# HG changeset patch
# User pjbriggs
# Date 1521455612 14400
# Node ID 5e133b7b79a69fd1854e19086d4fdff54a4c5da5
# Parent  a73c48890bde043b29b9c875add59cebf23d826c
Uploaded version 0.02.04.6 (uses conda dependency resolution).

diff -r a73c48890bde -r 5e133b7b79a6 README.rst
--- a/README.rst	Tue Jun 06 08:54:49 2017 -0400
+++ b/README.rst	Mon Mar 19 06:33:32 2018 -0400
@@ -61,6 +61,10 @@
 Version    Changes
 ---------- ----------------------------------------------------------------------
 
+0.02.04.6  - Update to get dependencies using ``conda`` when installed from the
+             toolshed (this removes the explicit dependency on Perl 5.16
+             introduced in 0.02.04.2, as a result the outputs from the tool are
+             now non-deterministic in some cases).
 0.02.04.5  - Update to handle large output files which can sometimes be generated
              by the ``pal_finder_v0.02.04.pl`` or ``pal_filter.py`` scripts (logs
              of hundreds of Gb's have been observed in production): log files
diff -r a73c48890bde -r 5e133b7b79a6 pal_finder_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pal_finder_macros.xml	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,38 @@
+<macros>
+  <!--
+       Set the path for the pal_finder data files
+  -->
+  <token name="@CONDA_PAL_FINDER_SCRIPT_DIR@">if [ -z "\$PALFINDER_SCRIPT_DIR" ]; then export PALFINDER_SCRIPT_DIR=\$(dirname \$(readlink -e \$(which pal_finder))); fi</token>
+  <token name="@CONDA_PAL_FINDER_DATA_DIR@">if [ -z "\$PALFINDER_DATA_DIR" ]; then export PALFINDER_DATA_DIR=\$(dirname \$(readlink -e \$(which pal_finder))); fi</token>
+  <xml name="output_illumina_microsat_summary">
+    <output name="output_microsat_summary">
+      <assert_contents>
+	<has_line line="allExtended:&#009;0" />
+	<has_line line="allSpan:&#009;0" />
+	<has_line line="broken:&#009;2" />
+	<has_line line="compound:&#009;2" />
+	<has_line line="readsWithMicrosat:&#009;13" />
+	<has_line line="totalBases:&#009;2320" />
+	<has_line line="totalReads:&#009;20&#009;(2 x 10)" />
+	<has_line line="Microsat Type&#009;monomer length&#009;total loci&#009;loci w/ primers&#009;reads with loci&#009;total bases&#009;extended&#009;extended w/ primers&#009;spanning&#009;spanning w/ primers" />
+	<has_line_matching expression="(AC|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" />
+	<has_line_matching expression="(AT|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" />
+	<has_line_matching expression="(AG|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" />
+      </assert_contents>
+    </output>
+  </xml>
+  <xml name="output_454_microsat_summary">
+    <output name="output_microsat_summary">
+      <assert_contents>
+	<has_line line="broken:&#009;1" />
+	<has_line line="compound:&#009;0" />
+	<has_line line="readsWithMicrosat:&#009;1" />
+	<has_line line="readsWithPrimers:&#009;0" />
+	<has_line line="totalBases:&#009;8639" />
+	<has_line line="totalReads:&#009;38" />
+	<has_line line="Microsat Type&#009;monomer length&#009;reads with loci&#009;total loci&#009;loci amplified&#009;total loci bases&#009;loci bases amplified" />
+	<has_line_matching expression="(AC|TG|AT|CG|AG|TC)\t.*" />
+      </assert_contents>
+    </output>
+  </xml>
+</macros>
diff -r a73c48890bde -r 5e133b7b79a6 pal_finder_wrapper.sh
--- a/pal_finder_wrapper.sh	Tue Jun 06 08:54:49 2017 -0400
+++ b/pal_finder_wrapper.sh	Mon Mar 19 06:33:32 2018 -0400
@@ -333,8 +333,16 @@
     exit 1
 fi
 #
-# Sort outputs into a consistent order regardless of Perl version
-echo "### Sorting outputs ###"
+# Sort microsat_summary output
+echo "### Sorting microsat summary output ###"
+head -n 7 Output/microsat_summary.txt | sort >microsat_summary.sorted
+grep "^$" Output/microsat_summary.txt>>microsat_summary.sorted
+grep "^Microsat Type" Output/microsat_summary.txt >>microsat_summary.sorted
+tail -n +11 Output/microsat_summary.txt >>microsat_summary.sorted
+mv microsat_summary.sorted Output/microsat_summary.txt
+#
+# Sort PAL_summary output
+echo "### Sorting PAL summary output ###"
 head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt
 if [ "$PLATFORM" == "Illumina" ] ; then
     grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt
diff -r a73c48890bde -r 5e133b7b79a6 pal_finder_wrapper.xml
--- a/pal_finder_wrapper.xml	Tue Jun 06 08:54:49 2017 -0400
+++ b/pal_finder_wrapper.xml	Mon Mar 19 06:33:32 2018 -0400
@@ -1,13 +1,18 @@
-<tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.5">
+<tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.6">
   <description>Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them</description>
+  <macros>
+    <import>pal_finder_macros.xml</import>
+  </macros>
   <requirements>
-    <requirement type="package" version="5.16.3">perl</requirement>
     <requirement type="package" version="0.02.04">pal_finder</requirement>
-    <requirement type="package" version="2.0.0">primer3_core</requirement>
+    <requirement type="package" version="2.7">python</requirement>
     <requirement type="package" version="1.65">biopython</requirement>
     <requirement type="package" version="2.8.1">pandaseq</requirement>
   </requirements>
-  <command interpreter="bash">pal_finder_wrapper.sh
+  <command><![CDATA[
+  @CONDA_PAL_FINDER_SCRIPT_DIR@ &&
+  @CONDA_PAL_FINDER_DATA_DIR@ &&
+  bash $__tool_directory__/pal_finder_wrapper.sh
   #if str( $platform.platform_type ) == "illumina"
     #set $paired_input_type = $platform.paired_input_type_conditional.paired_input_type
     #if $paired_input_type == "pair_of_files"
@@ -57,7 +62,7 @@
       $platform.assembly "$output_assembly"
     #end if
   #end if
-  </command>
+  ]]></command>
   <inputs>
     <param name="primer_prefix" type="text" value="test" size="25" label="Primer prefix" help="This prefix will be added to the beginning of all primer names" />
     <conditional name="platform">
@@ -169,18 +174,18 @@
     </data>
   </outputs>
   <tests>
+    <!-- Test with Illumina input -->
     <test>
-      <!-- Test with Illumina input -->
       <param name="platform_type" value="illumina" />
       <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
       <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
-      <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
-      <output name="output_pal_summary" file="illuminaPE_microsats.out" />
-      <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" />
+      <expand macro="output_illumina_microsat_summary" />
+      <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
+      <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats.out.re_match" />
       <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" />
     </test>
+    <!-- Test with Illumina input as dataset pair -->
     <test>
-      <!-- Test with Illumina input as dataset pair -->
       <param name="platform_type" value="illumina" />
       <param name="paired_input_type" value="collection" />
       <param name="input_fastq_pair">
@@ -189,64 +194,65 @@
 	  <element name="reverse" value="illuminaPE_r2.fq" ftype="fastqsanger" />
 	</collection>
       </param>
-      <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
-      <output name="output_pal_summary" file="illuminaPE_microsats.out" />
-      <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" />
+      <expand macro="output_illumina_microsat_summary" />
+      <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
+      <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats.out.re_match" />
       <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" />
     </test>
+    <!-- Test with Illumina input filter to loci with PandaSEQ assembly
+	 ('-assembly' option)
+    -->
     <test>
-      <!-- Test with Illumina input filter to loci with PandaSEQ assembly
-	   ('-assembly' option) -->
       <param name="platform_type" value="illumina" />
       <param name="filters" value="" />
       <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
       <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
-      <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
-      <output name="output_pal_summary" file="illuminaPE_microsats.out" />
+      <expand macro="output_illumina_microsat_summary" />
+      <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
       <output name="output_assembly" file="illuminaPE_assembly.out" />
     </test>
+    <!-- Test with Illumina input filter to loci with primers
+	 ('-primers' option) -->
     <test>
-      <!-- Test with Illumina input filter to loci with primers
-	   ('-primers' option) -->
       <param name="platform_type" value="illumina" />
       <param name="filters" value="-primers" />
       <param name="assembly" value="false" />
       <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
       <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
-      <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
-      <output name="output_pal_summary" file="illuminaPE_microsats.out" />
-      <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_primers.out" />
+      <expand macro="output_illumina_microsat_summary" />
+      <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
+      <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_primers.out.re_match" />
     </test>
+    <!-- Test with Illumina input filter to loci which appear only once
+	 ('-occurrences' option) -->
     <test>
-      <!-- Test with Illumina input filter to loci which appear only once
-	   ('-occurrences' option) -->
       <param name="platform_type" value="illumina" />
       <param name="filters" value="-occurrences" />
       <param name="assembly" value="false" />
       <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
       <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
-      <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
-      <output name="output_pal_summary" file="illuminaPE_microsats.out" />
-      <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_occurrences.out" />
+      <expand macro="output_illumina_microsat_summary" />
+      <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
+      <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_occurrences.out.re_match" />
     </test>
+    <!-- Test with Illumina input filter and rank loci with perfect motifs
+	 ('-rankmotifs' option) -->
     <test>
-      <!-- Test with Illumina input filter and rank loci with perfect motifs
-	   ('-rankmotifs' option) -->
       <param name="platform_type" value="illumina" />
       <param name="filters" value="-rankmotifs" />
       <param name="assembly" value="false" />
       <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
       <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
-      <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
-      <output name="output_pal_summary" file="illuminaPE_microsats.out" />
-      <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_rankmotifs.out" />
+      <expand macro="output_illumina_microsat_summary" />
+      <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
+      <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_rankmotifs.out.re_match" />
     </test>
+    <!-- Test with 454 input -->
     <test>
-      <!-- Test with 454 input -->
       <param name="platform_type" value="454" />
       <param name="input_fasta" value="454_in.fa" ftype="fasta" />
-      <output name="output_microsat_summary" file="454_microsat_types.out" />
-      <output name="output_pal_summary" file="454_microsats.out" />
+      <expand macro="output_454_microsat_summary" />
+      <output name="output_pal_summary" compare="re_match" file="454_microsats.out.re_match" />
     </test>
   </tests>
   <help>
diff -r a73c48890bde -r 5e133b7b79a6 test-data/454_microsat_types.out
--- a/test-data/454_microsat_types.out	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-totalBases:	8639
-readsWithPrimers:	0
-totalReads:	38
-compound:	0
-broken:	1
-readsWithMicrosat:	1
-
-
-Microsat Type	monomer length	reads with loci	total loci	loci amplified	total loci bases	loci bases amplified
-TC	2	0	0	0	0	0
-AC	2	1	2	0	48	0
-CG	2	0	0	0	0	0
-AT	2	0	0	0	0	0
diff -r a73c48890bde -r 5e133b7b79a6 test-data/454_microsat_types.out.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/454_microsat_types.out.re_match	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,14 @@
+
+broken\:\	1
+compound\:\	0
+readsWithMicrosat\:\	1
+readsWithPrimers\:\	0
+totalBases\:\	8639
+totalReads\:\	38
+
+
+Microsat\ Type\	monomer\ length\	reads\ with\ loci\	total\ loci\	loci\ amplified\	total\ loci\ bases\	loci\ bases\ amplified
+AC\	2\	1\	2\	\	48\	
+AT\	2\	0\	0\	0\	0\	0
+CG\	2\	0\	0\	0\	0\	0
+TG\	2\	0\	0\	0\	0\	0
diff -r a73c48890bde -r 5e133b7b79a6 test-data/454_microsats.out
--- a/test-data/454_microsats.out	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-SequenceID	Repeat Motif Size	Repeat Motif	Number Tandem Repeats	Primer Designed (1=y,0=n)	F Primer Name	Forward Primer	R Primer Name	Reverse Primer	Total Repeats In Amplicon	Occurances of Forward Primer in Reads	Occurances of Reverse Primer in Reads	Occurances of Amplifiable Primer Pair in Reads	Occurances of Amplifiable Primer Pair in PALs
-FW1N29Q04EP35X	2	AC	18	0									
diff -r a73c48890bde -r 5e133b7b79a6 test-data/454_microsats.out.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/454_microsats.out.re_match	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,2 @@
+SequenceID\	Repeat\ Motif\ Size\	Repeat\ Motif\	Number\ Tandem\ Repeats\	Primer\ Designed\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Total\ Repeats\ In\ Amplicon\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs
+FW1N29Q04EP35X\	2\	(AC|TG)\	18\	0\	\	\	\	\	\	\	\	\	
diff -r a73c48890bde -r 5e133b7b79a6 test-data/454_microsats.out.re_match~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/454_microsats.out.re_match~	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,2 @@
+SequenceID\	Repeat\ Motif\ Size\	Repeat\ Motif\	Number\ Tandem\ Repeats\	Primer\ Designed\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Total\ Repeats\ In\ Amplicon\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs
+FW1N29Q04EP35X\	2\	AC\	18\	0\	\	\	\	\	\	\	\	\	
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats.out
--- a/test-data/illuminaPE_filtered_microsats.out	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-readPairID	Motifs(bases)	Bases in all Motifs	Possible Extended	Possible Spanning	Primers found (1=y,0=n)	F Primer Name	Forward Primer	R Primer Name	Reverse Primer	Amplicon Motifs	Number motif bases in amplicon	Primers on sep reads	Extend with primers	Spand with primers	Occurances of Forward Primer in Reads	Occurances of Reverse Primer in Reads	Occurances of Amplifiable Primer Pair in Reads	Occurances of Amplifiable Primer Pair in PALs	R1_Sequence_ID	R1_Sequence	R2_Sequence_ID	R2_Sequence
-ILLUMINA-545855:49:FC61RLR:2:1:8157:1636	AC(12) 	12			1	test_5	AAGTACAGTGGGGAGGCTGG	test_6	TTTTCTACACAGCTCAAGTAGCCC	AC(12) 	12	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT	>ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
-ILLUMINA-545855:49:FC61RLR:2:1:1978:1220	AC(12) 	12			1	test_3	GCAGTAAACAAAGGCAAAGGG	test_4	CCTGGGCAGAGGTGTTCC	AC(12) 	12	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA	>ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
-ILLUMINA-545855:49:FC61RLR:2:1:10979:1695	TC(14) 	14			1	test_7	TTCTCCCACTATATTTTGCATTGG	test_8	TCCAGACTGAAGCTACCCTGG	TC(14) 	14	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA	>ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats.out.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_filtered_microsats.out.re_match	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,4 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	AAGTACAGTGGGGAGGCTGG\	test\_.*\	TTTTCTACACAGCTCAAGTAGCCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	GCAGTAAACAAAGGCAAAGGG\	test\_.*\	CCTGGGCAGAGGTGTTCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	(AG|TC)\(14\)\ \	14\	\	\	1\	test\_.*\	TTCTCCCACTATATTTTGCATTGG\	test\_.*\	TCCAGACTGAAGCTACCCTGG\	(AG|TC)\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats.out.re_match~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_filtered_microsats.out.re_match~	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,4 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	AC\(12\)\ \	12\	\	\	1\	test\_3\	AAGTACAGTGGGGAGGCTGG\	test\_6\	TTTTCTACACAGCTCAAGTAGCCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	AC\(12\)\ \	12\	\	\	1\	test\_7\	GCAGTAAACAAAGGCAAAGGG\	test\_4\	CCTGGGCAGAGGTGTTCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	AG\(14\)\ \	14\	\	\	1\	test\_5\	TTCTCCCACTATATTTTGCATTGG\	test\_1\	TCCAGACTGAAGCTACCCTGG\	AG\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_occurrences.out
--- a/test-data/illuminaPE_filtered_microsats_occurrences.out	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-readPairID	Motifs(bases)	Bases in all Motifs	Possible Extended	Possible Spanning	Primers found (1=y,0=n)	F Primer Name	Forward Primer	R Primer Name	Reverse Primer	Amplicon Motifs	Number motif bases in amplicon	Primers on sep reads	Extend with primers	Spand with primers	Occurances of Forward Primer in Reads	Occurances of Reverse Primer in Reads	Occurances of Amplifiable Primer Pair in Reads	Occurances of Amplifiable Primer Pair in PALs	R1_Sequence_ID	R1_Sequence	R2_Sequence_ID	R2_Sequence
-ILLUMINA-545855:49:FC61RLR:2:1:10979:1695	TC(14) 	14			1	test_7	TTCTCCCACTATATTTTGCATTGG	test_8	TCCAGACTGAAGCTACCCTGG	TC(14) 	14	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA	>ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
-ILLUMINA-545855:49:FC61RLR:2:1:1978:1220	AC(12) 	12			1	test_3	GCAGTAAACAAAGGCAAAGGG	test_4	CCTGGGCAGAGGTGTTCC	AC(12) 	12	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA	>ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
-ILLUMINA-545855:49:FC61RLR:2:1:8157:1636	AC(12) 	12			1	test_5	AAGTACAGTGGGGAGGCTGG	test_6	TTTTCTACACAGCTCAAGTAGCCC	AC(12) 	12	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT	>ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_occurrences.out.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_filtered_microsats_occurrences.out.re_match	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,4 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	(AG|TC)\(14\)\ \	14\	\	\	1\	test\_.*\	TTCTCCCACTATATTTTGCATTGG\	test\_.*\	TCCAGACTGAAGCTACCCTGG\	(AG|TC)\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	GCAGTAAACAAAGGCAAAGGG\	test\_.*\	CCTGGGCAGAGGTGTTCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	AAGTACAGTGGGGAGGCTGG\	test\_.*\	TTTTCTACACAGCTCAAGTAGCCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_occurrences.out.re_match~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_filtered_microsats_occurrences.out.re_match~	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,4 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	AG\(14\)\ \	14\	\	\	1\	test\_7\	TTCTCCCACTATATTTTGCATTGG\	test\_6\	TCCAGACTGAAGCTACCCTGG\	AG\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	AC\(12\)\ \	12\	\	\	1\	test\_5\	GCAGTAAACAAAGGCAAAGGG\	test\_2\	CCTGGGCAGAGGTGTTCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	AC\(12\)\ \	12\	\	\	1\	test\_8\	AAGTACAGTGGGGAGGCTGG\	test\_4\	TTTTCTACACAGCTCAAGTAGCCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_primers.out
--- a/test-data/illuminaPE_filtered_microsats_primers.out	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-readPairID	Motifs(bases)	Bases in all Motifs	Possible Extended	Possible Spanning	Primers found (1=y,0=n)	F Primer Name	Forward Primer	R Primer Name	Reverse Primer	Amplicon Motifs	Number motif bases in amplicon	Primers on sep reads	Extend with primers	Spand with primers	Occurances of Forward Primer in Reads	Occurances of Reverse Primer in Reads	Occurances of Amplifiable Primer Pair in Reads	Occurances of Amplifiable Primer Pair in PALs	R1_Sequence_ID	R1_Sequence	R2_Sequence_ID	R2_Sequence
-ILLUMINA-545855:49:FC61RLR:2:1:10979:1695	TC(14) 	14			1	test_7	TTCTCCCACTATATTTTGCATTGG	test_8	TCCAGACTGAAGCTACCCTGG	TC(14) 	14	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA	>ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
-ILLUMINA-545855:49:FC61RLR:2:1:1978:1220	AC(12) 	12			1	test_3	GCAGTAAACAAAGGCAAAGGG	test_4	CCTGGGCAGAGGTGTTCC	AC(12) 	12	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA	>ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
-ILLUMINA-545855:49:FC61RLR:2:1:8157:1636	AC(12) 	12			1	test_5	AAGTACAGTGGGGAGGCTGG	test_6	TTTTCTACACAGCTCAAGTAGCCC	AC(12) 	12	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT	>ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
-ILLUMINA-545855:49:FC61RLR:2:1:8899:1514	AC(12) AC(12) 	24			1	test_2	TCTTTATCTAAACACATCCTGAAATACC	test_1	AAACGCAATTATTTTGAGATGTCC	AC(12) AC(12) 	24	1			1	2	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 1:N:0:TCCTGA	TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC	>ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 2:N:0:TCCTGA	TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_primers.out.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_filtered_microsats_primers.out.re_match	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,5 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	(AG|TC)\(14\)\ \	14\	\	\	1\	test\_.*\	TTCTCCCACTATATTTTGCATTGG\	test\_.*\	TCCAGACTGAAGCTACCCTGG\	(AG|TC)\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	GCAGTAAACAAAGGCAAAGGG\	test\_.*\	CCTGGGCAGAGGTGTTCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	AAGTACAGTGGGGAGGCTGG\	test\_.*\	TTTTCTACACAGCTCAAGTAGCCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\	(AC|TG)\(12\)\ (AC|TG)\(12\)\ \	24\	\	\	1\	test\_.*\	TCTTTATCTAAACACATCCTGAAATACC\	test\_.*\	AAACGCAATTATTTTGAGATGTCC\	(AC|TG)\(12\)\ (AC|TG)\(12\)\ \	24\	1\	\	\	1\	2\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 1\:N\:0\:TCCTGA\	TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 2\:N\:0\:TCCTGA\	TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_primers.out.re_match~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_filtered_microsats_primers.out.re_match~	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,5 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	AG\(14\)\ \	14\	\	\	1\	test\_7\	TTCTCCCACTATATTTTGCATTGG\	test\_2\	TCCAGACTGAAGCTACCCTGG\	AG\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	TG\(12\)\ \	12\	\	\	1\	test\_5\	GCAGTAAACAAAGGCAAAGGG\	test\_3\	CCTGGGCAGAGGTGTTCC\	TG\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	TG\(12\)\ \	12\	\	\	1\	test\_4\	AAGTACAGTGGGGAGGCTGG\	test\_6\	TTTTCTACACAGCTCAAGTAGCCC\	TG\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\	TG\(12\)\ TG\(12\)\ \	24\	\	\	1\	test\_8\	TCTTTATCTAAACACATCCTGAAATACC\	test\_1\	AAACGCAATTATTTTGAGATGTCC\	TG\(12\)\ TG\(12\)\ \	24\	1\	\	\	1\	2\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 1\:N\:0\:TCCTGA\	TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 2\:N\:0\:TCCTGA\	TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_rankmotifs.out
--- a/test-data/illuminaPE_filtered_microsats_rankmotifs.out	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-readPairID	Motifs(bases)	Bases in all Motifs	Possible Extended	Possible Spanning	Primers found (1=y,0=n)	F Primer Name	Forward Primer	R Primer Name	Reverse Primer	Amplicon Motifs	Number motif bases in amplicon	Primers on sep reads	Extend with primers	Spand with primers	Occurances of Forward Primer in Reads	Occurances of Reverse Primer in Reads	Occurances of Amplifiable Primer Pair in Reads	Occurances of Amplifiable Primer Pair in PALs	R1_Sequence_ID	R1_Sequence	R2_Sequence_ID	R2_Sequence
-ILLUMINA-545855:49:FC61RLR:2:1:8157:1636	AC(12) 	12			1	test_5	AAGTACAGTGGGGAGGCTGG	test_6	TTTTCTACACAGCTCAAGTAGCCC	AC(12) 	12	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT	>ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
-ILLUMINA-545855:49:FC61RLR:2:1:8044:1926	AT(12) 	12			0														>ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 1:N:0:TCCTGA	TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG	>ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 2:N:0:TCCTGA	TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT
-ILLUMINA-545855:49:FC61RLR:2:1:6204:1090	TC(12) 	12			0														>ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 1:N:0:TCCTGA	TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA	>ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 2:N:0:TCCTGA	TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA
-ILLUMINA-545855:49:FC61RLR:2:1:5879:1238	AT(12) 	12			0														>ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 1:N:0:TCCTGA	TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC	>ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 2:N:0:TCCTGA	TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT
-ILLUMINA-545855:49:FC61RLR:2:1:1978:1220	AC(12) 	12			1	test_3	GCAGTAAACAAAGGCAAAGGG	test_4	CCTGGGCAGAGGTGTTCC	AC(12) 	12	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA	>ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
-ILLUMINA-545855:49:FC61RLR:2:1:17449:1584	AC(36) 	36			0														>ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 1:N:0:TCCTGA	TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA	>ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 2:N:0:TCCTGA	TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA
-ILLUMINA-545855:49:FC61RLR:2:1:10979:1695	TC(14) 	14			1	test_7	TTCTCCCACTATATTTTGCATTGG	test_8	TCCAGACTGAAGCTACCCTGG	TC(14) 	14	1			1	1	1	1	>ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA	>ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,8 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	AAGTACAGTGGGGAGGCTGG\	test\_.*\	TTTTCTACACAGCTCAAGTAGCCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 1\:N\:0\:TCCTGA\	TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 2\:N\:0\:TCCTGA\	TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\	(AG|TC)\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 1\:N\:0\:TCCTGA\	TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 2\:N\:0\:TCCTGA\	TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 1\:N\:0\:TCCTGA\	TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 2\:N\:0\:TCCTGA\	TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	GCAGTAAACAAAGGCAAAGGG\	test\_.*\	CCTGGGCAGAGGTGTTCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\	(AC|TG)\(36\)\ \	36\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 1\:N\:0\:TCCTGA\	TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 2\:N\:0\:TCCTGA\	TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	(AG|TC)\(14\)\ \	14\	\	\	1\	test\_.*\	TTCTCCCACTATATTTTGCATTGG\	test\_.*\	TCCAGACTGAAGCTACCCTGG\	(AG|TC)\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match~	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,8 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\	R1\_Sequence\_ID\	R1\_Sequence\	R2\_Sequence\_ID\	R2\_Sequence
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	AC\(12\)\ \	12\	\	\	1\	test\_3\	AAGTACAGTGGGGAGGCTGG\	test\_4\	TTTTCTACACAGCTCAAGTAGCCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\	TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\	TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 1\:N\:0\:TCCTGA\	TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 2\:N\:0\:TCCTGA\	TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\	TC\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 1\:N\:0\:TCCTGA\	TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 2\:N\:0\:TCCTGA\	TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 1\:N\:0\:TCCTGA\	TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 2\:N\:0\:TCCTGA\	TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	AC\(12\)\ \	12\	\	\	1\	test\_6\	GCAGTAAACAAAGGCAAAGGG\	test\_1\	CCTGGGCAGAGGTGTTCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\	TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\	TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\	AC\(36\)\ \	36\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 1\:N\:0\:TCCTGA\	TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 2\:N\:0\:TCCTGA\	TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	TC\(14\)\ \	14\	\	\	1\	test\_7\	TTCTCCCACTATATTTTGCATTGG\	test\_2\	TCCAGACTGAAGCTACCCTGG\	TC\(14\)\ \	14\	1\	\	\	1\	1\	1\	1\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\	TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\	\>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\	TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_microsat_types.out
--- a/test-data/illuminaPE_microsat_types.out	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-totalBases:	2320
-allSpan:	0
-totalReads:	20	(2 x 10)
-compound:	2
-broken:	2
-allExtended:	0
-readsWithMicrosat:	13
-
-
-Microsat Type	monomer length	total loci	loci w/ primers	reads with loci	total bases	extended	extended w/ primers	spanning	spanning w/ primers
-TC	2	2	1	2	26	0	0	0	0
-AC	2	7	4	7	116	0	0	0	0
-CG	2	0	0	0	0	0	0	0	0
-AT	2	8	0	6	106	0	0	0	0
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_microsat_types.out.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_microsat_types.out.re_match	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,16 @@
+allExtended\:\	0
+allSpan\:\	0
+broken\:\	2
+compound\:\	2
+readsWithMicrosat\:\	13
+totalBases\:\	2320
+totalReads\:\	20\	\(2\ x\ 10\)
+
+
+Microsat\ Type\	monomer\ length\	total\ loci\	loci\ w\/\ primers\	reads\ with\ loci\	total\ bases\	extended\	extended\ w\/\ primers\	spanning\	spanning\ w\/\ primers
+(AC\	2\	7\	4\	7\	116\	0\	0\	0\	0)?
+(AG\	2\	0\	0\	0\	0\	0\	0\	0\	0)?
+(AT\	2\	8\	0\	6\	106\	0\	0\	0\	0)?
+CG\	2\	0\	0\	0\	0\	0\	0\	0\	0
+TC\	2\	2\	1\	2\	26\	\	\	\	
+(TG\	2\	7\	4\	7\	116\	\	\	\	)?
\ No newline at end of file
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_microsat_types.out.re_match~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_microsat_types.out.re_match~	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,15 @@
+allExtended\:\	0
+allSpan\:\	0
+broken\:\	2
+compound\:\	2
+readsWithMicrosat\:\	13
+totalBases\:\	2320
+totalReads\:\	20\	\(2\ x\ 10\)
+
+
+Microsat\ Type\	monomer\ length\	total\ loci\	loci\ w\/\ primers\	reads\ with\ loci\	total\ bases\	extended\	extended\ w\/\ primers\	spanning\	spanning\ w\/\ primers
+AC\	2\	7\	4\	7\	116\	0\	0\	0\	0
+AG\	2\	0\	0\	0\	0\	0\	0\	0\	0
+AT\	2\	8\	0\	6\	106\	0\	0\	0\	0
+CG\	2\	0\	0\	0\	0\	0\	0\	0\	0
+TC\	2\	2\	1\	2\	26\	\	\	\	
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_microsats.out
--- a/test-data/illuminaPE_microsats.out	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-readPairID	Motifs(bases)	Bases in all Motifs	Possible Extended	Possible Spanning	Primers found (1=y,0=n)	F Primer Name	Forward Primer	R Primer Name	Reverse Primer	Amplicon Motifs	Number motif bases in amplicon	Primers on sep reads	Extend with primers	Spand with primers	Occurances of Forward Primer in Reads	Occurances of Reverse Primer in Reads	Occurances of Amplifiable Primer Pair in Reads	Occurances of Amplifiable Primer Pair in PALs
-ILLUMINA-545855:49:FC61RLR:2:1:10979:1695	TC(14) 	14			1	test_7	TTCTCCCACTATATTTTGCATTGG	test_8	TCCAGACTGAAGCTACCCTGG	TC(14) 	14	1			1	1	1	1
-ILLUMINA-545855:49:FC61RLR:2:1:17449:1584	AC(36) 	36			0													
-ILLUMINA-545855:49:FC61RLR:2:1:19063:1614	AT(14) AT(14) AT(14) AT(14) 	56			0													
-ILLUMINA-545855:49:FC61RLR:2:1:1978:1220	AC(12) 	12			1	test_3	GCAGTAAACAAAGGCAAAGGG	test_4	CCTGGGCAGAGGTGTTCC	AC(12) 	12	1			1	1	1	1
-ILLUMINA-545855:49:FC61RLR:2:1:5626:1554	AT(14) AC(16) AC(16) AT(12) 	58			0													
-ILLUMINA-545855:49:FC61RLR:2:1:5879:1238	AT(12) 	12			0													
-ILLUMINA-545855:49:FC61RLR:2:1:6204:1090	TC(12) 	12			0													
-ILLUMINA-545855:49:FC61RLR:2:1:8044:1926	AT(12) 	12			0													
-ILLUMINA-545855:49:FC61RLR:2:1:8157:1636	AC(12) 	12			1	test_5	AAGTACAGTGGGGAGGCTGG	test_6	TTTTCTACACAGCTCAAGTAGCCC	AC(12) 	12	1			1	1	1	1
-ILLUMINA-545855:49:FC61RLR:2:1:8899:1514	AC(12) AC(12) 	24			1	test_2	TCTTTATCTAAACACATCCTGAAATACC	test_1	AAACGCAATTATTTTGAGATGTCC	AC(12) AC(12) 	24	1			1	2	1	1
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_microsats.out.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_microsats.out.re_match	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,11 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	(AG|TC)\(14\)\ \	14\	\	\	1\	test\_.*\	TTCTCCCACTATATTTTGCATTGG\	test\_.*\	TCCAGACTGAAGCTACCCTGG\	(AG|TC)\(14\)\ \	14\	1\	\	\	1\	1\	1\	1
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\	(AC|TG)\(36\)\ \	36\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:19063\:1614\	AT\(14\)\ AT\(14\)\ AT\(14\)\ AT\(14\)\ \	56\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	GCAGTAAACAAAGGCAAAGGG\	test\_.*\	CCTGGGCAGAGGTGTTCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5626\:1554\	AT\(14\)\ (AC|TG)\(16\)\ (AC|TG)\(16\)\ AT\(12\)\ \	58\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\	(AG|TC)\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	(AC|TG)\(12\)\ \	12\	\	\	1\	test\_.*\	AAGTACAGTGGGGAGGCTGG\	test\_.*\	TTTTCTACACAGCTCAAGTAGCCC\	(AC|TG)\(12\)\ \	12\	1\	\	\	1\	1\	1\	1
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\	(AC|TG)\(12\)\ (AC|TG)\(12\)\ \	24\	\	\	1\	test\_.*\	TCTTTATCTAAACACATCCTGAAATACC\	test\_.*\	AAACGCAATTATTTTGAGATGTCC\	(AC|TG)\(12\)\ (AC|TG)\(12\)\ \	24\	1\	\	\	1\	2\	1\	1
diff -r a73c48890bde -r 5e133b7b79a6 test-data/illuminaPE_microsats.out.re_match~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/illuminaPE_microsats.out.re_match~	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,11 @@
+readPairID\	Motifs\(bases\)\	Bases\ in\ all\ Motifs\	Possible\ Extended\	Possible\ Spanning\	Primers\ found\ \(1\=y\,0\=n\)\	F\ Primer\ Name\	Forward\ Primer\	R\ Primer\ Name\	Reverse\ Primer\	Amplicon\ Motifs\	Number\ motif\ bases\ in\ amplicon\	Primers\ on\ sep\ reads\	Extend\ with\ primers\	Spand\ with\ primers\	Occurances\ of\ Forward\ Primer\ in\ Reads\	Occurances\ of\ Reverse\ Primer\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\	Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\	TC\(14\)\ \	14\	\	\	1\	test\_7\	TTCTCCCACTATATTTTGCATTGG\	test\_2\	TCCAGACTGAAGCTACCCTGG\	TC\(14\)\ \	14\	1\	\	\	1\	1\	1\	1
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\	AC\(36\)\ \	36\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:19063\:1614\	AT\(14\)\ AT\(14\)\ AT\(14\)\ AT\(14\)\ \	56\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\	AC\(12\)\ \	12\	\	\	1\	test\_6\	GCAGTAAACAAAGGCAAAGGG\	test\_1\	CCTGGGCAGAGGTGTTCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5626\:1554\	AT\(14\)\ AC\(16\)\ AC\(16\)\ AT\(12\)\ \	58\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\	TC\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\	AT\(12\)\ \	12\	\	\	0\	\	\	\	\	\	\	\	\	\	\	\	\	
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\	AC\(12\)\ \	12\	\	\	1\	test\_3\	AAGTACAGTGGGGAGGCTGG\	test\_4\	TTTTCTACACAGCTCAAGTAGCCC\	AC\(12\)\ \	12\	1\	\	\	1\	1\	1\	1
+ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\	AC\(12\)\ AC\(12\)\ \	24\	\	\	1\	test\_8\	TCTTTATCTAAACACATCCTGAAATACC\	test\_5\	AAACGCAATTATTTTGAGATGTCC\	AC\(12\)\ AC\(12\)\ \	24\	1\	\	\	1\	2\	1\	1
diff -r a73c48890bde -r 5e133b7b79a6 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 06 08:54:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,102 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="pal_finder" version="0.02.04">
-      <install version="1.0">
-	<actions>
-	  <action type="download_by_url">http://sourceforge.net/projects/palfinder/files/pal_finder_v0.02.04.tar.gz</action>
-	  <action type="move_file">
-	    <source>pal_finder_v0.02.04.pl</source>
-	    <destination>$INSTALL_DIR/bin</destination>
-	  </action>
-	  <action type="move_file">
-	    <source>config.txt</source>
-	    <destination>$INSTALL_DIR/data</destination>
-	  </action>
-	  <action type="move_file">
-	    <source>simple.ref</source>
-	    <destination>$INSTALL_DIR/data</destination>
-	  </action>
-	  <action type="set_environment">
-	    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-	  </action>
-	  <action type="set_environment">
-	    <environment_variable name="PALFINDER_SCRIPT_DIR" action="set_to">$INSTALL_DIR/bin</environment_variable>
-	  </action>
-	  <action type="set_environment">
-	    <environment_variable name="PALFINDER_DATA_DIR" action="set_to">$INSTALL_DIR/data</environment_variable>
-	  </action>
-	</actions>
-      </install>
-      <readme>pal_finder also needs Perl</readme>
-    </package>
-    <package name="perl" version="5.16.3">
-      <install version="1.0">
-        <actions>
-          <!-- install perl -->
-          <action type="download_by_url">http://www.cpan.org/src/5.0/perl-5.16.3.tar.gz</action>
-          <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action>
-          <action type="make_install" />
-          <action type="set_environment">
-            <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-          </action>
-        </actions>
-      </install>
-      <readme>
-        Perl 5 is a highly capable, feature-rich programming language with over 25 years of
-	development:
-
-        http://www.perl.org/
-      </readme>
-    </package>
-    <package name="primer3_core" version="2.0.0">
-      <install version="1.0">
-	<actions>
-	  <action type="download_by_url">https://sourceforge.net/projects/primer3/files/primer3/2.0.0-alpha/primer3-2.0.0-alpha.tar.gz</action>
-	  <action type="shell_command">make -C src -f Makefile</action>
-	  <action type="move_file">
-	    <source>src/primer3_core</source>
-	    <destination>$INSTALL_DIR/bin</destination>
-	  </action>
-	  <action type="set_environment">
-	    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-	  </action>
-	</actions>
-      </install>
-      <readme>primer3_core</readme>
-    </package>
-    <package name="biopython" version="1.65">
-      <install version="1.0">
-	<actions>
-	  <action type="shell_command">pip install  --install-option "--prefix=$INSTALL_DIR" https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz</action>
-	  <action type="set_environment">
-	    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
-	    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib64/python2.7/site-packages</environment_variable>
-	  </action>
-	</actions>
-      </install>
-      <readme>BioPython 1.65</readme>
-    </package>
-    <package name="pandaseq" version="2.8.1">
-      <install version="1.0">
-	<actions>
-	  <action type="download_by_url">https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz</action>
-	  <action type="shell_command">./autogen.sh</action>
-	  <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
-	  <action type="shell_command">make</action>
-	  <action type="shell_command">make install</action>
-	  <action type="set_environment">
-	    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-	    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
-	  </action>
-	</actions>
-      </install>
-      <readme>PANDASeq 2.8.1
-
-      PANDASEQ is a program to align Illumina reads, optionally
-      with PCR primers embedded in the sequence, and reconstruct
-      an overlapping sequence.
-
-      https://github.com/neufeld/pandaseq
-      </readme>
-    </package>
-</tool_dependency>