# 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:	0" />
+ <has_line line="allSpan:	0" />
+ <has_line line="broken:	2" />
+ <has_line line="compound:	2" />
+ <has_line line="readsWithMicrosat:	13" />
+ <has_line line="totalBases:	2320" />
+ <has_line line="totalReads:	20	(2 x 10)" />
+ <has_line line="Microsat Type	monomer length	total loci	loci w/ primers	reads with loci	total bases	extended	extended w/ primers	spanning	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:	1" />
+ <has_line line="compound:	0" />
+ <has_line line="readsWithMicrosat:	1" />
+ <has_line line="readsWithPrimers:	0" />
+ <has_line line="totalBases:	8639" />
+ <has_line line="totalReads:	38" />
+ <has_line line="Microsat Type	monomer length	reads with loci	total loci	loci amplified	total loci bases	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>