGAAAGTCCTTGAGAGGGATGATTTTAA\n+GTATTGATTGATAGGTAGTATGAGAGAGAGGATGATAATTTCATCTTCTCTTTTTTGCTT\n+TTATATTTTGGTACAGCCGATTCATGTAAAAAAAGGGTATACCCTAAATAGACAATGGGA\n+AATAGCTAGTATAAAGAATTTAATTTTGTAAATTTAGGTGTCAATGATTTAATAGTATAG\n+TTATACTAAAGTGGAAATTAAATAAAAAATTGCTTAAAATCAATACTGATAACGAAGAAT\n+CAATGATTGCTTTGAGTAATGTGGCGGATTGGAAGCAAATTATGAAGAATTAAATTTAAA\n+TTGATGGGCAAATGATTTAATAAAGAAATCTTTCAGGAGTCCACTTGTGATTATATCAAC\n+TTGACATATTAGTAACATCATTGTAACATTACTAATGTAAGCGGATACATATATAGTTGA\n+AGTACTTTAAGAAAAAAACAAAAGTATTGTAGCGTGGGATGTCGCGCTTTTAGGTAAAGG\n+AGATGGATAAAATGAAAAAAATTATTATTGGTGTGTTTTTCGGGATTCTTATTCTAGTTA\n+TTGTTGGTCTATATGTTTCATATGTCTATATGAATCAAAGCTTTATATGGGTTGCAGGGA\n+TACTTTTGTTGTTAGGTACATTATTCAATTGGTTTTTGTATAATAAGTATCTGTCTAAAA\n+AAACATAATAAGGGAGCGAGATAACCATGAAAAAAATCATTATAGTACTAGCATCAGTTA\n+TGTTAATGTCTCTTTCGGTTCTGCCACTGGCAACTTATGCATCAGAAACAGAGAACACTC\n+CTACTGAATCATATGACGGAGAAAATTTTATAGCAACTCAAATAGGTAATACTTTAGTTA\n+TTGAAGATAAGAAGACGGGCGAAACTGTAAAAATTGAAATGAATGACGAAGAAAACGGGG\n+TAATTACATCTGATGATGGTACAATAGAAAATGTACATAGGGATGAAGAAGGTAACGTTT\n+ATGTAGATAATGAGCTTGAACTAGAAGCACCTCCTTTAGACATTGAAGATGGCATAAATA\n+TCGCCACTCAGCCTCGGTTACTGAAAGCTTCTAAATGGATATATGTTCAAACAACTAAGT\n+ATAATACAACCACACAAGGCAATATGAGAAGTCTTGCATTGGGGATTCTATCATTCATGC\n+CAATTACAGGTCCAATCTTTGGAATAGTTGCAATTATTGATGCTGCTCGATCAATGGGGG\n+CGAAAACATTATATGTTAGAGTGAAACAATATCGTACTAGTGGTTATCAATTTTATAAGT\n+ATGATTCTTATTATTATGCCAATGCTAGTTTAACTAAGCTAGTTAAAAAAACATCCCAGA\n+CTAAACGAATGTGGTAGGGCATTATTAAAAAAACTAGTATAAACTAAAAGACCTTGCTCA\n+AAGATTAGCAAGGTCTTAGACTGGGGAAGAAAAAGTCTTCTCTTTTTCTGTTTTATGGAA\n+ATGTTATTCCGTATTTTAGACGAGTTTCTTCTATGGAAGAATACACAATTTTAGGGAATG\n+TGTCTGATATGGCAGCTAGATTCTCTGATAGTGAATAAGATTTGAAATTACCTAATGTTT\n+ACTACAGTGAAAAGCAAATTAGAGAAGAAGTGACTCGTTCTTTAGAAGCTTTAGCTTGAA\n+TCATAAAATTTGAGAGGAACGTAATTATGCAAAAAGATACATATAACGGCATTCGATTGA\n+GTGTAATCCAATTGATAGATTCAAAAAAAGAAAATCTGAAGGAGAATAATATAAAATTAA\n+CAATTATAAAGAATGAAAAAGACGGTTATGTTGTAGAACTGGATAATGACAAATGCATGG\n+CAGAAATTGTAGTTGAAGAACCTACTTATGCCCCATATCGCTATATTTCATTTGAAGTAG\n+TTTCTTTGATGGATGGAAAAGTTAAAATTATCTATTCTTGGTATGATGATGAAACAAGTC\n+AATGGAGCGATATTGAGAAAGAATTAAATAAAGGAATTCAATTTCTAAATAATTTT'..b'TATGTTTAATGCTTTTTAAATAACTATTCCAAGCGGTTGGTCTACTG\n+CTCGGCACGTTGCCAAACATACGCATGCTATATTCGCCGTTCGCAGTATTACGATAAATC\n+GTCCAGTAAGCACCTGAGCTTACCACTGTTAAATCCGAATCATCCGAATCAGCAACAGGC\n+TGCTCTCGAACATCTGGATTTTGCATCAACTCATCCGTAGTTGGGATTTCTTCTAGATTC\n+TCGACCTCGGCTGGTTTCTCTTGCGCAACTTCTTCTGCAATGAGATTAGAGGTATCCAGA\n+GAACCCAGCTCCTCTTCTGGAAGCTTATTCGTTGTATCCCTTTCTTGTGCGATAGAAACA\n+TTAGCGCTCCCAAAAGCAATAAAAAGCACAGAAATAATAAGGACCACTCGCATGGAAAAC\n+TTTTTCATCAGCTCCCCTCCTTCTTTCGTAGTTAATTTCTAGATGCAAACTTTCTAGCTG\n+CAACTTAATTATAGAGGAGTCGAGAAGCATTTCTGGCCATAAAATTTTAACTTCTTAAAA\n+TTTTACGGCTTAGTTGGTGTGTTTACTTTTTCCATTAGTATTGTACAAATGAAAAATAGA\n+AATAAAAAAATCCGAGTAACGATCATTACTCGGACAAGACCTTGGTTTTCCATTTAAACA\n+TTTTCCATATCCATTCCAACAAGTGTTTCCCTAATCTTTTTTATTAGCGATAAATTTTTT\n+TCTCGCTATTTTCGCCAGATTATCATTAATTTTGACATAATCAGATTCTAGCCATCTAGT\n+ATTTACATAGATTATTGGTTGATTGATACGTAAAGAGGTCAACACTTCGGGAGATACGGA\n+AAAATCACTTATATATAAATCCACCACCGGATCAACTTGATTAATTATTTCCAGATTGTA\n+GTAACTAGAAAAATACCTCATAAAATCAAATACGGCTGTTTCATTAGATATGGTCGATAA\n+AATAGTTACTTTAATAGGCAAGGTGTGTATAGAAAAATCAATCCGCTTATCCAAAATGAT\n+CAGATAATCTGAAGCAAGTCTTTCTTCAAACGGTTTTAATGAATCCATTTCTTTTAGATT\n+TACTAATTGGCTAATCAATGGTTCTAGGTGATTCACTTTATGGATTTTTCTTATATTTCG\n+ATCAAGATTTGTATACCCTGGCACAATATTATTGAACTTATTGATTAAATTATCAAGTAA\n+GAAATATCTATAATTTATACTCGCAAAGGAGTAACGGAGCAATTCCATCTCTTTCTCTGA\n+AAATGGAATAGAGAGATTATCATTTACTTGTTCACTGGCAAAATCAACTAGTTTCATGAA\n+GCCCATTTCTTCTAACTGTTCATCCATGTAGAAAAAAGAAGGCATTTTTTCAATGGAAGA\n+ATAACTACCGAAAGCAACAATGGTACTCAGTATAATTTGCGTCGTGTAGGTCATTTCTTT\n+ATAGTTCCTATTAGGAAGTTGTTTCGCTACCTTTTTAATGAACGCACTTTCTGATTTCTT\n+AGACTCCTCGGTGCAAGCCTTATATAGGGCCACTTTAAACTGCCTAGTTGTATCAATTTG\n+ACAATTCATTCGATCTCTTAATAAATGCATAGCGACATAATAATGAATCATCATCGCCTT\n+ATCTATCGAGTTTGCTCTATAAATTTCTTTTGGACAACTCTCTAATAAGTCAGTGATTTC\n+ATCATATCGAACAAAAGAAAATGGCCAACGATCCCCGCTATATGCGACTAAAAAAAGGAA\n+GGTATAGAATATTCTTAATGAAAATTCATCCCCCATTATTTCTACCTGATTTCCTGTAGA\n+AATATACAAGTTCCGTTCACTTAGCTCTTCATTCAATTCTTTTATTTCTTTCTTTATCCC\n+AGAATAAGAAACATGTACTTTTTTTGCCAATGCTTGTAGATTAGGGAAGGAAGCCAGCAA\n+TAAAGTTTCGAGAATTTGAAATTTGGGCGATTCTCTAATATAGGCGTTGATAATGAGTTG\n+AATACTACAATTATCCGATATTTTTAAGGTATAGGACAAATTTGGCGCGGAGTGAAC\n+>.12673_8_24.11\n+CTTTACGTCTCATTGCTTTTCGTCTTCTTCTTTGTTCAGTTTTCAAAGGTCACTTTTTCT\n+TCTTCGTTGCCTTTAGCAGCAACTCTTATATCTTACTCTATTCTCTAAACAATGTCAACA\n+CATTTTTAGAAATAATTTGGTGGAGCCTAGCGGGATCGAACCGCTGACCTCCTGCGTGCA\n+AAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCATAATAAAAATCAAACAATCGGGAAGA\n+CAGGATTCGAACCTGCGACCCCTTGGTCCCAAACCAAGTGCTCTACCAAGCTGAGCTACT\n+TCCCGTTTAATAAAGTGCGCCCAAGAGGAGTCGAACCTCTAACCGCTTGATTCGTAGTCA\n+AGTACTCTATCCAGTTGAGCTATGGGCGCATATAAAAATAATGCCGAGGACCGGAATCGA\n+ACCGGTACGGATATCACTATCCGCAGGATTTTAAGTCCTGTGCGTCTGCCAGTTCCGCCA\n+CCCCGGCATATTGGAACTTTTGTAAACAAGCGGAAGACGGGGTTCGAACCCGCGACCCCC\n+ACCTTGGCAAGGTGATGTTCTACCACTGAACTACTTCCGCATATTTAAAATAAGTGCGGG\n+TGAAGGGACTTGAACCCCCACGCCTCGCGGCGCCAGATCCTAAATCTGGTGCGTCTGCCA\n+ATTCCGCCACACCC\n+>.12673_8_24.12\n+TTCTTCGGCTCCTAGTGCCAAGGCATCCACCGTGCGCCCTTTCTAACTTAACCAATTTAC\n+TTCTACGAAGTAAAGGTTGTTTTTCTGATTTTCTGTATCAGCGATGATACTTCCAATCAG\n+ATGAAAGATTCACTTTCAGATGATTCTCGGTTACTTGTGTCATAGATAATCACTTATCTA\n+TGCTAACTTTACTAACTTTCTTATCTAGTTTTCAAAGAACAATTTTGGTGGAGCCTAGCG\n+GGATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCC\n+CGTAAAAGGGTATCATTATTTATATTTCTTGTGTCAGAAAGAAAAAGTGGGCCTAAATGG\n+ACTCGAACCATCGACCTCACGCTTATCAGGCGTGCGCTCTAACCAGCTGAGCTATAGGCC\n+CGTCAAAAATGTAGTGGCGCGATGCTTCAAGCATGGTGCCTTGCATACTTTATCTGACAT\n+AAAAAGAGAGTAACCTCTCAAAACTGAACAAATGTAGAAGAACGAAAACTCACAGGTTTC\n+CTTTTCCTTAGAAAGGAGGTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGAC\n+TTCAC\n+>.12673_8_24.13\n+GGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAAAAGGAAACCTGTG\n+AGTTTTCGTTCTTCTCTATTTGTTCAGTTTTGAGAGGTTACTCTCTTTTATGTCAGATAA\n+AGTATGCAAGGCACTATGCTTGAAGCATCGCGCCACTACATTTTTGACGGGCCTATAGCT\n+CAGCTGGTTAGAGCGCACGCCTGATAAGCGTGAGGTCGATGGTTCGAGTCCATTTAGGCC\n+CACTTTTTCTTTCTGACGCAAGAAATACAAATAATCATATCCTTTTACGGGGCCTTAGCT\n+CAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAGGCTCC\n+ACCAAAATTGTTCTTTGAAAACTAGATAAGAAAGTTAGTAAAGTTAGCATAGATAAGTAA\n+TTATCTATGACACAAGTAACCGAGAATCATCTGAAAGTGAATCTTTCATCTGATTGGAAG\n+TATCATCGCTGATACGGAAAATCAGAAAAACAAC\n'
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/12673_8_34.contigs_velvet.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/test-data/12673_8_34.contigs_velvet.fa Thu May 16 11:08:09 2019 -0400
b
b'@@ -0,0 +1,48882 @@\n+>.12673_8_34.1\n+CAGTGGTTGAGGTGTTCATTTCAGAGGATGATTTGGATGTCAGTGAAGAAAACATACAGG\n+AGATCCCTAAAAAAGAACTGGCAGCCTCTTCCGATAAGGATAACAAACAACCCATATTAC\n+CTAAAGCAGGTGATACAGTAACTAACTATACCTTGTTGGGTTTAGTGCTCATCCTTATTT\n+GGTTGATAATGCAAAGAAAGAGGAAGAAGAAAGAATAACCCCCTGTGACAGCATCGTAAT\n+GTAGCAAGTAAAAAAGGAAAGAAAATTTCTGTATTAGATAGGAAGTGATAGGTATGGCTC\n+GAATTGAATATGGAGAAGAAATTCAAAAAAGCCTACTGGTTTTATACTTTAGGGGGTCTA\n+CCATACAGTCTATCTGCAGGGAGTATGGTATTCCTCGTTACGAATTTCACAAATGGATGA\n+AGTTACATGATAGCGATAAACTTGAAACAAAAGAGGTGGAGACTTTTCTACAGATAAGAG\n+AATTAAAACAGCAAAAAAACAAATTAGAAGAAGAGATTTTGTTTTTAAATGAAGCAATCA\n+ATCTGTTGGAAAGTCCTTGATAGGGATGATTTCAAGAATCAGCTGTAGGAAAAGTGAGCA\n+ATCATTTTTTCTACAGCTTTTTTTAAAATGGGGAGGTTTTTATGTTACTTTTATATAGAT\n+GCCATGTTTACTTTTCTCAGATGCCCAATCATTCATTTCACGTACTTTTTCTGAAAGCTC\n+ATCCGCCGGAATAAGCCGCCCATCCACCAAAACAGAAGGATTAATCAAGCGCATTTTCTT\n+CTTATGATGATAAGTAAAGTCCACCTCATTTTCTTCCAAATGGGGACTCTCGAGCAACTG\n+AATTTTCTCCCGAGCATCTGAATTCGCATTCAATTTAGCTAACAATTCAGCATCAGTCAA\n+CCGAAGATCCGCATTTGTAATCGTCTCCTGCTGAAACGCAATGCGCATTGCTTCAGCCAA\n+AATCTCATAACTATAAACATTCAGCGGATCATAAAAATAATCAATCACTTCCGAATAATA\n+TTGCGCAACAAACCATTCTGCAAGAGCGATATTTGCCAAATAAAGCCGCCCATCAACCAT\n+TACTAAAGCCTGCAAAAATTCTTCCACCTCAGCCAAACTAATTTTCCCATGTCGATACAA\n+ATCTTGCAACGTATAATCAATCCGGTCAGCACAAAGCTCCGGGGCTTCTTGCTCCAAAAT\n+TTTCCACTTCGAAATATCATCAAAAATCCCTTCAAAAGAATAACCATACTTCTCTAAAAT\n+GGCAGGAATCGTCGAAGTTTTTACAAAGTCCTCAAAAATCTGCTCATGATAATCTTCCTC\n+TTCAAAATCAAGCGCATAATCCACCACATGCGAAAAAGCAGTGTGCGATACATCGTGCAG\n+TAAGCCAGCAATTTGCTCCTCCAAAGAGCCACCGAACTTCCTAATAAAAAGCATCACACC\n+AATCGAATGATCAAGCCGGCTAAGGTCCCAAAGCGGATTTACTAAATAACTCGAGCCACC\n+TTGATGCACGTATGCTAGCCGTGAAACCAATGGGCTCTGGATTAGTTCAGCCAAAACAGG\n+TTCTATTTCAAATGTTCCGTAGAGCGGGTCTGTTATTTTCATCATATTCACCTCTTTTTT\n+TAATTATATATTAGCGAACAAACGTTTTCCATGTTTTCCCTAGCAATTCCAATTTTGCTG\n+AGAAAGCTTATAAAAAATTACTGAAATGACCGAAGATGCGATTGATAAAATGAAAAACAG\n+TTCGGTAGTGTAATTATTCCAGACGAAACCTCTGTTGTTGCACAAATTTTCCGCGATAAA\n+ATCGACCTAGTTGCCAACGCAATCGGCGAATCTATTTCCCAAATCAAGCGGGATGAAGCG\n+CTGCAAAATGGCGAGCAAAAGCGAGAGAATAAGTAACCTTGGCCGGTACAGTGACTGACT\n+CGGTTGAAGTAGTGGAAGAAATCCCATTGGTGCATCATCTGGCTAATGCGCCCAGGTTGC\n+GCATGAAAGTTGTGGGGAATTTGGTTTAAGGGAAGTAAATAGTGGAACATTCCAATCATT\n+TTTTATAAAGTAATCCCACGTGTATAAAAATACGGTTTATACACGTGGGATTATGGTTCT\n+ATATGAAATAGGTTATTTATTAGAAGGTTTAAATGGCTTATTTTATTTTTCAATGTATAA\n+AATTATGTATATTGACACAATTTGTGTTATTTTGAACATAAATTTAAGTAAATCAATTCT\n+TAATGTATTGATTTTCGCCTAAAATAGGTCGTTCATGACAAGAATCGGACATTTCATTAC\n+ATTTTTGGTTATACATTCATTTTCTATGCTATGGTTTTAGTAGGAACAACTATTTGATTA\n+ATGCATAGAAAAGAGGGAGCATAATGAAAAAAAGGTTAATAGGTATTATTACAGCATTAT\n+TGTTAGTAAGTGGGATTTTGCTATCTCCGCAGATGGCTCAGGCGGAAACAAAAGTGGATT\n+ATGACGCATTGTATCAACAGGGAGTATCTGAAGGGATTATTAATAAAGCAGATGTAAGCT\n+TAGAAACATGGATAAAAGAGAATGAAAGTGAGTATAATCAAGTCTATCAAGATGGTTTAA\n+AAGATGGTGTCTATGATGCATCATTGTCGTATGAAGAATGGATAAAGTTAAACAACTATG\n+GACAACCTCCTGTAGTAGATGAAAATTGGGAAGAAGTTCCACAGAAGCCAATGCTTAAAG\n+GTGTGTATAAAGGTTATAATATTAAAAAAGGGGACATTCTGATTACAAATGGAACATCTT\n+CTTCCGGATTATTGGGACATGCTGCTATTGCGAATGGGAATGAGTATATATTAGATATTC\n+CTGGGGCTGGAAAAACGACAAGGCAAGTACCTACAAGTAAATGGATGAGTGATTATGATC\n+CAGAAGGATGGGTAAAAGTTTATCGCCTGAAGGATAGTTCTGTTGCTAATGCCGCAGCCA\n+ATTGGGCGGACAAAAACTATTATTCCACCAAAGGCACATCCAAACAAAATATTTTCCCAA\n+AATACGGTATGACAGGAAGTCGATATAGTAAGAACCCTACTTATTGTTCTAAAATTGTAC\n+TTCAAGCCTATTATTTCGGAACAGGAAATAAGCCTGTTGTGCAAGTATTTCCGTCCTTAG\n+TTACTGTGTATGATTTACCAAACTATTTTTCAAAAGCATATAAGCCACAACAAGTGAAAT\n+ACTTTAAATAAATCTCATGTATTAGGAAGTGTCGCTGAATGAAAAAGTATAAAAAGTGGT\n+GGATAACGATTGGATTAGTGTTAATTATTTGCATTATCGGATATATTTATTGGTTTGCAA\n+TCCCTAAACATACAGCAAATGAAGCAGTAGATGATTACTTAGCAGCGCAAAAGATAAATT\n+CAACGCAAGTTAAAACGAGGGATATTCAAAAAGATTGGACTAGAGGAGGATACTATGTCA\n+CGATAGTGTTTAAGGATGACCCTAATTTAGTGTATGAATACAACTACAATAGTAAAAGGA\n+ATACGCCTTACCATATTAATCTACTTGTTTTTAAAGATGGCTCGAGTCAAGAAGATGACC\n+AAGTGAAGCATCCACCACTACAAGAGCAAAAGGATTAAAGCAGAAACCCAAGCATTTTAA\n+GTAAGCAGTGCTACTACTGCTTACTTTTTTGTATTACTTTTATATAAGCTCCACATAAAA\n+AGTATCACGCCGATCGAATAATCAAGCCGGCTAAGGTCCCAAAGTGAATTTACTAAATAA\n+CTTGAGACACCTTAATGCACGCGAGCTAGCCGGGAAGCCAAAAAGCTTTGGATTAGTTCA\n+ACTAAAATCTATCATTTTCATTCAAGGAGATAATAAAGCACCAACCTCTCCCATGC'..b'ACATGTTTGCTGCTTGTAAAAGTCTTGAAGAGCTAGATTTAAGT\n+ACCTTGGATACCAGTTCAGTTACTAATATGTACAGCATGTTTTCTTATTGTTATAATTTT\n+GAAGAGTTAGATCTAAGTAATTTTGATACGAGTTCCGTTACTAATATGCAACAAATGTTT\n+TATGGTAGTTACAATCTTGAAGAGTTAGATTTAAGCAACTTTGATACGAGTTCCGTTACT\n+AATATGCACCTAATGTTTGGTGGCTGTAAAAGTCTTGAAGAGCTAGATGTAAGCACCTTT\n+GATACCAGTTCAGTGACTAACATGCGTGGTGTGTTTTCTGAGTGCAATAGTCTTGGAGAG\n+CTAGATTTAAGTACCTTTGATACTAGTTCAGCAACTACTATGCAGATCATGTTTTATGAT\n+TGTACTAGCCTTGAAGAGCTAGATTTAAGTACCTTTGATACTAGTTCCGTGACTACTATG\n+GCTTCCATGTTTGAAAATTCTACAGCGTTAAAATCTTTATATTTAGATAATTTTACAG\n+>.12673_8_34.12\n+CCACCAAATACTCTCTATACACCGTTATTTCCTCAGTAGTTTTTACTGTACGATAATTTC\n+CATCTAAGAAGGAATCTATTACTCCCTAAGGTAGAATTTCTCTATCCATTTCAATAACTT\n+ACTTTATCATCTATTTTAGTTCTATATTTAGCCGCTCATTAAGTTAATTTAAAGGTATAT\n+TTTTTCGTTCCTTCTTAATCTTTACTTCATTTTTCGGTACCCATTTTTCATAATAATATT\n+TATCAGTTCTTTCAAAATTTAATTCTTTAGCTATTTCTGTATTTATAGTACCAATTCTAA\n+AAAAATCTTTGGTTTCAGTAATAGATTCAAATTCCTTTTCTTTATACACGACTATATCTG\n+ATATTTCATACAGCTCTTTTATACAAGAAAAGTCAACTTCACATATATATAAGTCTGGCA\n+ATTTTTCTTTATTTAAATAGTTATCTGGGTATTCTTTCTTTACAAATCCCTTTTGTATAT\n+CTTGCTCATTACTACTAACAAGTCTTACTGTATTATCACCAATTTTACTAACTTTATAAA\n+TAACTTCTTTGTATTTAGCAAATTTTGTACTCATAGTTAGCAATCCCCTTTCTAAAGCTG\n+CTCAAGTAGTTCCTAAAGAACACAGAGTAGTTGACTTTTCCCTGCTATTTATACAAAATT\n+GTCAAACTGTTGATAAATAGGTAGTAGCATATAACGAACTCCTTGCATGCATTACCTTAT\n+ATTATAAAAAATATCTATACTACTTATATTACTTCTTGGATCATATTCAGAAATTATTTT\n+TCCCCAATTATAACTTACATTATTTTGAATACCGTTCTCACTTAATATTTTATCGTGTAT\n+TGTTTTCCTATCTATTTCATTAGATTCAGAAATGTTTTGATCACAATTAATAAGAGAAAC\n+ACTATATAATTGCTTTTCTTTAAAAAATAAGTTTACAAAGTAATGATACGTATCAATTTT\n+TTGTATTTTCTCCAGATAAATTATTTTAATCCCGTCTTGTCCATCATAATACTCTGTGTT\n+CTTAAATTCATCAAATTGATATTCAGGATGAACAATCAATTCATCATTTATCTTCAATTC\n+TCCATTTACAGTATTTAACATTTATTTAGCTCCTCAATCAATTAATTTTATCTCATCAAT\n+AGGTATTAAAATGCCTTTTTCTATTAATTCATTTACATTTGGAACAAAAACTTGAAGTGC\n+TCCACCCTCACCAAATTGTGGATTAGCTTTCGTAAATCCAGATGCTGCATCAACTTCACT\n+ATTCACTTTATATCCTGTCATACTTTTCCGATAGCCATAAATAGGATGTTTTTCGACTTG\n+TAATCCTTCAAAAATTTTAGTCGCACTAATATCAGCATTTTCTATGACTTCCTTATAGGA\n+ATCTTCGACTATAGTTATATATATTTATATTTTCTTCAAACACATGGTTTTTTTTGCAGT\n+CTCAAGTATTCTTTCGGTCACTGTGTACATATCTCTGATTATCTCTTCTTGTTGTGATTT\n+CCCAGTGTACTCTTCGTTGATAGCATTCAAAACATTTTGCGCATATTTTATTAAATCTTC\n+CATAAGATCCTCCACCCTTATTTATTAGGAACACTCTTAATATTAATAATCCAATCGGAA\n+GACCAATTTCTTGGAAGAACAATTTGGTCTACTCCGCCTTTTAATATTGTACCTGTCGAC\n+TCAATTGCTTGAGGTGCTACTTTACCAATATTAATTTGCTGGCCTTTAGGAATAATTATT\n+TCTGCTTCGTACATGCGAGTATTCTTCCATCCAGGTAATAATGCCATATCTATTTTTGCG\n+TCTATTCGACTTATTGTCTTCTCTGAAGTCACAAAACTTCCTGTAGACTTTGCATTTCCA\n+CCAAATACTCTCTATACACCGTTATTTCCTCAGTAGTTTTTACTGTACGATAATTTCCAT\n+CTAAGAAGGAATCTATTACTCCCT\n+>.12673_8_34.13\n+CTGCCGGGCAGTATTTCTGGAGGTTTAGCTCAGCTGGGAGAGCATCTGCCTTACAAGCAG\n+AGGGTCAGCGGTTCGATCCCGTTAACCTCCATTTTTTATGCCGGCTTAGCTCAGTTGGTA\n+GAGCAACTGATTTGTAATCAGTAGGTCGCGAGTTCGACTCTTGCAGCCGGCACCATTAAT\n+ATTAACTTTATGATAATACATATTTTTATTGTAGAGAGCCGTTAGCTCAGTTGGTAGAGC\n+ATCTGACTTTTAATCAGAGGGTCGCTGGTTCGAACCCAGCACGGCTCACTTTTGCGGGTG\n+TGGCGGAATTGGCAGACGCACCAGATTTAGGATCTGGCGCCGCGAGGCGTGGGGGTTCAA\n+GTCCCTTCACCCGCACTTATTTTAAATATGCGGAAGTAGTTCAGTGGTAGAACATCACCT\n+TGCCAAGGTGGGGGTCGCGGGTTCGAACCCCGTCTTCCGCTTGTTTACAAAAGTTCCAAT\n+ATGCCGGGGTGGCGGAACTGGCAGACGCACAGGACTTAAAATCCTGCGGATAGTGATATC\n+CGTACCGGTTCGATTCCGGTCCTCGGCATTATTTTTATATGCGCCCATAGCTCAACTGGA\n+TAGAGTACTTGACTACGAATCAAGCGGTTAGAGGTTCGACTCCTCTTGGGCGCACTTTAT\n+TAAACGGGAAGTAGCTCAGCTTGGTAGAGCACTTGGTTTGGGACCAAGGGGTCGCAGGTT\n+CGAATCCTGTCTTCCCGATTGTTTCATTTTTATTATGGGGCCTTAGCTCAGCTGGGAGAG\n+CGCCTGCTTTGCACGTAGGAGGTCAGCGGTTCGATCCCGCTAGGCTCCACCAAATTATTT\n+CTAAAAATGTGTTGACATTGTTTAGAGAATAGAGTAAGATATAAGAGTTGCTGCTAAAGG\n+CAACGAAGAAGAAAAAGTGACCTTTGAAAACTGAACAAAGAAG\n+>.12673_8_34.14\n+TTATCTATGCTAACTTTACTAACTTTCTTATCTAGTTTTCAAAGAACAATTTTGGTGGAG\n+CCTAGCGGGATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCT\n+AAGGCCCCGTAAAAGGGTATGATTATTTGTATTTCTTATGTCAGAAAGAAAAAGTGGGCC\n+TAAATGGACTCGAACCATCGACCTCACGCTTATCAGGCGTGCGCTCTAACCAGCTGAGCT\n+ATAGGCCCGTCAAAAATGTAGTGGCGCGATGCTTCAAGCATAGTGCCTTGCATACTTTAT\n+CTGACATAAAAGAGAGTAACCTCTCAAAACTGAACAAATAGAGAAGAACGAAAACTCACA\n+GGTTTCCTTTTCCTTAGAAAGGAGGTGATCCAGCCGCACCTTCCGATACG\n'
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/12673_8_43.contigs_velvet.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/test-data/12673_8_43.contigs_velvet.fa Thu May 16 11:08:09 2019 -0400
b
b'@@ -0,0 +1,50063 @@\n+>.12673_8_43.1\n+AATGATCAGATAATCTGAAGTAAGTCTTTCTTCAAACGGTTTTAATGGATCCATTTCTTT\n+TAAATTTACTAATTGACTAATCAATGGTTCTAGGTGATTCACTTTATGGATTTTTCTTAT\n+ATTTCGATCAAGATCTGTATACCCTGGCACAATATTATTGAACTTATTGATTAGATTATC\n+AAGTAAGAAATATCTATAATTTATACTCGCAAAGCAGTAACGGAGCAATTCCATCTCTTT\n+CTCTGAAAATGGAATAGAGAGATTATCATTTACTCGTTCACTGGCAAAATCAACTAGTTT\n+CATGAAGCCCATTTCTTCTAACTGTTCATCCATGTAGAAAAAAGAAGGCATTTTTTCAAT\n+CGAAGAATAACTACCGAAAGCAACAATGGTACTCAGTATAATTTGCGTCGTGTAGGTCAT\n+TTCTTTATAGTTCCTATTAGGAAGTTGTTTCGCTACCTTTTTAATGAACGCGCTCTCTGA\n+TTTCTTAGACTCCTCGGTGCAAGCCTTATATAGGGCCACTTTAAACTGCCTAGTTGTATC\n+AATTTGACAATTCATTCGATCTCTTAATAAATGCATAGCGACATAATAATGAATCATCAT\n+CGCCTTATCTATCGAGTTTGCTCTATAAATTTCTTTTGGGCAACTCTCTAATATGTCGGT\n+GATTTCATCATATTGAACAAAAGAAAAGGGCCAACGATCCCCACTATATGCGACTAAAAA\n+GAGGAAGGTATAGAATATTCTTAATGAAAATTCGTCCCCCGTTATTTCTACCTGACTTCC\n+TGTAGAAATAGACAAGTTCCGTTCCCTTAGCTCTTCATTCAATTCCTTTATTTCTTTCTT\n+TATCCCAGAATAAGAAACATGTACTTCGTTTGCCAATACTTGTAAGTTAGGGAAGGAGGC\n+CAGCAATAAAGTTTCGAGAATTTGAAATTTGGGTGACTCTCTAATATAGGCGTTGATAAT\n+AAGTTGAATACTACAATTATCCGATATTTTTAAGGTATAGGACAAATTAGGCGCGGAGTG\n+AACAATCGAAAACGCTTTATAGCCAAAGCGTTCAATATCAAAATTAATTGTTTTAATCGT\n+AGAAATGAGGGTTGGATACGTGATGTTCAAATCATTTAATAGTTCCTCTTGTGTACTTGT\n+ATGATTTTCCGCATAAAAAATCTTCTCAAGAAGTGCTACCTTTTTTTGGCTTTTTGAATC\n+TAAATATTCTCTCATTAAAACACTTCCTTTCAATGTTTACTTTTTATGTAAAATCCAGGT\n+AACAGCAATAAGATGTTCCTCTAAGTCATCGTATTCGCTCCATTGGCTCTTAAGGTATCC\n+TTCAAAAAGGGCTTTTTTCTCTGGATATTGTTGAATTAATTCATTGGCTCTTGTTAATAA\n+GTGTTGCTTTTCCAGTTCAAAATCCACTTCTGCTGTTCCCTCTAGCTCTTCCACCAATTG\n+TAATTGATTCTGTTCAAATAAATTCAGCCATTCGTTTCGAGTGAGATATTCATAATTTTG\n+ATACTTCACCTGGTTATTGTGCGCTAATTCAGGCACATAGGCTTCATCTATAATAATATA\n+ACCGCCTTCTTTAACAGTTCCCTGCAATTTTTCCAACGTTTCTGCTGGATTTCCAAGTAT\n+ATCCGCTGCTGCACCAAATATAACGGCATCATAATTTTTTTCGTTTTGAACCGATTTATT\n+TACATCTCCTACTTCAAATTGGCACAGTGACTCTACTTGCGCTTCTTTCGCTTTGCATTT\n+TGCTTCTTCTATAAATGCCGGAATTAAATCTATTCCTTTGACAGGATTTCCTAGTTCCTT\n+AGCGATACCAATGGAAACAGCGCCTTTTCCGCAAGCTAAATCCAAAAAATTACTTTCAGC\n+TGATAACGGCATATGTTGCTTAATTAAATAAGTAATATCTTTCGGACTACTACCCAATTC\n+AAAAAAATCTTGTAAAAAATACGGAATAAACGGTAATATTTCTATTGATTGAGAAGTGAG\n+TGACGCAGCAAGCTTTCGTTCGGTTTCTTTATTCATTTATTTACCCTCCTAAAATATTTT\n+TCGTTAGCACTGGGTCTGTTTTTCTACATAATCAGCTATAGAATGTATTAATATATCCAA\n+AGTCTCTTCTTTCGCTTTTTTGGCAGTTTCTACATAACTCCTTGTCGCAGTGTAAGTTAA\n+ACAATCTAGTAACATCACTAAAGCCTCCCATTGAGCTCTCGTAAGATCGATATACGTCAT\n+GGCAGTTTCCAGGACTTCACTTGTCATTCTTTCTTCTCTTTCCGTATATGTTGGAGGGAG\n+TTTTTGGAGTATTGCGTGGAAATCTTCCGGTGAAAAGTAGTTGTTTATACTCTTTTCCGA\n+AAGATAGACTTCTTTCAAAAAACGAGTCATCTTGCTTTTTAACGAACCTTTCTCCTCCAT\n+AATTTTTTTAAATGCCTCTAATTGTGCTTGATAGGAATATTCCACAACCTCAAATAGGCA\n+TGCTTCTTTGGAGGGAAAACACGTATAGAATTTTCTCTTTCCAATCCTAGCTGCTCGAGT\n+AATATCCTCCACAGTAAAACCTTGAATTCCTTTTTTTATATAAATTAAATGGCTTGTATG\n+TTCGATAATGAGGTTTTTAGTTTGTTGACGCTCATATCCCGTAACGAGTTTTGGCATTTT\n+GCTCCTCCTTAAAAATTTCTCGCATAACGCTTTTAATGGAACTATTTATTAATTTCCAGT\n+TCTACAAAAACACCTTAAACTAAATATTTAACAATGTCAAATGAGGTGAAATGGATTTTC\n+CACGGTTCTTATATCGAATACGTTTACTAATAGTTTAGTATTAGATTTGAAAAAAATATT\n+TTATCAGGTATATCTTATCTTTTACATTTTTCCAATCTTACATAACCGCTCCCATCGATG\n+AAGCAAGTAAGATTCAAAGTAAACCAAGAAAAAAGAGAAGACAAAAATTTGTCTTCTCTC\n+TTAGAACGCCAATGTTTCACGCTATTTCTATGAATTTGACTCAATGCCATTGAGTAAGAT\n+TGGTGTTTATTTGTTTTTTAGCCAATTAGAACTTTTTTATAGATTTATATATTTAATTTT\n+CTGAAAAATGGGACAAAATATCCATCTCAGTGGTATATAAGTGCAGTTAATTTGTTCCAT\n+TTACATATATGGATTGGTGATTATCAAAAAATTTCTGGAAAATGCGACAAATCACCCTCT\n+TACCTGTATCTATTTATATATTTAATGAAAGGTGGGAAGACTCATGAAAATAATCCTAGA\n+ATTTTTACTTAAAGAGTTATTGTCTTTAGCTATTGAATACGGAATAAATTGGCTTATTTT\n+AAATGATCACATCTATATATTGATCATTATAGTTAGCTTTATTGTTCGTTGTTTTGTAGA\n+AACTCGCGATAAAAAATATTTTTAGTACATAACCATAGCATTTAACCTTTTTCCAAAAGA\n+GTTTCAATGCTATACAAAAAGAGTAAGCAAGTTTATGGTGGTGGCTAGCTCTTACAACAA\n+GAAAGGGTGATGCTATGAATATTTTTGTTAGGATTGCCTGGAAAGGATAACCCATGACTG\n+TTTATGAAGCACTGTCTTTTGCAACCCTGGTGTTGCTATTGAACAGTCAAAATAACAAAA\n+AATAACCACTCATAAACTTTGGTCGGTTTAGTGGTTATTTTTATAATCTATTAAGCTAGC\n+TGCCACCTTAAATGGGCTTATACTTGAGAGTCATCTTAGCGCATGACTCTCTTTTCATAT\n+TTAATAATAACATAAGACCATTTGACAACATATGACATTAGGTACTACTCATTACTATAT\n+CTGAAACGAAAGCAGCAACTGCTTTCGTTTTTATTTTAAATAGCCAATTTCAATCC'..b'AACAATGGAAGAAG\n+CACTTGCAAGCAAAGTGAAAGAGCAGACAAATATCGATATAGAAATAGAGTCTATCCTAC\n+ACTGCAAAGAGCGCCGTGCTACATGGGAGCATGTTTGTACATTCGTTTTTCGAGCAAAAC\n+CTGTTGGTAATGCACTTCTTGCTTCCAATGATGACAATGTGTTTCGAGTGAAGTGGATAC\n+CTATCCCGCTCGCAGATGATTTATTAGCTGTAGACCAATTATCATTAAATGAACTAGTAA\n+GAAGCGAAGGCGTCTTGTATGAAAACTATACCTAAATTTCAAAAAGGCTCAAATTTCACA\n+AGGTCAAGCCTTGCTAAAAAGCACTGATTGATATAAAGTTAATAAAGAAACTTTTTTAAA\n+ATTTGGAGGGAAAACAATGACACATATTAAATTTGATTATTCCAAAGCGCTCCGTTTTTT\n+TGAAGAACGCGAACTTGATTATCTTGAACCAGCAGTAAAAGCAGCTCATGATTCATTACA\n+TAATGGTACAGGTGCTGGTAATGATGCACTTGGTTGGATTAACTTACCAACAGATTACGA\n+CAAAGAAGAATTTGCTCGTATCAAAAAAGCAACAGAAAAAATCCACAGCGACTCCGACGT\n+ATTAATCGTTATCGGTATCGGTGGTTCTTATCTTGGGGCACGTGCTGCAATCGAAACTTT\n+AAATCATTCCTTCTATAATGTACTTGAAAAAGGTGCTCGTAAAACACCTCAAGTATTCTT\n+TGCAGGAAATAGCATTAGTTCCTCTTACTTACATGACTTAATTGAAGTAGTTGGCGACCG\n+TGACTTCTCTGTTAACGTTATTTCTAAATCCGGAACAACAACAGAGCCAGCAATCGCTTT\n+CCGTGTTTTCAAAGAACTTTTAATCAAAAAATATGGCGAAGAAGGCGCGAAAAAACGCAT\n+TTACGCTACAACTGATAAAGCAAAAGGCGCTCTAAAAACATTAGCTGACAATGAAGGCTA\n+CGAAACATTTGTTGTTCCAGATGACGTTGGCGGACGTTTCTCTGTTTTAACTGCAGTAGG\n+TTTACTTCCAATCGCAGTTAGTGGTGTTGATATCGATGCTCTTATGAATGGAGCAGCAGC\n+AGCAAGCAAAGATTTCGACAAACCTGAACTAAAAAATAACATTGCATACCAATACGCAGC\n+AGCTCGTAACGTTCTTTACCGTAAAGGCAAAGTAACAGAACTTCTAATCAGCTATGAACC\n+AGGCTTACAATACTTTAACGAGTGGTGGAAACAATTATTCGGCGAAAGTGAAGGTAAAGA\n+CAAAAAAGGTATTTACCCATCCAGCGCAAACTTCTCCACTGACTTGCACTCTATCGGTCA\n+ATATATCCAAGACGGCCGTCGTAACCTTTTTGAAACAGTTATCAAAGTGGATAAACCACG\n+CCACAACTTAACTATCAATAAAGAAGAGGTAGATCTAGATGGCTTAAATTATCTTGCTGG\n+CGAAACAGTTGATTTCGTTAACACAAAAGCATTCGAAGGAACACTTCTAGCACATACAGA\n+CGGCGAAGTTCCAAACTTTGTTGTAGAAGTTCCAGAACTAGATGCATACACTTTCGGTTA\n+CCTAGTATACTTCTTTGAAAAAGCAGTAGCTATCAGCGGCTACCTAAATGGCGTAAATCC\n+ATTTGACCAACCAGGCGTAGAAGCATACAAAGCCAACATGTTCGCATTACTTGGCAAACC\n+AGGCTTCGAAGACAAAAAAGCAGAATTAGAAAAACGCTTAAACGATTAATTTTCATTTCC\n+AAACCTTGGGGCCAATCGCTCCAAGGTTTTTTGTTTGTTTGCGATTTTCTTCCATTGGAG\n+TTACCATATAGTTAAACAAAAGGAGGGGAAGAAGTGCTATCTATCGAACGAAAACGCGCC\n+ATCGTCCAATATGTCAAAAGCCGAAAAATAGCAACAGTTAGCGAATTAGCTAAACATTTT\n+GAAGTCCACGAAGCAACCATTCGCCGCGATTTAACCTCTTTAGAAAAAGACAAAAAGCTA\n+AAAAGAACCCACGGCGGAGTTATGATAGAAGAAAAAGTAGTTTCCGAACCAAATTGGAAA\n+AAACGAAGCGAAGTGCGCTACGAAGAAAAACAACGCATCGCCACATTAGCAGCGACAATG\n+GTCAAAGACGGCGATACAATCATTCTTGACGCTGGAACAACAACCGGACACATCGCAACC\n+GCATTAAAAGACCGATCCAAACTAACCGTCATAACAAACGATATCAACGTAGCTTCCATT\n+ATGCGCTTTTCCCCGTCTAAAGTAATTGTGACAGGTGGCGTCATCTACCCAGAAACTTTC\n+ATCCTTAACGGTATGATTACGAGCGGAACCTTGCAGAGCATTCACGTACATAAAGCATTT\n+GTAACCACACCGGCACTCGATATCGACAAAGGCTTAATGCACTACGACGAATACCTAATC\n+CCAGCTAAGCAACAAATGCTCCACTCAGCCGATGAAGTCATCTTAGTAACAGACCACACC\n+AAGTTTGGCCGCATTTCACTTTACAAATACGCAGCCCTAGACGAAATCTCTTCTATTATC\n+ACTGGAAAAGAAATAGACCCAGTATTAAAAGAACAATTTGAAGAAAAAGGAATGCAAATT\n+TATACAACATAATGTTTTAAAAACTCCATTTAATCACCAATTTATGCACCAAATTCATCT\n+TTTTTCATCTTTATTTAAAAAACTTTGTAAAAAGTATTGACGAAAGGCAAAAATCTTGGT\n+ATATTTATAAACGTTGCTGATGCGGACAAAACGCTTTCGCAACAAAAGAAATTGA\n+>.12673_8_43.11\n+ATATTGTCTGGTAGTTATGGCGAGAAGGTCACACCCGTTCCCATCCCGAACACGGTAGTT\n+AAGCTTCTCTGCGCCAATGGTAGTTGGGGGCTTCCCCCTGCGAGAGTAGGTCGCTGCCGG\n+GCAGTATTTCTGGAGGTTTAGCTCAGCTGGGAGAGCATCTGCCTTACAAGCAGAGGGTCA\n+GCGGTTCGATCCCGTTAACCTCCATTTTTTATGCCGGCTTAGCTCAGTTGGTAGAGCAAC\n+TGATTTGTAATCAGTAGGTCGCGAGTTCGACTCTTGCAGCCGGCACCATTAATATTAACT\n+TTATGATAATACATATTTTTATTGTAGAGAGCCGTTAGCTCAGTTGGTAGAGCATCTGAC\n+TTTTAATCAGAGGGTCGCTGGTTCGAACCCAGCACGGCTCACTTTTGCGGGTGTGGCGGA\n+ATTGGCAGACGCACCAGATTTAGGATCTGGCGCCGCGAGGCGTGGGGGTTCAAGTCCCTT\n+CACCCGCACTTATTTTAAATATGCGGAAGTAGTTCAGTGGTAGAACATCACCTTGCCAAG\n+GTGGGGGTCGCGGGTTCGAACCCCGTCTTCCGCTTGTTTACAAAAGTTCCAATATGCCGG\n+GGTGGCGGAACTGGCAGACGCACAGGACTTAAAATCCTGCGGATAGTGATATCCGTACCG\n+GTTCGATTCCGGTCCTCGGCATTATTTTTATATGCGCCCATAGCTCAACTGGATAGAGTA\n+CTTGACTACGAATCAAGCGGTTAGAGGTTCGACTCCTCTTGGGCGCACTTTATTAAACGG\n+GAAGTAGCTCAGCTTGGTAGAGCACTTGGTTTGGGACCAAGGGGTCGCAGGTTCGAATCC\n+TGTCTTCCCGATTGTTTGATTTTTATTATGGGGCCTTAGCTCAGCTGGGAGAGCGCCTGC\n+TTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAGGCTCCACCAAATTATTTCTAAAAA\n+TGTGTTGACATTGTTTAGAGAATAGAGTAAGATATAAGAGTTGCTGCTAAAGGCAACGAA\n+GAAGAAAAAGTGACCTTTGAAAACTGAACAAAGAAGAAGACGAAAAGCAATGAGACGTAA\n+AG\n'
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/12754_4_71.contigs_velvet.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/test-data/12754_4_71.contigs_velvet.fa Thu May 16 11:08:09 2019 -0400
b
b'@@ -0,0 +1,49241 @@\n+>.12754_4_71.1\n+AAACAGCTTTCTGTTTTCTGCCCTGCGATTACCAGTGAGACTTTACGTCTCATTGCTTTT\n+CGTCTTCTTCTTTGTTCAGTTTTCAAAGGTCAGTTGCTTTGTTAACGCAACTTTTAAATC\n+TTACCATAAAGTTTAAATCACGTCAACAACTATTTTTAAAATGTTTTTTGATGAATCAAT\n+TTGTATCAATTCAGCTTTATCATTATATAACAGCTTTATACTAAATACAAGCCTTTTAAG\n+TTATATTTTTAATTCTTTCTCTAGTGCATGTATAAAATCCTGCATAATTTTTTGTTTTTC\n+TCCTGCAAGTTCCCGACCAGTCTTTGTTTTTAGTTGCGTTTGAATTAAGAGTAATTTATC\n+GTAAAAGTGTTGTAAAGTGGTATTTTCTGGGTGATCTCGATTAGCGATTTCTCTATTGTG\n+TGCTCCTCCATAAGTAAATGTTCGAGCTATACCGATTGCACCAATTGCATCCAAACGGTC\n+TGCATCTTGAACTATTTTTTCTTCTATTGTAGAAGCTTGGATAGGATTTTTTCCATTTTT\n+AAAAGAAACTGCTTGGATAATTCGGATGATTTTACTGATTACATCTTCAGGTATTTCTTT\n+TTCTCTCAGCCAAGTTGTGATTATTTCAGTTGCTTGTAATGGGTCTTCTGTTAGTTTGCT\n+ATCATTATAGTCGTGAAACAATGCTGCTAATTCGATTGCAAATTTGTCCCCACCTTCTGT\n+TACTTGGATTTGTTTACTTAAATGCCAGACTCGTTTAATATGTTCCCAGTCGTGTCCAGT\n+AGTTTCCTTTTCAAAATGAGACTGCATCCATTTTTGCGCGGCAATTATTATTTCTTCTTG\n+CTTCATTAGTATTTGCTCCTTTTTTACGTTATTTTCATGTACAATAGTAGAAAATGGAAA\n+TGAGGTATTCGATGTTTGCTTTTAAGAACGTTTATTTAAAGCGCGATAATAAAATGATTT\n+TGTCGGATATTAATTGGGTGGTTAATGATAAGGAATACTGGGCAATACTAGGACTTAACG\n+GTTCTGGAAAAACAACTTTGTTGCAACTTTTAAATGGGTATCTTTGGCCTAGCAGTGGAA\n+ATCTTCAAGTACTTGGGCATATTTTTGGGAAGACTTCTTTGCCGGAGTTACGTAAATCGA\n+TTGGTTGGGTTAGTAATGCGCTTGACCATCAGCTGAAAGAGTATGAGTTAAGCGAGCAAA\n+TTGTACTTAGTGGAAAATTTGCAAGTATTGGTATTTATGAAAAAGTCACTACTGCGGAGA\n+TTGACCAAGCGAAAAAGCTGCTTACTGATTGTGGCGGTATCACGCTTATTGGAAAGCCGT\n+ATAAAATTTTATCGCAAGGTGAGCGTCAAATTGTTTTAATTGCACGTGCTTTAATGGCCA\n+GTCCTAAGTTACTTATTTTAGATGAGCCTTGTAACGGGCTTGATTTATTTGCAAAGAATC\n+GTTTGTTAGAAAGAATTAAGAAAATTGCAGAACTTCCTGAATCACCAACGATGCTCTTTG\n+TTACGCATCATACGGAAGAAATTCTTCCCTGCTTCGATAATATCATTTTACTGCGTGACG\n+GGGAAATAACTCATCACGGAAAAACAGAAAAACTTTTAACAGAGGAAGTCCTTCAAGATT\n+TTTATCAAAAGCCGGTCGAATTAATTCGGATAAAAGATGGCTCCATTGCAGTCTATCCGA\n+AGTAAGTGGTATAGTTAGAATACGAAAAATGCGTATGTAGAGGGGCGAAAAATTTTGTAT\n+GAAACGATGATTGCAAAAGCAGGTGTCCGTGAGCTTCTCGGGATGGATACTAGTCTGATT\n+TATGGTTCATTTGCTTATGAAATGGAAGACGAATGGATGGATTTAACAGGGCTTTGGATT\n+TCGAATGAGAATGCACTGATTTTTTACTTAGAAAATGAAGATGTCTATTTACTGAAGAAA\n+TTCGCTTATGAAATGATAGACAGTTTAGAACAAAAAGTGAGTATCCTTTCCATGACGAAA\n+AAATTGATTTTACATCTTAATAATAAAGAAAGCTATACATTACTAGTAGCAAACGGTGAA\n+GCGAAACTATTTGCTGCTAGGGTAAATGAGCGCATAGAAAAAGTGAGTCTAGGATGAACT\n+AGACTCACTTTTTTATTATTCTTTTTCTTCAAACAAACGAGCCACTTCAATGATTACTTC\n+TGTTGCTTTAACCATACTTTCTAATGCAACATATTCAAATTTACCGTGGAAGTTCTCTCC\n+TCCACCAAAAATATTAGGTGTTGGTAGTCCTTTGTAGGAAAGTTGAGCGCCGTCTGTTCC\n+GCCACGAATTGGACTGATTTTCGGTTCAATGTCTAGATTTCTCATCGCCGCACTGACGAT\n+ATCCACAATTTCTTTTACTGGTTCGATTTTTTCGCGCATATTGTAATATTGATCGTTCAG\n+TTTTAATTCTACCGATCCTTCGCCGTATTTTTCTTCTAACTCTTTAGCGATACTAGCAAT\n+ATGTGTTTTTCTTTCCACAAATTTCAAGTGATCGAAGTCGCGGATAATATAGTAGGATCT\n+GGCTTGTTCTACGTCGCCGTTTAGGGAGATTAAATGATAAAAGCCTTCGTAACCTTCTGT\n+GTACTCTGGTGCTTCGTCTTTTGGAATGCGCGCATCGAATTCCATCGCCATTTTAACAGC\n+ATTAACCATTTTGTTTTTGGCTGTACCAGGGTGAACACTATTACCTTTAAAAGTGATTTT\n+GGCAGAAGCCGCGTTAAAACTTTCATATTCGAGTTCGCCAAGTGGGCCACCATCCATTGT\n+ATAAGCATATTTTGCGCCAAATGCTTCTACATCAAAACGTTCTGGGCCTCGGCCGATTTC\n+TTCATCTGGTGTAAAAGCAATACGAATTTTACCGTGTTTGATTTCGGGATGGTTAATTAA\n+ATGGTTCATTGCCACCATAATTTCGGTAATGCCAGCTTTGTCGTCTGCGCCAAGTAGCGT\n+TGTTCCGTCAGTTGTGATTAGTGTTTTCCCTTTGTACCCAGCTAGTTCTGGAAATTGTTT\n+TGGTGAAAGCACTACATTTAAGTCTTTGTTTAGAATGATATCTTTACCATCATAATTATC\n+GTGAACTTGTGGTTGGACGTTTTTACCTGTTAAATCTGTTGCTGTATCTAAATGGGCTAA\n+AAATCCGATTACTGGGACTTCTTTCGTTGAATTAGATGGAAGTGTTGCCATGACATAACC\n+AAATTCGTCAACAGTGACTTCTTGCATTCCGATTTCTTTTAGTTCTGTAACGAGAATGTT\n+TGCCAGTTCCATTTGACCTGGGGTTGTTGGACAAACTGTGCTTTCTTCATTCGATTGAGT\n+ATCTACTTTTACATATTTTGTAAATCGTTTTAATAGTTCTTCTTTCATTCCGACCACTCC\n+CTTAAATTGATTCTTTTTCATTATAAACTTGATTTTCGAAAAATTCTATTCCTGACTGTC\n+GAGTAGTGTTTTTAATTGAAGCGTCGTTCGCCAATTCCGCGTTGTCGTTAGAGCCATTTT\n+ATATTGACCAAGGAAAACTGGTAATTTTAAGGTGTGGATTTGGTTGGAGAAAACATGGAC\n+ATAAAGGACGCGGCCAATTGCGATTACTTCGGCTTGGTCGTTTTTTTGTCTTGGGATATC\n+AATATTTTCATTATAAAAAGCAGCCATCCAGCGTTCTTCTTCGCCAATTGTTTCTGGCGG\n+AAATGGATTGTTTGCGATGATTTGCTTATAATTTTGTTCTGAAAATACGAATACATCAAT\n+AGTTAGTTCACATATCGCTTTGATTACTTTCGTTATCTTCGCCGCTACTTCTGTTTCTGT\n+TTGTAAAATAGAACTTAGTACGAGGTTCCCACTTTGGATATAAGTTACTACGTTTT'..b'CATAATACTCAAATTCGTGTTGCGCGAGTA\n+AAGTTCGTCCAGATGTTAGTGCGAGTTTCGTTATGTCTGGTGTTAATTGATTAAAATCAG\n+TTCCAACAGGTACATCAATGGTATATCCAGGTGTTGTAGTTAGTTGGTCTTGCTTTTGAT\n+AGTTGTTATCGTAAAATTCTAATAGGTTATTCCCATTATTAAACTGGCTTACATAGTTGG\n+CAGGAATATTGGTTACAATCTGGTTCCCTGCAGCCATTAAGTCTAAGTCTCCACCAGTTG\n+CATTTGTCCAGTTCGTAGTGAAAATTACGTCTGGAACCTTCACTAAATGGTTATTTAATA\n+CCCCTAAGAATTTCAAATGACTCGCCATATTTGTTATTGTTGCAGGGATTTCTTCTATTG\n+TTCCCCCAGAAACTTGTAATTCTTCTAACTTAGGTAGTTGGAAAACAATCATTGGAAAGG\n+TGCTTAAATGATTATCATTCAGAACTAAGATTTTTAACTCCTTTAAATTCCCCACTGAGT\n+TAGATACAGAAGATAATGTTCCATTTTTAACTTCTAACGTAGTTAAATGAGTTAACATAT\n+CGATATTAGTCGGAATATCACTTGCCCCTGTTACTCGCAAGGCGGTTATAGCTTCTAAAT\n+CTGTCTGTGTAATATTCGCTCTCGTTTTACCAGTTTCTTTTTCAATCTCTTTTATAAATG\n+GTTCATTACTATTCATGGTTTGTTCTAACCATGTAGGTGTGCTTGCAGAAACAGTCGTAA\n+AACTAACTGTATTGATAATAACTACAAGCGCAATTAATGCAATAAATATTTTCTTTAAAA\n+TAACAATCTTCCTCCTTTTAACGCTAAATTTGCAGTGTCAGTTGGCAATTTGTTCCTTTG\n+CCAAAGCCCCTCCCTTCACTGTCCATGTGGCTTTAAGCCGTACTTCAGTCTATATAATAC\n+TATGCGGAGTCTTAAAATTTTCTAATGTCGCATATATACTACTCAAAAAAAGAAAACCAA\n+AAAGAATAGTCCTTTTTAGCTTTCATTCCATCGTTTTTATATCGTTGTTTTCCCTCGCAA\n+ATTGTCGGTACATGGTTTCATACTCTGCCGCTTTATTTTCATAACCTAATGCCCGCAAAA\n+TAGCTACTGCCTGCTCGATTTCTTCGCCACCTTCGCGCTCTTCGCCTTCTCCCCACCGCA\n+CAATTCCACGATAATACATACAAAGAATTTTGAAATAAGTACCATCACAGTCCT\n+>.12754_4_71.8\n+CTCGATAGCCTCATCTTTTGTATCAAAATATGTGATTGATTCCCATCGCCCGCCGTAACT\n+ACCGTTTAACATCCATTGCCCTTGTTTCATTCCGCCACCTCCATTACTAATTCGTATCGG\n+CTTTCTAGTTGCCAATAACTCTTTTTAGAGCTATCAGGAATCTTGTCATGCAAGTCAATA\n+CGTCGTAAATCGTAACTAATACCTTCCACAAGTGCTTCATAATCATAACTGTATAAAGAA\n+ATATTTATTCCCATTCTTGCACCTTCCCTTTCAATGGATTTATTCCCATCACCACATAAT\n+TTTCTTTTTGCTCATAATCTGTGATGTAGGTAACTTCTACGGTTATCTTCCATCCGGTAT\n+GTTTTTCCTCTTTAAATTCTTTTAAAATCAGGTAATCTCCAACTTGGAAATTTCTGTCAT\n+TCTTTCTAATCTCAAACGTTTTTCGCCCTTCTGCGATGTCCCAGAAGTATTCTGACAATA\n+TTTTTAGTTCATGTGTTTTACTCATTTGAGTACCTCCAACTTACTTTTTATCTCGGTCAG\n+CAATTCCCTTACCATTTTCACTTCGTATGCCAATTCTTCAAAACTACTAATATCTGATGT\n+TCTGATGTGATGTTCAGTAAAGGCGTCTAAAGCTTTCTCTACAGTAGGAAAATAGCCAAT\n+ATCACTATATTGTTCCGCTCCGTTTTTATCTGGTCCTTTTGGCTTTGATAATACATATTG\n+ATATTGACTGCTTCTAATTACGTAATCTTCGTTTATTTTAATTTTCATTCTGTCTCCTCC\n+ACTTCTTCAACAGGCACAGCGAAATCCCAATATCGTGTGTCTATATTTTTTATTTCTGAT\n+TCAGTGAATTTAGTTTTATACCCTTCACTTCCCAGATGACAACTTAAAAGTCGTACGCCA\n+TTAAAATAAACATTGAGAAAACCTAATCCCCCATCGAAAAATCTTACATAATAAAGCGGT\n+TCTCCCACCTCGTAGTCTCCCATCCAAGCACGGGCGAAAAGCTCTTGATTTTCATGACAA\n+TCTGCAAGCCAGTCCGTTACTTCTTCGGGCATGCAACTATTTTCATAAGTATCTTCTAAA\n+GCCTCAGACAATCCCCAACGATGTTTTTCACAATACTCAATCCAATCAGCTACAAATTTC\n+GGCACTTTCACAAGTTCGACTTTGCTAACTTGATTTTGTTTAAATAAATAATCTATCGCG\n+GGCTTCTTAGCTAATTTAACCATTAATTCGTCAGTTAATTCGTCAGTTAATTCAATAACC\n+TCTTCTACCAAGCCCTGATGCAACTCACTTCGCCAAATAACTTCTACTCTGCCACCTTTT\n+TTAAATTTCATTGTTTTCCTCCTTCTCTCCGCCCTATTGCACTCTGTATCCGTTACAGTC\n+TGAACTCGGTCACCTTTTTTGATTATATTCATTTAAAGCCGCCACCCTCATATTTTGCAA\n+TAAAATCAGAAACTAATTCTCCACAATTTCT\n+>.12754_4_71.9\n+GTGTGGCGGAATTGGCAGACGCACCAGATTTAGGATCTGGCGCCGCGAGGCGTGGGGGTT\n+CAAGTCCCTTCACCCGCACTTATTTTAAATATGCGGAAGTAGTTCAGTGGTAGAACATCA\n+CCTTGCCAAGGTGGGGGTCGCGGGTTCGAACCCCGTCTTCCGCTTGTTTACAAAAGTTCC\n+AATATGCCGGGGTGGCGGAACTGGCAGACGCACAGGACTTAAAATCCTGCGGATAGTGAT\n+ATCCGTACCGGTTCGATTCCGGTCCTCGGCATTATTTTTATATGCGCCCATAGCTCAACT\n+GGATAGAGTACTTGACTACGAATCAAGCGGTTAGAGGTTCGACTCCTCTTGGGCGCACTT\n+TATTAAACGGGAAGTAGCTCAGCTTGGTAGAGCACTTGGTTTGGGACCAAGGGGTCGCAG\n+GTTCGAATCCTGTCTTCCCGATTGTTTTGAATTTTATTATGGGGCCTTAGCTCAGCTGGG\n+AGAGCGCCTGCTTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAGGCTCCACCAAATT\n+ATTTCTAAAAATGTGTTGACATTGTTTAGAGAATAGAGTAAGATATAAGAGTTGCTGCTA\n+AAGGCAACGAAGAAGAAAAAGTGACCTTTGAAAACTGAACAAAGAAGAAGACGAAAAGCA\n+ATGAGACGTAAAG\n+>.12754_4_71.10\n+TATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAAAAGGAAACCTGTGAGTTTTCG\n+TTCTTCTCTATTTGTTCAGTTTTGAGAGGTTACTCTCTTTTATGTCAGATAAAGTATGCA\n+AGGCACTATGCTTGAAGCATCGCGCCACTACATTTTTGACGGGCCTATAGCTCAGCTGGT\n+TAGAGCGCACGCCTGATAAGCGTGAGGTCGATGGTTCGAGTCCATTTAGGCCCACTTTTT\n+CTTTCTGACGCAAGAAATACAAATAATCATATCCTTTTATGGGGCCTTAGCTCAGCTGGG\n+AGAGCGCCTGCTTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAGGCTCCACCAAAAT\n+TGTTCTTTGAAAACTAGATAAGAAAGTTAGTAAAGTTAGCATAGATAATTTATTATTTAT\n+GACACAAGTAACCGAGAATCATCTGAAAGTG\n'
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/12754_4_77.contigs_velvet.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/test-data/12754_4_77.contigs_velvet.fa Thu May 16 11:08:09 2019 -0400
b
b'@@ -0,0 +1,50049 @@\n+>.12754_4_77.1\n+AAAAAGTTCAAGAATTTGAACCATCCATTTAGCCTCCGTTCTCACGCATAATTCTTAACC\n+TCTTCTAGCTTTTCAATCAGTTGTTCGTGTGTTAATTCAAGCAAAATATCTTTTATAGAG\n+TTTTTTCCGTCATGAGACTTTACAAGTACGAGTGATACAAAATTAGAGTCAAGATTTTCT\n+ATCACTCTCGCTTGATAGCCATTTTCAAAACTATAAGCAGTTAGTTCTAAGCCGTTATCA\n+CTTAATCTTGTTCTTTCTGTGATGTATTCTTTATACTCATTTGCGATTGTTTTCACGTCT\n+GCACCTCATTCCTAGCCGCTAACTGCGCTTTAATTTCAGCGACTCTCTTTTCTAAGTCTT\n+CGCTTGATTCTGTTGTTGAAGCTTCTTGTTTTGTTTGTTTCTGCTCTTTGTCGAACCAGT\n+CCGGCAATACTTCTTCTTTAACTGGTTTGTTATATTTGTTGTAAGTGGGCTTGTTATATT\n+TTTGCTCTAGCTCTATCTGTCGTTGTTTTTCCGCTGCATCAACATCAGCTATTGTTTTAA\n+ATCCTCTGTTTTCCCAGTTTTTAAGAATTTTATTAACGTAAGCGTAATTACGTTTGTTAG\n+CTCCTTGCTCTGATGTAACTTCTAAAGCCTTCATGACAATTTCTCGATTACCTGCAAAAT\n+CATCTACCCAAGCAAGTAGTTTTTCGAGTTCGATTGGAAGCATCATTCCGAATCCGTTTT\n+GTTCCCAAAAATCTTTGAAATTTAAATCGCTGTTGTTGTTGTTTTTATTACATTCTTTAG\n+TTCTTACATTCTTGTTAGTTGTTAGCTGTTTGTTAGCTGTTTGTGAGTCGTTTGTTAGCT\n+GTTTGTTAGCAAGTGTGTTAGATTTATTTTCCGAGTCTTGATAAACGCCCCAGTTCACTA\n+TGTTTATAAGGGTGTTTACCTTTGTTGATTCCTTTGTTAGAAATCCGTAATTTTCAAATC\n+TTTTTAGAGCTGTCCTGACATTTTGCGAAGAGATACCTTTGCCGCATTCCTCCGTAATTG\n+ACTTAATACTTGTGACGAATTCACCTGGTTTTGCTTTGAAAGGTTTCCCCATCCACTCCC\n+ACTCGTTTTCCTTGTGATTTGCCATCATTAACAAAGTCACAAGGATGGTTTTTTGCTCGG\n+GTGTAGAGCTTCTCCATATAGGCTTTTCTTTCAAATCTCTATGCAATTTAACCCACCCAT\n+GTGACATGCTTCTTTTCTCCTTTCAAATTAGATCATTGACCCTTGAACTACCGAGCCAGC\n+TTCTAACGTGTCAGACGGCGTTATAGGCGCCTCTATAATGTCCGGTATTGATTCATCGTC\n+TGTAACGTCTTTTCGTTCTCTAGGCTCTGCTTCGTCCTCTGTAACCGCTGTTTGCATGTC\n+GATGGATAAGATGCCCCATTTACTTAACATGTTTCTAAGAACAGTCTTTTTAGCCATTGC\n+ATCGTAATCTTTTTTCCATCCAAAGTCTGATTTACTAAATTTCTTTTTATGTGCTTCAAT\n+TTCTTTGCGAGTCCAATAGACCGTTTTTTCAAAGCCATTTATCAACTGAAAATAACCACA\n+GTAACCAACGACTTTTTCACTTGTATTGTTGTCTAAATCTAGTTCGATTTCTTCAGTAAG\n+TCGATTCCATTTTAGTAACTCGCCTTCTCGCACTTCGATAACATTAATACTTTTATATTG\n+TCCTGTGCGTAGTGCTAACTGGATGTATCCTTTATAACCAAGCTGAAACTGTGCTCTGCC\n+TTTGTAAGGAACAATCCACGCATAACCTAAATTTTTGTCAATCGGTAAATCTAGTGTTGC\n+CGCTACCATGGCAGAAGTAACAACCGTCATTGGGTCTGTTTTTTGTAAATAGTCGTCGCC\n+ATTGTAAAGGTTTAAAAGGGAAGTTAAAAATTGAGGTGCTTTTTTATCTAGTACACTTTC\n+GAATTTCTTGCGCATTGTAGGTGCTTCTAGCAATCCTTTTAAACCTAATGATTGTGCGCT\n+TGCTACTTGTCCCCCATTTTGTTTGTTTGCTAATTGATTTTTTAATTCATCGTTAGTTGC\n+CATAATTATTTATTCTCCTTCACCACAAATTTTCTATAACTAGTTTCTTTCTGGAATTTT\n+TTGTAAATATCTGGATGTTCTTCTTTTAAACGTTTATCATCTACTCTTGAAGTCGTAACA\n+GGATTCCAAGTAATCTTAAAATCATCTGTGATGCCCGTTTCAGCTTCTTTTAAATCATTC\n+TTGATATTATTATCAATTTCTTTCTTTCGTGTCTCTAAAAGCTTTATATCGCGTTCTAAA\n+TTTGCTCTTTCAGCCAAAAATTCGTTATATTTTTTTGATAAAATAACTTGTTTAGCTTCT\n+GACTTAGCAAAACGATCTTTTAAATATTTTTCTGCGGCACTTGAACCGTCTAGCGCCGGC\n+GCTACATGTCCTTTTACGTTCGTTTCCCAAAAATCTAACTCAAAAGCAATTATTTGATTG\n+ATTAACTCGTCATCGCGTTCAATTTCTTTCCAAATAAATTTATTTCCTCCAATTAGAACA\n+GCTACATAGGCTTTGCTTTTACCTGTGACCGCTAAATAGTGTTGTATTTGCACTAGATAA\n+GTCGCTGGTACTTCGTCAGCTTCCCATTCCTTTGCTAAGTATGCTGATGCTGTTTTACAT\n+TCCAAAATAGCGTCTTCACCAACCACAAACCTATCAACGTTTGCCAACATAAAATCATGC\n+TCTGGATGTTGATACATCATGTTGCTACGTCTTACTTTCTTGCCAGTTCGCTTTTCGAAT\n+TCTTTTGCGACAACTTCTTCCATTTGATTGCCCCAGTATGCGGCTTCTCCCGCTGATTCA\n+TCTGGCAAAACTTGGTCTGTTTTATCTAGCCACAGCTCAAATGCTGTTTTGTACTGATTT\n+AACCCCATGATGATTCCCGCATCGCTTCCGCCAATGCCTAAACGTCGAGTTAGCAACCAT\n+TGTGTTCTATCCATGTCTTTCACGCTTGCTAAAATGTTCATTGTCTTTTCTTTTGCAATA\n+GCCATATATGTTACCTCCATTGATTTTTTAATGGACCTGAGGTATAATTTTGTTAAGGTA\n+ATATCTCAAATCTCGGACCTGCGCTGCTACGCGGGTCTTTTTTAATGCCTAAAACCATCG\n+TCCCAAAGATCATCAACAACCATCGGATTTTCAACCATGTTTTTTATCACTTCCTCTCAG\n+CCAGTAGCCTGCAATTAGCGACATAAACGACACGAAAATCATTACCATAAATACATCCAT\n+TATCTTGTGACCTCCTCGTATCCCTTTAGTTTCAGCTCTTCGATATAGTCCGCCATGCTG\n+TCGCAACCTGTTTCATTTAAAGGGATTTTCTGCTGAAATGCCGGATTAGCAATCATTTTT\n+GTTCTGCTATCTGTATGAATTTCACTATCACCGAAGTTTGTCGCCTTTCTGAAAACTCTT\n+TCTGTCATTGCTGTAACCCTCCTTTATTTTTCTCCGCCTTGAGCTACCCATGCTTCAAGT\n+TCTCTTTTGCTAAAAATCCATGTCTTGCCATTTATTTTTTTGCCGGGTAATCCCGCATTT\n+CTAGCCCAAGACTGAATAGTCCTCTTTTTCATTCCTAACATCTCCGCCGCTTCTTCAGCT\n+GTTAAAATATCCTTTTCCATCGTTTCCATTGTTTCTCACTCCTTCACCAAACCATTTTTT\n+TGATAGAATTTATCTCGACTTTCTAAAATTTGTTGTAAATTAATGTTGAATGCCTTCGCT\n+ATACTTGTGTTAAGCGTTAATGCTGTTGCGATTACATCTGTTATTTCTGAAATTGCTTGT\n+TTTGCGGCTTCTCGTTGTAGCATGTCACCTTTTCTTAAATTGAATGTCATCGTTTC'..b'TCCGTTTTTTTGAAGAACGCGAACTTGATTATCTTGAACCAGCAGTAAAAGCAGCTCAT\n+GATTCATTACATAATGGTACAGGTGCTGGTAATGATGCACTTGGTTGGATTAACTTACCA\n+ACAGATTACGACAAAGAAGAATTTGCTCGTATCAAAAAAGCAACAGAAAAAATCCACAGC\n+GACTCCGACGTATTAATCGTTATCGGTATCGGTGGTTCTTATCTTGGGGCACGTGCTGCA\n+ATCGAAACTTTAAATCATTCCTTCTATAATGTACTTGAAAAAGGTGCTCGTAAAACACCT\n+CAAGTATTCTTTGCAGGAAATAGCATTAGTTCCTCTTACTTACATGACTTAATTGAAGTA\n+GTTGGCGACCGTGACTTCTCTGTTAACGTTATTTCTAAATCCGGAACAACAACAGAGCCA\n+GCAATCGCTTTCCGTGTTTTCAAAGAACTTTTAATCAAAAAATATGGCGAAGAAGGCGCG\n+AAAAAACGCATTTACGCTACAACTGATAAAGCAAAAGGCGCTCTAAAAACATTAGCTGAC\n+AATGAAGGCTACGAAACATTTGTTGTTCCAGATGACGTTGGCGGACGTTTCTCTGTTTTA\n+ACTGCAGTAGGTTTACTTCCAATCGCAGTTAGTGGTGTTGATATCGATGCTCTTATGAAT\n+GGAGCAGCAGCAGCAAGCAAAGATTTCGACAAACCTGAACTAAAAAATAACATTGCATAC\n+CAATACGCAGCAGCTCGTAACGTTCTTTACCGTAAAGGCAAAGTAACAGAACTTCTAATC\n+AGCTATGAACCAGGCTTACAATACTTTAACGAGTGGTGGAAACAATTATTCGGCGAAAGT\n+GAAGGTAAAGACAAAAAAGGTATTTACCCATCCAGCGCAAACTTCTCCACTGACTTGCAC\n+TCTATCGGTCAATATATCCAAGACGGCCGTCGTAACCTTTTTGAAACAGTTATCAAAGTG\n+GATAAACCACGCCACAACTTAACTATCAATAAAGAAGAGGTAGATCTAGATGGCTTAAAT\n+TATCTTGCTGGCGAAACAGTTGATTTCGTTAACACAAAAGCATTCGAAGGAACACTTCTA\n+GCACATACAGACGGCGAAGTTCCAAACTTTGTTGTAGAAGTTCCAGAACTAGATGCATAC\n+ACTTTCGGTTACCTAGTATACTTCTTTGAAAAAGCAGTAGCTATCAGCGGCTACCTAAAT\n+GGCGTAAATCCATTTGACCAACCAGGCGTAGAAGCATACAAAGCCAACATGTTCGCATTA\n+CTTGGCAAACCAGGCTTCGAAGACAAAAAAGCAGAATTAGAAAAACGCTTAAACGATTAA\n+TTTTCATTTCCAAACCTTGGGGCCAATCGCTCCAAGGTTTTTTGTTTGTTTGCGATTTTC\n+TTCCATTGGAGTTACCATATAGTTAAACAAAAGGAGGGGAAGAAGTGCTATCTATCGAAC\n+GAAAACGCGCCATCGTCCAATATGTCAAAAGCCGAAAAATAGCAACAGTTAGCGAATTAG\n+CTAAACATTTTGAAGTCCACGAAGCAACCATTCGCCGCGATTTAACCTCTTTAGAAAAAG\n+ACAAAAAGCTAAAAAGAACCCACGGCGGAGTTATGATAGAAGAAAAAGTAGTTTCCGAAC\n+CAAATTGGAAAAAACGAAGCGAAGTGCGCTACGAAGAAAAACAACGCATCGCCACATTAG\n+CAGCGACAATGGTCAAAGACGGCGATACAATCATTCTTGACGCTGGAACAACAACCGGAC\n+ACATCGCAACCGCATTAAAAGACCGATCCAAACTAACCGTCATAACAAACGATATCAACG\n+TAGCTTCCATTATGCGCTTTTCCCCGTCTAAAGTAATTGTGACAGGTGGCGTCATCTACC\n+CAGAAACTTTCATCCTTAACGGTATGATTACGAGCGGAACCTTGCAGAGCATTCACGTAC\n+ATAAAGCATTTGTAACCACACCGGCACTCGATATCGACAAAGGCTTAATGCACTACGACG\n+AATACCTAATCCCAGCTAAGCAACAAATGCTCCACTCAGCCGATGAAGTCATCTTAGTAA\n+CAGACCACACCAAGTTTGGCCGCATTTCACTTTACAAATACGCAGCCCTAGACGAAATCT\n+CTTCTATTATCACTGGAAAAGAAATAGACCCAGTATTAAAAGAACAATTTGAAGAAAAAG\n+GAATGCAAATTTATACAACATAATGTTTTAAAAACTCCATTTAATCACCAATTTATGCAC\n+CAAATTCATCTTTTTTCATCTTTATTTAAAAAACTTTGTAAAAAGTATTGACGAAAGGCA\n+AAAATCTTGGTATATTTATAAACGTTGCTGATGCGGACAAAACGCTTTCGCAACAAAAGA\n+A\n+>.12754_4_77.10\n+AGACTTTACGTCTCATTGCTTTTCGTCTTCTTCTTTGTTCAGTTTTCAAAGGTCACTTTT\n+TCTTCTTCGTTGCCTTTAGCAGCAACTCTTATATCTTACTCTATTCTCTAAACAATGTCA\n+ACACATTTTTAGAAATAATTTGGTGGAGCCTAGCGGGATCGAACCGCTGACCTCCTGCGT\n+GCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCATAATAAAAATCAAACAATCGGGA\n+AGACAGGATTCGAACCTGCGACCCCTTGGTCCCAAACCAAGTGCTCTACCAAGCTGAGCT\n+ACTTCCCGTTTAATAAAGTGCGCCCAAGAGGAGTCGAACCTCTAACCGCTTGATTCGTAG\n+TCAAGTACTCTATCCAGTTGAGCTATGGGCGCATATAAAAATAATGCCGAGGACCGGAAT\n+CGAACCGGTACGGATATCACTATCCGCAGGATTTTAAGTCCTGTGCGTCTGCCAGTTCCG\n+CCACCCCGGCATATTGGAACTTTTGTAAACAAGCGGAAGACGGGGTTCGAACCCGCGACC\n+CCCACCTTGGCAAGGTGATGTTCTACCACTGAACTACTTCCGCATATTTAAAATAAGTGC\n+GGGTGAAGGGACTTGAACCCCCACGCCTCGCGGCGCCAGATCCTAAATCTGGTGCGTCTG\n+CCAATTCCGCCACACCCGC\n+>.12754_4_77.11\n+AATAAGTGCGGGTGAAGGGACTTGAACCCCCACGCCTCGCGGCGCCAGATCCTAAATCTG\n+GTGCGTCTGCCAATTCCGCCACACCCGCAAAAGTGAGCCGTGCTGGGTTCGAACCAGCGA\n+CCCTCTGATTAAAAGTCAGATGCTCTACCAACTGAGCTAACGGCTCTCTACAATAAAAAT\n+ATGTATTATCATAAAGTTAATATTAATGGTGCCGGCTGCAAGAGTCGAACTCGCGACCTA\n+CTGATTACAAATCAGTTGCTCTACCAACTGAGCTAAGCCGGCATAAAAAATGGAGGTTAA\n+CGGGATCGAACCGCTGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAAACC\n+TCCAGAAATACTGCCCGGCAGCGACCTACTCTCGCAGGGGGAAGCCCCCAACTACCATTG\n+GCGCAGAGAAGCTTAACTACCGTGTTCGGGATGGGAACGGGTGTGACCTTCTCGCCATAA\n+CTACCAGACAATAT\n+>.12754_4_77.12\n+TAATCAATAAGTTCAATAATATTGTGCCAGGGTATACAGATCTTGATCGAAATATAAGAA\n+AAATCCATAAAGTGAATCACCTAGAACCATTGATTAGTCAATTAGTAAATTTAAAAGAAA\n+TGGATCCATTAAAACCGTTTGAAGAAAGACTTACTTCAGATTATCTGATCATTTTGGATA\n+AGCGGATTGATTTTTCTATACACACCTTGCCTATTAAAGTAACTATTTTATCGACCATAT\n+CTAATGAAACAGCCGTATTTGATTTTATGAGGTATTTTTCTAGTTACTACAATCTGGAAA\n+TA\n'
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/clusters.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/test-data/clusters.csv Thu May 16 11:08:09 2019 -0400
b
@@ -0,0 +1,6 @@
+Taxon,Cluster
+12754_4_77.contigs_velvet.fa,1
+12673_8_34.contigs_velvet.fa,1
+12673_8_43.contigs_velvet.fa,1
+12673_8_24.contigs_velvet.fa,1
+12754_4_71.contigs_velvet.fa,2
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/distances.png
b
Binary file tools/PopPUNK/test-data/distances.png has changed
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/gmm_contours.pdf
b
Binary file tools/PopPUNK/test-data/gmm_contours.pdf has changed
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/gmm_fit.png
b
Binary file tools/PopPUNK/test-data/gmm_fit.png has changed
b
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/test-data/refs.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/test-data/refs.txt Thu May 16 11:08:09 2019 -0400
b
@@ -0,0 +1,2 @@
+12673_8_24.contigs_velvet.fa
+12754_4_71.contigs_velvet.fa