# HG changeset patch
# User mheinzl
# Date 1543224380 18000
# Node ID e486f84adbec67b4c0deee6da992069b7580f101
# Parent  238a712418766cf3d4590256d1b13167700191c3
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d

diff -r 238a71241876 -r e486f84adbec fsd_beforevsafter.xml
--- a/fsd_beforevsafter.xml	Mon Oct 08 05:55:14 2018 -0400
+++ b/fsd_beforevsafter.xml	Mon Nov 26 04:26:20 2018 -0500
@@ -1,6 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <tool id="fsd_beforevsafter" name="FSD Before/After" version="1.0.0">
     <description>: Family Size Distribution of duplex sequecning tags during DuNovo analysis</description>
+    <macros>
+        <import>fsd_reg_macros.xml</import>
+    </macros>
     <requirements>
 		<!-- galaxy version 16.04 -->
         <requirement type="package" version="2.7">python</requirement>
@@ -8,13 +11,13 @@
         <requirement type="package" version="1.71">biopython</requirement>
     </requirements>
     <command>
-        python2 '$__tool_directory__/fsd_beforevsafter.py' --inputFile_SSCS '$file1' --inputName1 '$file1.name' --makeDCS '$makeDCS' --afterTrimming '$afterTrimming' --alignedTags '$alignedTags' --output_pdf $output_pdf --output_tabular $output_tabular
+        python2 '$__tool_directory__/fsd_beforevsafter.py' --inputFile_SSCS '$file1' --inputName1 '$file1.name' --makeDCS '$makeDCS' --afterTrimming '$afterTrimming' --bamFile '$bamFile' --output_pdf $output_pdf --output_tabular $output_tabular
     </command>
     <inputs>
         <param name="file1" type="data" format="tabular" label="Dataset 1: input tags of whole dataset" optional="false" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family."/>
         <param name="makeDCS" type="data" format="fasta" label="Dataset 2: tags after making DCSs" help="Input in fasta format with the tags of the reads, which were aligned to DCSs, and their family sizes of both strands (reverse and forward) in the header, as well as the read itself in the next line."/>
         <param name="afterTrimming" type="data" format="fasta" optional="true" label="Dataset 3: tags after trimming" help="Input in fasta format with the tags of the reads, which were not filtered out after trimming, and their family sizes of both strands (reverse and forward) in the header, as well as the read itself in the next following line."/>
-        <param name="alignedTags" type="data" format="txt" optional="true" label="Dataset 4: input tags aligned to the reference genome" help="Input in txt format with the regions of the reference genome and the tags, which were aligned to the reference genome."/>
+        <param name="bamFile" type="data" format="bam" optional="true" label="Dataset 4: input tags aligned to the reference genome" help="Input in BAM format with the reads that were aligned to the reference genome."/>
     </inputs>
     <outputs>
         <data name="output_pdf" format="pdf" />
@@ -22,12 +25,12 @@
     </outputs>
     <tests>
         <test>
-            <param name="file1" value="Test_data.tabular"/>
-            <param name="makeDCS" value="Test_data_DCS.fasta"/>
-            <param name="afterTrimming" value="Test_data_trimming.fasta"/>
-            <param name="alignedTags" value="Test_data_regions.txt"/>
-            <output name="output_pdf" file="output_file.pdf" lines_diff="183"/>
-            <output name="output_tabular" file="output_file.tabular"/>
+            <param name="file1" value="fsd_ba_data.tab"/>
+            <param name="makeDCS" value="fsd_ba_DCS.fna"/>
+            <param name="afterTrimming" value="fsd_ba_trimmed.fna"/>
+            <param name="bamFile" value="fsd_ba.bam"/>
+            <output name="output_pdf" file="fsd_ba_output.pdf" lines_diff="183"/>
+            <output name="output_tabular" file="fsd_ba_output.tab"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -56,32 +59,15 @@
   >AAAAAAAAGGCAGAAGATATACGC 11-3
   CNCNGGCCCCCCGCTCCGTGCACAGACGNNGCNACTGACAA
 	
-**Dataset 4 (optional):** Finally, a TXT file with the regions and all tags that were aligned to the reference genome can be given as input. This file can be obtained by the tool "Duplex Sequencing Analysis: range2tag"::
-
- 87_636   AAATCAAAGTATGAATGAAGTTGCCT
- 87_636   AAATTCATAGCATTAATTTCAACGGG
- 656_1143 GGGGCAGCCATATTGGCAATTATCAT
+**Dataset 4 (optional):** BAM file of the aligned reads. This file can be obtained by the tool "Map with BWA-MEM".	
 
 **Output**
         
 The output is a PDF file with the plot and a tabular file with the data of the plot.
          
-**About Author**
-        
-Author: Monika Heinzl
-Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
-Contact: monika.heinzl@edumail.at
+@author@
         
 ]]> 
-
     </help>
-    <citations>
-        <citation type="bibtex">
-            @misc{duplex,
-            author = {Heinzl, Monika},
-            year = {2018},
-            title = {Development of algorithms for the analysis of duplex sequencing data}
-         }
-        </citation>
-    </citations>
+    <expand macro="@citation@" />
 </tool>
diff -r 238a71241876 -r e486f84adbec test-data/Test_data.tabular
--- a/test-data/Test_data.tabular	Mon Oct 08 05:55:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-10	AAAAAACATCCCAATAAGAAATCA	ab
-9	AAAAAACATCCCAATAAGAAATCA	ba
-4	AAAAAAGTCCTTCGACTCAAGCGG	ab
-5	AAAAAAGTCCTTCGACTCAAGCGG	ba
-5	AAAAAATAGTTAAGCCGACACACT	ab
-7	AAAAAATAGTTAAGCCGACACACT	ba
-7	AAAAAATGTGCCGAACCTTGGCGA	ab
-10	AAAAAATGTGCCGAACCTTGGCGA	ba
-7	AAAAACAACATAGCTTGAAAATTT	ab
-4	AAAAACAACATAGCTTGAAAATTT	ba
-81	ATTCGGATAATTCGACGCAACATT	ab
-11	ATTCGGATAATTCGACGCAACATT	ba
-41	ATTCGTCGACAATACAAAGGGGCC	ab
-226	ATTCGTCGACAATACAAAGGGGCC	ba
-6	ATTGCCAGTGTGGGCTGGTTAGTA	ab
-41	ATTGCCAGTGTGGGCTGGTTAGTA	ba
-50	ATTTCGCGACCATCCGCCACTTTG	ab
-332	ATTTCGCGACCATCCGCCACTTTG	ba
-64	CAAACTTTAGCACAGTGTGTGTCC	ab
-57	CAAACTTTAGCACAGTGTGTGTCC	ba
-85	ATAAACGGCCTTCGACATTGTGAC	ab
-15	ATAAACGGCCTTCGACATTGTGAC	ba
-11	ATAAAGTCACCTGTGAATACGTTG	ab
-35	ATAAAGTCACCTGTGAATACGTTG	ba
-83	ATAAATCGAAACCGTGCCCAACAA	ab
-63	ATAAATCGAAACCGTGCCCAACAA	ba
-9	ATTTAGATATTTTCTTCTTTTTCT	ab
-7	ATTTAGATATTTTCTTCTTTTTCT	ba
-7	ATTTAGTTATCCGTCGGCGACGAA	ab
-3	ATTTAGTTATCCGTCGGCGACGAA	ba
-8	ATTTAGTTTGAATTGCCCTGCGTC	ab
-9	ATTTAGTTTGAATTGCCCTGCGTC	ba
\ No newline at end of file
diff -r 238a71241876 -r e486f84adbec test-data/Test_data_DCS.fasta
--- a/test-data/Test_data_DCS.fasta	Mon Oct 08 05:55:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
->AAAAAAGGACCCTACCACCAACGT 8-5
-CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGNGTCCAACGCGTCCATGAGCTNCNACNCNCCACTGGTGCGCNNCGCNNGNCTNNNNNCAGNNNANNNCCNCANNNNNNCCNNNNNCNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNN
->AAAAAAGGATTCCAAATCTCTGGA 3-7
-TACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGNCCCTGGGGACACGGGCTCCTCAGACGGGNTGCCAGGCNCNGGAGGNCCGCNCAGCCGGNNNCCACCGCNNSNNNCCNNNNCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNN
->AAAAAAGGCCAGTTTAAAAAAACT 37-3
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTNGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCNNNTGGGCCTGGCANCCCNNCNGAGGAGCCNGNNNCCNCAGGTCCCCTGTACNNNCTNGTG
->AAAAAAGGCCCAGATCTCTTAAAA 194-31
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGAGCCCGTGTCCCCAGGGCCCCTGTACGTGCTGGTGGAGTACGCGGCCAAGGGTAACCTGCGGGAGTTTCAGTCATTTTAAG
->AAAAAAGGGGCCTCATGCGTCAGT 4-3
-CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCNGGAAGNGGGAGANCTTGTGCACGGTGGNNGANCCNAGGCCTTNCTTGGGGGGNNTGCGNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNGGNNNANNNGNNNNNNNNNNNNNNNNT
->AAAAAAGTCCTTCGACTCAAGCGG 4-5
-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTNCTGCCAGGTACCGGCNTCTNCTGCTGCTGNNGNNCNNCNNTNNCNNNNNNNNNNTNNCNNNNNNNNNNNN
->AAAAAAGTGGGATCGGGTTGCAGC 11-6
-CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCNGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGGTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGCNCCCCAGGGCCGGGCNCACGTTGGTTGTCTTCTTGNANTAGTCNNNNTNGTGCNCGTNNNNNNNCNNNNNNNNNNNNNCNNNN
->AAAAAATAATTTCGCCCTCGAGTA 16-4
-CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCANCNCACCACTGGNNNGNNTCNCANNGCTNTCNNCAGNNNNNGGCCNNNNNCTGNNCNANNTCNCC
->AAAAAATAGTTAAGCCGACACACT 5-7
-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGNGTACACCTGCCTGGCGGGCAATTCTATNGGGTTTTCTCATCACTCTGCGTGGNNGGTGGTGCTGCCAGGTACCGGCNTCTGCTGCTNNNGCTGNNCCGCNNNNNNNNNNNNNNNNNGNNNNNNNNNNCN
->AAAAAATCAGAATAGAGCGCTTTC 4-3
-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGNGGACGCCGGGGAGTANACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGNCTGGTGGNGCTGCCNGNNNCCNNNNNCTNNNNNNNNNGCTNNNNNNNNNTNNNNNNNNNNNNNNNNNCTNNCNNNNNNNN
->AAAAAATCATAAACATTTTAACAA 65-21
-CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGTGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGTGCGCATCGCAAGGCTGTCCTCAGGGGAGGGCCCCACGCTGGCCAATGTCTCCNNNCNNGNGCNGCCTGCCNNNNNCAAANGG
->AAAAAATCTTGACTCGGTACACAA 9-3
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGMCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNNCNGAGGAGCCNNNNTCNCCAGGNCCNNTGNANNNNCNGGNGGAGTANNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
->AAAAAATGACGAACGATTCGTCAT 3-6
-CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACNNTGGGCACAGGGNCAGGAGNNNNNGCNCAAGNANNNNNNNNNNNNNNNNNNTCNNNNNNNNNNNCNNNNNNNNNNKNNNNNNNNNNNNNNNNNNNCNNNNNNNN
->AAAAAATGTGCCGAACCTTGGCGA 7-10
-CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGNNGNNNGNAAGTCNCAGGATTNNNNNCNNNNNTNNNANNTTTGGCNNNNNNNNNNNNANN
->AAAAAATTGAATCCGTGGATATAG 3-8
-CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGNNCCNNNCCNGGCCNNAACGCCCATNTCTTTNCNGCNNNGNNNGANCNGGTGGAGGNNNGACNAGGCGGGNNGTGNNTNNNNMNGNCNNNNNNNNNNNNGNNNNGNGNNNNNNNNNTGTNNNTCMNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
->AAAAAATTGCATGCATCGTCCCTG 6-9
-CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGTGCGNATCGCAAGGCTGTCCTCAGGGGNGGNCCNCNNNNTGNCNNATNNCNCCGNGCNNNNGCNNCCTGCNNNNNNCNNNN
->AAAAAATTGGCATTGTGTATGCAT 18-5
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCNGNNCNNNNGNNNANNCCGTGNCCCCAGGGNCNNTGNNNNNNNNGGTNNNNNACGNNNNCNANNNTANCCNNNNNNNGT
->AAAAAATTTTCCCACCAAAATTTC 18-3
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTNNNGGNTNGGCGGCCCTCCTGGGCCTGGCNGCNCGTCTGAGGNNCCNNNGTCNNCAGGNNNNCNNTNNNNNNNGGNGNNNNANNNNGNNNNGNNNNNNNNNNNNNNNNNNCNGNNNNNNNNNNNN
->AAAAAATTTTTCTTTACCACCTGT 4-4
-CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGGCCNGGCNNNNCNNNAACGCCCANNNTNTTTNNANCNNNNGNGNNNNNGNNNNNNNSNNNCNNNNNNNNNNGNNNNNNNNNNNNNCNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
->AAAAACAACATAGCTTGAAAATTT 7-4
-CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCNCAGGGCCAGGAGTGAGGGCNCNAGNAGCNGGACGGNNGTAAGTNNNNNNANTNNNNNNNNTNNNNGCNNNNNTNNNNNNNCNNNNNNNAGN
->AAAAACAACCAACGTTCTATCTCT 18-4
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNNNNGNGGNNNNNGNGTCCCCAGGGCCCCTGNNNNNNNNGGNNGNNNNNNNGGNCNNGNNNNNCNTGNNNNANNNNNNNNNNNNNNNNNNN
->AAAAACAAGATAATTGGCGCCCGT 5-22
-CTGCCATACACCCGTCCCAGGAGCATGTCCACAGAACCCCAGCCACACCCAACATCCGCCACATCCCTGACGGCCCCTAAACCCAGCCGGGCCTCTGACTGGTGGCTGTTTCACCCCCACCACCAAGCCCCCTACAGCCAACGCTGGCCCTCAGCACCACTGACCGGGCCCGAGACAGCTCCCATTTGGGGTCGGCAGGCAGCTCGAGCTCGGANACATTGGCCAGCGTGGNGNNNNNCCCNNNGNNCNNCCNTNNNNNNYNNNNNANNNNNNNNNNNNNNNMNNN
->AAAAACAAGCATCTGTCGACACTA 69-60
-TGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTAACAGAAAGTAGATACCAGGTTCTGAGCTGCCTGCCCGCCAGGCCTCCTGGAGCCCCACCTCGGCCCACGCTGGTCCTGGGCTGTGTGAGCCCTCTCTGCAGCCAGGCGGGCTCCCCTCTCCTCGTCTCTGCTCACCATGTAGAGCCTAGGGAGTCATAGTGTCGACAG
->AAAAACAATCTTAACCGCGATCTA 10-4
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGNGCCNGNNTCCCCNGGTCCCCTGTNNGTGCTGGNGGANTACNNGGNCNAGGGTNNCCNGCNNNNGNTNNTGNNNGNNNNNNNN
->AAAAACACGCGGACTTTCCGCATT 4-7
-ACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGCCCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGNGGGCCGCCCAGCCGGCACCACCGCCGCTACCGCNNCTACCNCCNNNNCGTGCNNNNNNCNNNCAGNNNNNN
\ No newline at end of file
diff -r 238a71241876 -r e486f84adbec test-data/Test_data_regions.txt
--- a/test-data/Test_data_regions.txt	Mon Oct 08 05:55:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-87_636 AAAAAACATCCCAATAAGAAATCA
-87_636 AAAAAAGTCCTTCGACTCAAGCGG
-87_636 AAAAAATAGTTAAGCCGACACACT
-87_636 AAAAAATGTGCCGAACCTTGGCGA
-87_636 AAAAACAACATAGCTTGAAAATTT
-656_1143 ATTCGGATAATTCGACGCAACATT
-656_1143 ATTCGTCGACAATACAAAGGGGCC
-656_1143 ATTGCCAGTGTGGGCTGGTTAGTA
-656_1143 ATTTCGCGACCATCCGCCACTTTG
-656_1143 CAAACTTTAGCACAGTGTGTGTCC
-1141_1564 ATAAACGGCCTTCGACATTGTGAC
-1141_1564 ATAAAGTCACCTGTGAATACGTTG
-1141_1564 ATAAATCGAAACCGTGCCCAACAA
-1892_2398 ATTTAGATATTTTCTTCTTTTTCT
-1892_2398 ATTTAGTTATCCGTCGGCGACGAA
-1892_2398 ATTTAGTTTGAATTGCCCTGCGTC
-
diff -r 238a71241876 -r e486f84adbec test-data/Test_data_trimming.fasta
--- a/test-data/Test_data_trimming.fasta	Mon Oct 08 05:55:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
->AAAAAGAAAAACGATGCTTGACCA 4-6
-CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCGGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGGTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGC
->AAAAAGAAAAGTTTGCTTTTTCTT 13-17
-CTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGACCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGAGGGCCGCCCAGCCGGCACCACCGCCGCT
->AAAAAGAAATGAATTGGTCCTAGA 24-7
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTNTGAGGAGCC
->AAAAAGACAGCCTGAATTCCTTGT 17-4
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGNGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCNCCTGGGCCTGGCAGCCCGTCNGAG
->AAAAAGACGATTACACAATAACCT 16-7
-CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGTGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGT
->AAAAAGATACGGGAGGTGAATTGT 75-6
-CTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACGCCAAAGCTGCCAGGACGGACGGGAATCCTGTGACTTACGGCCGTCCCGCTTCTTGAGCCCTCACTCCTGGCCCTGTGCCCAGTGTGGGGACAAAGTTGGCCTGGCCCGGTCCTGGTCCCAGAGGGGC
->AAAAAGATATTTTAATCGGCCCGA 7-6
-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTMTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGC
->AAAAAGATTACACTGAAATCTTTT 25-5
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNTCTGAGGAGCCCNTGTCCCCAGGGCC
->AAAAAGCCATATGGTCGAAGAGAT 13-10
-ACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGACCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGAGGGCCGCCCAGCCGGCACCACCGCC
->AAAAAGCGAAAGTGCCCCATATTT 13-16
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNTCTGAGGAGCCCGTGTCCCCAGGGCCCCTGTACGTNCTGGTGG
->AAAAAGCGATTTAACTGAAATTAT 5-4
-CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGC
->AAAAAGCGGGGTGGCCTTACGCCC 17-10
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGAGCCCGNGTCCCCAGGGCCNCTGTACGT
->AAAAAGCTCTACCCCCACGAAGCG 5-10
-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGNCTTCTGCTGCTGCTGC
->AAAAAGGATATGTCTAACATCCCT 15-16
-CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCACGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGAAGCCCACCCCGT
->AAAAAGGTACACCCGAGATGAACT 13-9
-CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGNGCCCGTGTCCCCAGGTCCCCTGTACGTGCTGGTGGAGTAC
->AAAAAGTAGCTTCGGTTCGGGTCT 12-4
-GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGANTACACCTGCCTGGCGGGCANTTCTATTGGGTTTTCTCATCACTCTGCGTG
->AAAAAGTAGGGACATAATTGACTT 4-4
-CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCGGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGRTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGCACCCCA
\ No newline at end of file
diff -r 238a71241876 -r e486f84adbec test-data/fsd_ba.bam
Binary file test-data/fsd_ba.bam has changed
diff -r 238a71241876 -r e486f84adbec test-data/fsd_ba_DCS.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fsd_ba_DCS.fna	Mon Nov 26 04:26:20 2018 -0500
@@ -0,0 +1,50 @@
+>AAAAAAGGACCCTACCACCAACGT 8-5
+CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGNGTCCAACGCGTCCATGAGCTNCNACNCNCCACTGGTGCGCNNCGCNNGNCTNNNNNCAGNNNANNNCCNCANNNNNNCCNNNNNCNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNN
+>AAAAAAGGATTCCAAATCTCTGGA 3-7
+TACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGNCCCTGGGGACACGGGCTCCTCAGACGGGNTGCCAGGCNCNGGAGGNCCGCNCAGCCGGNNNCCACCGCNNSNNNCCNNNNCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNN
+>AAAAAAGGCCAGTTTAAAAAAACT 37-3
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTNGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCNNNTGGGCCTGGCANCCCNNCNGAGGAGCCNGNNNCCNCAGGTCCCCTGTACNNNCTNGTG
+>AAAAAAGGCCCAGATCTCTTAAAA 194-31
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGAGCCCGTGTCCCCAGGGCCCCTGTACGTGCTGGTGGAGTACGCGGCCAAGGGTAACCTGCGGGAGTTTCAGTCATTTTAAG
+>AAAAAAGGGGCCTCATGCGTCAGT 4-3
+CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCNGGAAGNGGGAGANCTTGTGCACGGTGGNNGANCCNAGGCCTTNCTTGGGGGGNNTGCGNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNGGNNNANNNGNNNNNNNNNNNNNNNNT
+>AAAAAAGTCCTTCGACTCAAGCGG 4-5
+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTNCTGCCAGGTACCGGCNTCTNCTGCTGCTGNNGNNCNNCNNTNNCNNNNNNNNNNTNNCNNNNNNNNNNNN
+>AAAAAAGTGGGATCGGGTTGCAGC 11-6
+CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCNGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGGTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGCNCCCCAGGGCCGGGCNCACGTTGGTTGTCTTCTTGNANTAGTCNNNNTNGTGCNCGTNNNNNNNCNNNNNNNNNNNNNCNNNN
+>AAAAAATAATTTCGCCCTCGAGTA 16-4
+CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCANCNCACCACTGGNNNGNNTCNCANNGCTNTCNNCAGNNNNNGGCCNNNNNCTGNNCNANNTCNCC
+>AAAAAATAGTTAAGCCGACACACT 5-7
+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGNGTACACCTGCCTGGCGGGCAATTCTATNGGGTTTTCTCATCACTCTGCGTGGNNGGTGGTGCTGCCAGGTACCGGCNTCTGCTGCTNNNGCTGNNCCGCNNNNNNNNNNNNNNNNNGNNNNNNNNNNCN
+>AAAAAATCAGAATAGAGCGCTTTC 4-3
+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGNGGACGCCGGGGAGTANACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGNCTGGTGGNGCTGCCNGNNNCCNNNNNCTNNNNNNNNNGCTNNNNNNNNNTNNNNNNNNNNNNNNNNNCTNNCNNNNNNNN
+>AAAAAATCATAAACATTTTAACAA 65-21
+CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGTGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGTGCGCATCGCAAGGCTGTCCTCAGGGGAGGGCCCCACGCTGGCCAATGTCTCCNNNCNNGNGCNGCCTGCCNNNNNCAAANGG
+>AAAAAATCTTGACTCGGTACACAA 9-3
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGMCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNNCNGAGGAGCCNNNNTCNCCAGGNCCNNTGNANNNNCNGGNGGAGTANNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+>AAAAAATGACGAACGATTCGTCAT 3-6
+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACNNTGGGCACAGGGNCAGGAGNNNNNGCNCAAGNANNNNNNNNNNNNNNNNNNTCNNNNNNNNNNNCNNNNNNNNNNKNNNNNNNNNNNNNNNNNNNCNNNNNNNN
+>AAAAAATGTGCCGAACCTTGGCGA 7-10
+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGNNGNNNGNAAGTCNCAGGATTNNNNNCNNNNNTNNNANNTTTGGCNNNNNNNNNNNNANN
+>AAAAAATTGAATCCGTGGATATAG 3-8
+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGNNCCNNNCCNGGCCNNAACGCCCATNTCTTTNCNGCNNNGNNNGANCNGGTGGAGGNNNGACNAGGCGGGNNGTGNNTNNNNMNGNCNNNNNNNNNNNNGNNNNGNGNNNNNNNNNTGTNNNTCMNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+>AAAAAATTGCATGCATCGTCCCTG 6-9
+CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGTGCGNATCGCAAGGCTGTCCTCAGGGGNGGNCCNCNNNNTGNCNNATNNCNCCGNGCNNNNGCNNCCTGCNNNNNNCNNNN
+>AAAAAATTGGCATTGTGTATGCAT 18-5
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCNGNNCNNNNGNNNANNCCGTGNCCCCAGGGNCNNTGNNNNNNNNGGTNNNNNACGNNNNCNANNNTANCCNNNNNNNGT
+>AAAAAATTTTCCCACCAAAATTTC 18-3
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTNNNGGNTNGGCGGCCCTCCTGGGCCTGGCNGCNCGTCTGAGGNNCCNNNGTCNNCAGGNNNNCNNTNNNNNNNGGNGNNNNANNNNGNNNNGNNNNNNNNNNNNNNNNNNCNGNNNNNNNNNNNN
+>AAAAAATTTTTCTTTACCACCTGT 4-4
+CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGGCCNGGCNNNNCNNNAACGCCCANNNTNTTTNNANCNNNNGNGNNNNNGNNNNNNNSNNNCNNNNNNNNNNGNNNNNNNNNNNNNCNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+>AAAAACAACATAGCTTGAAAATTT 7-4
+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCNCAGGGCCAGGAGTGAGGGCNCNAGNAGCNGGACGGNNGTAAGTNNNNNNANTNNNNNNNNTNNNNGCNNNNNTNNNNNNNCNNNNNNNAGN
+>AAAAACAACCAACGTTCTATCTCT 18-4
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNNNNGNGGNNNNNGNGTCCCCAGGGCCCCTGNNNNNNNNGGNNGNNNNNNNGGNCNNGNNNNNCNTGNNNNANNNNNNNNNNNNNNNNNNN
+>AAAAACAAGATAATTGGCGCCCGT 5-22
+CTGCCATACACCCGTCCCAGGAGCATGTCCACAGAACCCCAGCCACACCCAACATCCGCCACATCCCTGACGGCCCCTAAACCCAGCCGGGCCTCTGACTGGTGGCTGTTTCACCCCCACCACCAAGCCCCCTACAGCCAACGCTGGCCCTCAGCACCACTGACCGGGCCCGAGACAGCTCCCATTTGGGGTCGGCAGGCAGCTCGAGCTCGGANACATTGGCCAGCGTGGNGNNNNNCCCNNNGNNCNNCCNTNNNNNNYNNNNNANNNNNNNNNNNNNNNMNNN
+>AAAAACAAGCATCTGTCGACACTA 69-60
+TGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTAACAGAAAGTAGATACCAGGTTCTGAGCTGCCTGCCCGCCAGGCCTCCTGGAGCCCCACCTCGGCCCACGCTGGTCCTGGGCTGTGTGAGCCCTCTCTGCAGCCAGGCGGGCTCCCCTCTCCTCGTCTCTGCTCACCATGTAGAGCCTAGGGAGTCATAGTGTCGACAG
+>AAAAACAATCTTAACCGCGATCTA 10-4
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGNGCCNGNNTCCCCNGGTCCCCTGTNNGTGCTGGNGGANTACNNGGNCNAGGGTNNCCNGCNNNNGNTNNTGNNNGNNNNNNNN
+>AAAAACACGCGGACTTTCCGCATT 4-7
+ACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGCCCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGNGGGCCGCCCAGCCGGCACCACCGCCGCTACCGCNNCTACCNCCNNNNCGTGCNNNNNNCNNNCAGNNNNNN
\ No newline at end of file
diff -r 238a71241876 -r e486f84adbec test-data/fsd_ba_data.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fsd_ba_data.tab	Mon Nov 26 04:26:20 2018 -0500
@@ -0,0 +1,32 @@
+10	AAAAAACATCCCAATAAGAAATCA	ab
+9	AAAAAACATCCCAATAAGAAATCA	ba
+4	AAAAAAGTCCTTCGACTCAAGCGG	ab
+5	AAAAAAGTCCTTCGACTCAAGCGG	ba
+5	AAAAAATAGTTAAGCCGACACACT	ab
+7	AAAAAATAGTTAAGCCGACACACT	ba
+7	AAAAAATGTGCCGAACCTTGGCGA	ab
+10	AAAAAATGTGCCGAACCTTGGCGA	ba
+7	AAAAACAACATAGCTTGAAAATTT	ab
+4	AAAAACAACATAGCTTGAAAATTT	ba
+81	ATTCGGATAATTCGACGCAACATT	ab
+11	ATTCGGATAATTCGACGCAACATT	ba
+41	ATTCGTCGACAATACAAAGGGGCC	ab
+226	ATTCGTCGACAATACAAAGGGGCC	ba
+6	ATTGCCAGTGTGGGCTGGTTAGTA	ab
+41	ATTGCCAGTGTGGGCTGGTTAGTA	ba
+50	ATTTCGCGACCATCCGCCACTTTG	ab
+332	ATTTCGCGACCATCCGCCACTTTG	ba
+64	CAAACTTTAGCACAGTGTGTGTCC	ab
+57	CAAACTTTAGCACAGTGTGTGTCC	ba
+85	ATAAACGGCCTTCGACATTGTGAC	ab
+15	ATAAACGGCCTTCGACATTGTGAC	ba
+11	ATAAAGTCACCTGTGAATACGTTG	ab
+35	ATAAAGTCACCTGTGAATACGTTG	ba
+83	ATAAATCGAAACCGTGCCCAACAA	ab
+63	ATAAATCGAAACCGTGCCCAACAA	ba
+9	ATTTAGATATTTTCTTCTTTTTCT	ab
+7	ATTTAGATATTTTCTTCTTTTTCT	ba
+7	ATTTAGTTATCCGTCGGCGACGAA	ab
+3	ATTTAGTTATCCGTCGGCGACGAA	ba
+8	ATTTAGTTTGAATTGCCCTGCGTC	ab
+9	ATTTAGTTTGAATTGCCCTGCGTC	ba
\ No newline at end of file
diff -r 238a71241876 -r e486f84adbec test-data/fsd_ba_output.pdf
Binary file test-data/fsd_ba_output.pdf has changed
diff -r 238a71241876 -r e486f84adbec test-data/fsd_ba_output.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fsd_ba_output.tab	Mon Nov 26 04:26:20 2018 -0500
@@ -0,0 +1,45 @@
+Dataset:	fsd_ba_data.tab
+	AB	BA
+max. family size:	81	226
+absolute frequency:	1	1
+relative frequency:	0.100	0.100
+
+
+total nr. of reads before SSCS building	1312
+
+
+Values from family size distribution
+	before SSCS building	after DCS building	after trimming	after alignment to reference
+FS=1	0	0	0	0
+FS=2	0	0	0	0
+FS=3	1	8	0	0
+FS=4	2	10	6	2
+FS=5	2	5	3	2
+FS=6	1	3	3	0
+FS=7	5	5	3	4
+FS=8	1	2	0	1
+FS=9	3	2	1	3
+FS=10	2	2	3	2
+FS=11	2	1	0	2
+FS=12	0	0	1	0
+FS=13	0	0	4	0
+FS=14	0	0	0	0
+FS=15	1	0	1	0
+FS=16	0	1	3	0
+FS=17	0	0	3	0
+FS=18	0	3	0	0
+FS=19	0	0	0	0
+FS=20	0	0	0	0
+FS>20	12	8	3	4
+sum	32	50	34	20
+
+
+In the plot, the family sizes of ab and ba strands and of both duplex tags were used.
+Whereas the total numbers indicate only the single count of the formed duplex tags.
+total nr. of tags (unique, FS>=1)	16
+DCS (before SSCS building, FS>=1)	16
+total nr. of tags (unique, FS>=3)	16
+DCS (before SSCS building, FS>=3)	16
+after DCS building	25
+after trimming	17
+after alignment to reference	10
diff -r 238a71241876 -r e486f84adbec test-data/fsd_ba_trimmed.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fsd_ba_trimmed.fna	Mon Nov 26 04:26:20 2018 -0500
@@ -0,0 +1,34 @@
+>AAAAAGAAAAACGATGCTTGACCA 4-6
+CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCGGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGGTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGC
+>AAAAAGAAAAGTTTGCTTTTTCTT 13-17
+CTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGACCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGAGGGCCGCCCAGCCGGCACCACCGCCGCT
+>AAAAAGAAATGAATTGGTCCTAGA 24-7
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTNTGAGGAGCC
+>AAAAAGACAGCCTGAATTCCTTGT 17-4
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGNGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCNCCTGGGCCTGGCAGCCCGTCNGAG
+>AAAAAGACGATTACACAATAACCT 16-7
+CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGTGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGT
+>AAAAAGATACGGGAGGTGAATTGT 75-6
+CTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACGCCAAAGCTGCCAGGACGGACGGGAATCCTGTGACTTACGGCCGTCCCGCTTCTTGAGCCCTCACTCCTGGCCCTGTGCCCAGTGTGGGGACAAAGTTGGCCTGGCCCGGTCCTGGTCCCAGAGGGGC
+>AAAAAGATATTTTAATCGGCCCGA 7-6
+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTMTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGC
+>AAAAAGATTACACTGAAATCTTTT 25-5
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNTCTGAGGAGCCCNTGTCCCCAGGGCC
+>AAAAAGCCATATGGTCGAAGAGAT 13-10
+ACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGACCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGAGGGCCGCCCAGCCGGCACCACCGCC
+>AAAAAGCGAAAGTGCCCCATATTT 13-16
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNTCTGAGGAGCCCGTGTCCCCAGGGCCCCTGTACGTNCTGGTGG
+>AAAAAGCGATTTAACTGAAATTAT 5-4
+CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGC
+>AAAAAGCGGGGTGGCCTTACGCCC 17-10
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGAGCCCGNGTCCCCAGGGCCNCTGTACGT
+>AAAAAGCTCTACCCCCACGAAGCG 5-10
+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGNCTTCTGCTGCTGCTGC
+>AAAAAGGATATGTCTAACATCCCT 15-16
+CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCACGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGAAGCCCACCCCGT
+>AAAAAGGTACACCCGAGATGAACT 13-9
+CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGNGCCCGTGTCCCCAGGTCCCCTGTACGTGCTGGTGGAGTAC
+>AAAAAGTAGCTTCGGTTCGGGTCT 12-4
+GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGANTACACCTGCCTGGCGGGCANTTCTATTGGGTTTTCTCATCACTCTGCGTG
+>AAAAAGTAGGGACATAATTGACTT 4-4
+CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCGGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGRTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGCACCCCA
\ No newline at end of file
diff -r 238a71241876 -r e486f84adbec test-data/output_file.pdf
Binary file test-data/output_file.pdf has changed
diff -r 238a71241876 -r e486f84adbec test-data/output_file.tabular
--- a/test-data/output_file.tabular	Mon Oct 08 05:55:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-Dataset:	Test_data.tabular
-	AB	BA
-max. family size:	85	332
-absolute frequency:	1	1
-relative frequency:	0.062	0.062
-
-
-
-total nr. of reads	1312
-
-
-Values from family size distribution
-	before SSCS building	after DCS building	after trimming	after alignment to reference
-FS=1	0	0	0	0
-FS=2	0	0	0	0
-FS=3	1	8	0	1
-FS=4	2	10	6	2
-FS=5	2	5	3	2
-FS=6	1	3	3	1
-FS=7	5	5	3	5
-FS=8	1	2	0	1
-FS=9	3	2	1	3
-FS=10	2	2	3	2
-FS=11	2	1	0	2
-FS=12	0	0	1	0
-FS=13	0	0	4	0
-FS=14	0	0	0	0
-FS=15	1	0	1	1
-FS=16	0	1	3	0
-FS=17	0	0	3	0
-FS=18	0	3	0	0
-FS=19	0	0	0	0
-FS=20	0	0	0	0
-FS>20	12	8	3	12
-sum	32	50	34	32
-
-
-In the plot, the family sizes of ab and ba strands and of both duplex tags were used.
-Whereas the total numbers indicate only the single count of the formed duplex tags.
-total nr. of tags (unique, FS>=1)	16
-DCS (before SSCS building, FS>=1)	16
-total nr. of tags (unique, FS>=3)	16
-DCS (before SSCS building, FS>=3)	16
-after DCS building	25
-after trimming	17
-after alignment to reference	16