# HG changeset patch
# User artbio
# Date 1553080636 14400
# Node ID 3a4694d4354fd5f93bca6a8d61cc2b0f355ba6e1
# Parent  6f54dc6b37daadcb93b740444875e63a85c89e95
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 618a7892f6af26278364a75ab23b3c6d8cdc73db

diff -r 6f54dc6b37da -r 3a4694d4354f catWrapper.xml
--- a/catWrapper.xml	Sun Mar 11 18:19:40 2018 -0400
+++ b/catWrapper.xml	Wed Mar 20 07:17:16 2019 -0400
@@ -1,43 +1,246 @@
-<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="0.3">
-    <description>tail-to-head</description>
+<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.0">
+    <description>tail-to-head by specifying how</description>
     <command><![CDATA[
-        #if $headers == "No":
-            cat
-            #for $file in $input
-                "$file"
-            #end for
-            > "$out_file1"
+        #if $headers == 0:
+            #set $concat_command = "cat"
         #else:
-            #for $file in $input
-                printf "# ${file.element_identifier}\n" >> "$out_file1" &&
-                cat "$file" >> "$out_file1" &&
-            #end for
-            sleep 1
+            #set $concat_command = 'tail -q -n +'+ str(int($headers)+1)
+        #end if
+        #if $global_condition.input_type == "singles":
+            #if $dataset_names == "No":
+                $concat_command
+                #for $file in $global_condition.inputs
+                    '$file'
+                #end for
+                > '$out_file1'
+            #else:
+                #for $file in $global_condition.inputs
+                    #if $file.ext[-2:] == "gz":
+                        printf "# ${file.element_identifier}\n" | gzip -c >> '$out_file1' &&
+                        gzip -dc "$file" | $concat_command |gzip -c >> '$out_file1' &&
+                    #else:
+                        printf "# ${file.element_identifier}\n" >> '$out_file1' &&
+                        $concat_command "$file" >> '$out_file1' &&
+                    #end if
+                #end for
+                sleep 1
+            #end if
+        #else if $global_condition.input_type == "paired_collection":
+            #if $global_condition.paired_cat_type == "by_strand":
+                #if $dataset_names == "No":
+                    #for $file in $global_condition.inputs
+                        $concat_command
+                        $file['forward']
+                        >> '$forward' &&
+                        $concat_command
+                        $file['reverse']
+                        >> '$reverse' &&
+                    #end for
+                    sleep 1
+                #else:
+                    #for $file in $global_condition.inputs.keys()
+                        printf "# ${file}_forward\n" >> '$forward' &&
+                        $concat_command
+                        $global_condition.inputs[$file]['forward']
+                        >> '$forward' &&
+                        printf "# ${file}_reverse\n" >> '$reverse' &&
+                        $concat_command
+                        $global_condition.inputs[$file]['reverse']
+                        >> '$reverse' &&
+                    #end for
+                    sleep 1
+                #end if
+            #else if $global_condition.paired_cat_type == "by_pair":
+                mkdir concatenated &&
+                #if $dataset_names == "No":
+                    #for $file in $global_condition.inputs.keys()
+                        $concat_command
+                        $global_condition.inputs[$file]['forward']
+                        > concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
+                        $concat_command
+                        $global_condition.inputs[$file]['reverse']
+                        >> concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
+                    #end for
+                    sleep 1
+                #else:
+                    #for $file in $global_condition.inputs.keys()
+                        printf "# ${file}_forward\n" > concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
+                        $concat_command
+                        $global_condition.inputs[$file]['forward']
+                        >> concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
+                        printf "# ${file}_reverse\n" >> concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
+                        $concat_command
+                        $global_condition.inputs[$file]['reverse']
+                        >> concatenated/'${file}.${global_condition.inputs[$file]['reverse'].ext}.listed' &&
+                    #end for
+                    sleep 1
+                #end if
+            #else if $global_condition.paired_cat_type == "all":
+                #if $dataset_names == "No":
+                    #for $file in $global_condition.inputs.keys()
+                        $concat_command
+                        $global_condition.inputs[$file]['forward']
+                        >> $out_file1 &&
+                        $concat_command
+                        $global_condition.inputs[$file]['reverse']
+                        >> $out_file1 &&
+                    #end for
+                    sleep 1
+                #else:
+                    #for $file in $global_condition.inputs.keys()
+                        printf "# ${file}_forward\n" > $out_file1 &&
+                        $concat_command
+                        $global_condition.inputs[$file]['forward']
+                        >> $out_file1 &&
+                        printf "# ${file}_reverse\n" >> $out_file1 &&
+                        $concat_command
+                        $global_condition.inputs[$file]['reverse']
+                        >> $out_file1 &&
+                    #end for
+                    sleep 1
+                #end if
+            #end if
         #end if
         ]]>
     </command>
     <inputs>
-        <param name="headers" type="select" label="include dataset names">
-                <option value="No" selected="true">No</option>
-                <option value="Yes">Yes</option>
-        </param>
-        <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
+        <conditional name="global_condition">
+            <param name="input_type" type="select" label="What type of data do you wish to concatenate?" help="Depending on the type of input selected the concatenation options will differ">
+                <option value="singles">Single datasets</option>
+                <option value="paired_collection">Paired collection</option>
+            </param>
+            <when value="singles">
+                <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" help="All inputed datasets will be concatenated tail-to-head."/>
+            </when>
+            <when value="paired_collection">
+                <param name="inputs" type="data_collection" collection_type="list:paired" label="Input paired collections to concatenate"/>
+                <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?">
+                    <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option>
+                    <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option>
+                    <option value="all">Concatenate all datasets into a single file regardless of strand (outputs a single file)</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="dataset_names" type="boolean" label="Include dataset names?" truevalue="Yes" falsevalue="No" checked="false" help="If 'Yes' is selected '#name of dataset' will be added when concatenating."/>
+        <param name="headers" type="integer" label="Number of lines to skip at the beginning of each concatenation:" value="0" help="This paremeter exists so as to not concatenate comments or headers contained at the start of the files."/>
     </inputs>
     <outputs>
-        <data name="out_file1" format_source="input" metadata_source="input"/>
+        <data name="out_file1" format_source="inputs" metadata_source="inputs" label="Concatenated datasets">
+            <filter>global_condition['input_type'] == 'singles' or (global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all')</filter>
+        </data>
+        <collection name="paired_output" type="paired" label="Concatenation by strtand">
+            <data name="forward" />
+            <data name="reverse" />
+            <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter>
+        </collection>
+        <collection name="list_output" type="list" label="Concatenation by pairs">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;[^\._]+\.?[^\._])\.listed" visible="false" directory="concatenated"/>
+            <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair'</filter>
+        </collection>
     </outputs>
     <tests>
-        <test>
-            <param name="headers" value="No" />
-            <param name="input" value="1.bed,2.bed"/>
+        <!-- Single files concatenation -->
+        <test> <!-- Test 2 single files concatenation with no other option -->
+            <param name="input_type" value="singles" />
+            <param name="inputs" value="1.bed,2.bed"/>
+            <param name="dataset_names" value="No" />
+            <param name="headers" value="0" />
             <output name="out_file1" file="cat_wrapper_out1.bed"/>
         </test>
-        <test>
-            <param name="headers" value="Yes" />
-            <param name="input" value="1.bed,2.bed"/>
+        <test> <!-- Test 2 single files concatenation with dataset names activated -->
+            <param name="input_type" value="singles" />
+            <param name="inputs" value="1.bed,2.bed"/>
+            <param name="dataset_names" value="Yes" />
+            <param name="headers" value="0" />
             <output name="out_file1" file="cat_wrapper_out2.bed"/>
         </test>
-
+        <test> <!-- Test 2 single files concatenation skipping 1 line -->
+            <param name="input_type" value="singles" />
+            <param name="inputs" value="1.bed,2.bed"/>
+            <param name="dataset_names" value="No" />
+            <param name="headers" value="1" />
+            <output name="out_file1" file="cat_wrapper_out3.bed"/>
+        </test>
+        <test> <!-- Test gz handling with no options -->
+            <param name="input_type" value="singles" />
+            <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
+            <param name="dataset_names" value="No" />
+            <param name="headers" value="0" />
+            <output name="out_file1" file="1.fastq.gz" decompress="True"/>
+        </test>
+        <test> <!-- Test gz handling with options -->
+            <param name="input_type" value="singles" />
+            <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/>
+            <param name="dataset_names" value="Yes" />
+            <param name="headers" value="4" />
+            <output name="out_file1" file="1_options.fastq.gz" decompress="True"/>
+        </test>
+        <!-- Test paired options -->
+        <test> <!-- Test paired collection concatenation by_pair with no other option -->
+            <param name="input_type" value="paired_collection" />
+            <param name="paired_cat_type" value="by_pair"/>
+            <param name="inputs">
+                <collection type="list:paired">
+                    <element name="2">
+                        <collection type="paired">
+                            <element name="forward" value="2_f.fastq"/>
+                            <element name="reverse" value="2_r.fastq"/>
+                        </collection>
+                    </element>
+                    <element name="3">
+                        <collection type="paired">
+                            <element name="forward" value="3_f.fastq"/>
+                            <element name="reverse" value="3_r.fastq"/>
+                        </collection>
+                    </element>
+                    <element name="4">
+                        <collection type="paired">
+                            <element name="forward" value="4_f.fastq"/>
+                            <element name="reverse" value="4_r.fastq"/>
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="dataset_names" value="No" />
+            <param name="headers" value="0" />
+            <output_collection name="list_output" type="list" >
+                <element name="2" file="2.fastq"/>
+                <element name="3" file="3.fastq"/>
+                <element name="4" file="4.fastq"/>
+            </output_collection>
+        </test>
+        <test> <!-- Test paired collection concatenation by_strand with no other option -->
+            <param name="input_type" value="paired_collection" />
+            <param name="paired_cat_type" value="by_strand"/>
+            <param name="inputs">
+                <collection type="list:paired">
+                    <element name="2">
+                        <collection type="paired">
+                            <element name="forward" value="2_f.fastq"/>
+                            <element name="reverse" value="2_r.fastq"/>
+                        </collection>
+                    </element>
+                    <element name="3">
+                        <collection type="paired">
+                            <element name="forward" value="3_f.fastq"/>
+                            <element name="reverse" value="3_r.fastq"/>
+                        </collection>
+                    </element>
+                    <element name="4">
+                        <collection type="paired">
+                            <element name="forward" value="4_f.fastq"/>
+                            <element name="reverse" value="4_r.fastq"/>
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="dataset_names" value="No" />
+            <param name="headers" value="0" />
+            <output_collection name="paired_output" type="paired" >
+                <element name="forward" file="f.fastq"/>
+                <element name="reverse" file="r.fastq"/>
+            </output_collection>
+        </test>
     </tests>
     <help>
 
@@ -45,15 +248,23 @@
 
 **WARNING:** This tool does not check if the datasets being concatenated are in the same format.
 
+**WARNING:** The paired collection operations do not handle gziped files.
+
 -----
 
 **What it does**
 
-Concatenates datasets
+Concatenates datasets and paired collections with multiple options:
+
+ - It's possible select either a concatenation by strand, by pair or a whole collection concatenation, when the input is a paired collection.
+
+ - Skipping lines before concatenation to avoid headers
+
+ - Add the name of the concatenated files as separator
 
 -----
 
-**Example**
+**Single datasets concatenation example**
 
 Concatenating Dataset::
 
@@ -83,6 +294,98 @@
 
 -----
 
+**Paired collection concatenation example**
+
+1rst pair::
+
+    forward - reverse
+
+2nd pair::
+
+    forward - reverse
+
+Concatenation by strand::
+
+    concatenates:
+
+    1rst forward + 2nd forward
+    1rst reverse + 2nd reverse
+
+    outputs:
+
+    1 pair
+
+Concatenation by pair::
+
+    concatenates:
+
+    1rst forward + 1rst reverse
+    2nd forward + 2nd reverse
+
+    outputs:
+
+    2 datasets
+
+Concatenate all::
+
+    concatenates:
+
+    1rst forward + 1rst reverse + 2nd forward + 2nd reverse
+
+    outputs:
+
+    1 dataset
+
+-----
+
+**When selecting "Include dataset names" when concatenating files**:
+
+1rst file name="first_tabular"::
+
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+
+2nd file name="second_tabular"::
+
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+
+output::
+
+    # first_tabular
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+    # second_tabular
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+
+-----
+
+**Skiping lines**
+
+1rst file::
+
+    chrX  151087187  151087355  A  0  -
+    chrX  151572400  151572481  B  0  +
+
+2nd file::
+
+    chr1  151242630  151242955  X  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+
+skipping 1 line
+
+output::
+
+    chrX  151572400  151572481  B  0  +
+    chr1  151271715  151271999  Y  0  +
+    chr1  151278832  151279227  Z  0  -
+
+-----
+
 Adapted from galaxy's catWrapper.xml to allow multiple input files.
 
     </help>
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/1.fastq.gz
Binary file test-data/1.fastq.gz has changed
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/1_f.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1_f.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,12 @@
+@NS500801:189:HWGFJBGX5:1:11101:18757:1118 1:N:0:GCCAAT
+CACCGTTACATCACACCAACCAAGATTACATCACACCACTCAGGATGACAGACAGTAATCCTGTTTGTTATATANG
++
+AAAAAEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE<EEEEEEEEE#A
+@NS500801:189:HWGFJBGX5:1:11101:21956:1118 1:N:0:GCCAAT
+CTTACAACCAACTTGATATCACATTCAGCCTGAGGATTTGTTGCTTCATCTTCAGTTCTGTAACATTAAATGGANT
++
+AAAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEEEEEEEEE#E
+@NS500801:189:HWGFJBGX5:1:11101:17695:1118 1:N:0:GCCAAT
+GGGTAATTGATCATCTGTCATGCCAACAGCAAGCAAGGTCTTCCCAGTGCAGCAACAACGTTCAGAATGGATACNG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEE/AEE/EEEEEEAEEEEE#E
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/1_f.fastq.gz
Binary file test-data/1_f.fastq.gz has changed
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/1_options.fastq.gz
Binary file test-data/1_options.fastq.gz has changed
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/1_r.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1_r.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,12 @@
+@NS500801:189:HWGFJBGX5:1:11101:18757:1118 2:N:0:GCCAAT
+CCAAAATCTGNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGAGAAGCTGCAGCTCGAGNNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE############################EEEEEEEEEEEEEEEEEE<E###############
+@NS500801:189:HWGFJBGX5:1:11101:21956:1118 2:N:0:GCCAAT
+ATTTAAGATTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGCTTTGGGAGGATTATTTTNNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE############################EEEEEEEEEEEEEEEEEEEE###############
+@NS500801:189:HWGFJBGX5:1:11101:17695:1118 2:N:0:GCCAAT
+AACTTGCATGNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGTTGTTGCTGCACTGGGANNNNNNNNNNNNNNN
++
+AAAAAEEAEE#EE############################EAEEEEEEEEEEAAEEEEEE###############
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/1_r.fastq.gz
Binary file test-data/1_r.fastq.gz has changed
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,24 @@
+@NS500801:189:HWGFJBGX5:1:11101:3766:1118 1:N:0:ACAGTG
+ATCCCATACTGCTCAAAATAATCTCGTAGGTGATGTTCTTCAGTGTCTTCTTTAATACCACCAACAAAGATCTTNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE#E
+@NS500801:189:HWGFJBGX5:1:11101:25700:1118 1:N:0:ACAGTG
+GTGCCGTTGAATTTGCCGTGAGTGGAGTCATACTGGAACATGTAGACCATGTAGTTGAGGTCAATGAAGGGGTCNT
++
+AAAAAAAEAEEAEEEEAE/</EEEEAEEEEAAEEEEEEEEEEE6EE<6EEEEEEEEAEEE///EAEEEE<AEEE#E
+@NS500801:189:HWGFJBGX5:1:11101:24308:1119 1:N:0:ACAGTG
+CACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGGCGGTTCACCCCTCCTTAGGCAACCNG
++
+AAAAAEAAEE/EAA/AE//EE6/EEAEEEEE<EE<EEEEEEEEE6<E/////E/E//E</A<EEEE6E6EEEEE#A
+@NS500801:189:HWGFJBGX5:1:11101:3766:1118 2:N:0:ACAGTG
+ACCACACCTTNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTGAAGTCATTTTTCCTTNNNNNNNNNNNNNNN
++
+/AAAAEEE6E#EE############################EEEEEEEEEEEEAEEEEEAE###############
+@NS500801:189:HWGFJBGX5:1:11101:25700:1118 2:N:0:ACAGTG
+GCCGCATCTTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAATGGTGAAGGTCGGTGTGNNNNNNNNNNNNNNN
++
+AAAAAEEEE6#E/############################/EEA/EE6/EEEEE6E/AEE###############
+@NS500801:189:HWGFJBGX5:1:11101:24308:1119 2:N:0:ACAGTG
+GGAGGATCGCNTGNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATGCCGATCGGGTGTCCGCNNNNNNNNNNNNNNN
++
+A//AA/EEEE#EE###########################/E//AAEAEE//EEEE<EA/E###############
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/2_f.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_f.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,12 @@
+@NS500801:189:HWGFJBGX5:1:11101:3766:1118 1:N:0:ACAGTG
+ATCCCATACTGCTCAAAATAATCTCGTAGGTGATGTTCTTCAGTGTCTTCTTTAATACCACCAACAAAGATCTTNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE#E
+@NS500801:189:HWGFJBGX5:1:11101:25700:1118 1:N:0:ACAGTG
+GTGCCGTTGAATTTGCCGTGAGTGGAGTCATACTGGAACATGTAGACCATGTAGTTGAGGTCAATGAAGGGGTCNT
++
+AAAAAAAEAEEAEEEEAE/</EEEEAEEEEAAEEEEEEEEEEE6EE<6EEEEEEEEAEEE///EAEEEE<AEEE#E
+@NS500801:189:HWGFJBGX5:1:11101:24308:1119 1:N:0:ACAGTG
+CACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGGCGGTTCACCCCTCCTTAGGCAACCNG
++
+AAAAAEAAEE/EAA/AE//EE6/EEAEEEEE<EE<EEEEEEEEE6<E/////E/E//E</A<EEEE6E6EEEEE#A
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/2_r.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_r.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,12 @@
+@NS500801:189:HWGFJBGX5:1:11101:3766:1118 2:N:0:ACAGTG
+ACCACACCTTNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTGAAGTCATTTTTCCTTNNNNNNNNNNNNNNN
++
+/AAAAEEE6E#EE############################EEEEEEEEEEEEAEEEEEAE###############
+@NS500801:189:HWGFJBGX5:1:11101:25700:1118 2:N:0:ACAGTG
+GCCGCATCTTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAATGGTGAAGGTCGGTGTGNNNNNNNNNNNNNNN
++
+AAAAAEEEE6#E/############################/EEA/EE6/EEEEE6E/AEE###############
+@NS500801:189:HWGFJBGX5:1:11101:24308:1119 2:N:0:ACAGTG
+GGAGGATCGCNTGNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATGCCGATCGGGTGTCCGCNNNNNNNNNNNNNNN
++
+A//AA/EEEE#EE###########################/E//AAEAEE//EEEE<EA/E###############
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/3.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,24 @@
+@NS500801:189:HWGFJBGX5:1:11101:15584:1117 1:N:0:TGACCA
+GTTGATTCATAAAATTGTTTTTAGGTAGCTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTAGAAGNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEA#E
+@NS500801:189:HWGFJBGX5:1:11101:26457:1117 1:N:0:TGACCA
+CTTTTACAGTAACTCCGGGCATCGTGCGGCCTCCGCGCTGCCAGCCAGGGGAAAGGGAACGACGGGGTTTCCCGNG
++
+/AAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEE6EEEEEEEEEEEEEEEEEEEAE#E
+@NS500801:189:HWGFJBGX5:1:11101:25352:1117 1:N:0:TGACCA
+GTCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCNG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEA#E
+@NS500801:189:HWGFJBGX5:1:11101:15584:1117 2:N:0:TGACCA
+GTAAGAACAANCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACTAACTAGAAAACTTCNNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEE###############
+@NS500801:189:HWGFJBGX5:1:11101:26457:1117 2:N:0:TGACCA
+GCGAGACTCGNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTTCCCTTTCCCCTGGCTGNNNNNNNNNNNNNNN
++
+AAAAAEEEEE##E############################EEEE/EEEEEEEEEEEEAAE###############
+@NS500801:189:HWGFJBGX5:1:11101:25352:1117 2:N:0:TGACCA
+GGGGGACCACNAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTCGGAAACGGAGCAGGTCNNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEA###############
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/3_f.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_f.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,12 @@
+@NS500801:189:HWGFJBGX5:1:11101:15584:1117 1:N:0:TGACCA
+GTTGATTCATAAAATTGTTTTTAGGTAGCTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTAGAAGNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEA#E
+@NS500801:189:HWGFJBGX5:1:11101:26457:1117 1:N:0:TGACCA
+CTTTTACAGTAACTCCGGGCATCGTGCGGCCTCCGCGCTGCCAGCCAGGGGAAAGGGAACGACGGGGTTTCCCGNG
++
+/AAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEE6EEEEEEEEEEEEEEEEEEEAE#E
+@NS500801:189:HWGFJBGX5:1:11101:25352:1117 1:N:0:TGACCA
+GTCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCNG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEA#E
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/3_r.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3_r.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,12 @@
+@NS500801:189:HWGFJBGX5:1:11101:15584:1117 2:N:0:TGACCA
+GTAAGAACAANCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACTAACTAGAAAACTTCNNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEE###############
+@NS500801:189:HWGFJBGX5:1:11101:26457:1117 2:N:0:TGACCA
+GCGAGACTCGNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTTCCCTTTCCCCTGGCTGNNNNNNNNNNNNNNN
++
+AAAAAEEEEE##E############################EEEE/EEEEEEEEEEEEAAE###############
+@NS500801:189:HWGFJBGX5:1:11101:25352:1117 2:N:0:TGACCA
+GGGGGACCACNAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTCGGAAACGGAGCAGGTCNNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEA###############
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/4.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,24 @@
+@NS500801:189:HWGFJBGX5:1:11101:7257:1118 1:N:0:GATCAG
+CCTAATAAAACTATAGAGCATTATCCCACCATGGTAGCAAATATGGCCCACAAAGGGATAAAAACTTCAATCACNC
++
+AA/AAAEE66EEEAEEEA/EEAEEE<EEEEEE/EEEAEEEEEEEEEEEEEEEEEE/<E/EAEEEAAEAEAEEEA#<
+@NS500801:189:HWGFJBGX5:1:11101:6563:1118 1:N:0:GATCAG
+CCAGCTTTTTCACACGAAGTTTGTGATTTCTGGCCTGGCGAAGAATGGTATTCCTGCGCATAGTCTTGGCGTAANG
++
+AAAAAEEEEEEAEE/EEEAEAEEEEEEEEEEEEE<EEEEEEEAEEEEAEEEEEEEE/EEEEEEEEEA/AEA/EE#A
+@NS500801:189:HWGFJBGX5:1:11101:14965:1119 1:N:0:GATCAG
+CGATCTTGAGCATTTTCCAGGCCAGTTTTAGGAGCAAAGCCATTTTCAACTAATGGAGGACCTAGGAGCTCTTTNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/E6#E
+@NS500801:189:HWGFJBGX5:1:11101:7257:1118 2:N:0:GATCAG
+ATAAAATGTANTANNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAACCAGAATAACTGCATCNNNNNNNNNNNNNNN
++
+AAAAAE66AA#EE############################EEEEEE/<AE/EEE/AAEEE###############
+@NS500801:189:HWGFJBGX5:1:11101:6563:1118 2:N:0:GATCAG
+GAAGAAGAATNCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACCCTTACGCCAAGACTNNNNNNNNNNNNNNN
++
+AAAA/EE/EE#/A############################EEA/EEEEEEEE/EAE</EE###############
+@NS500801:189:HWGFJBGX5:1:11101:14965:1119 2:N:0:GATCAG
+GCCTTACTGGNATNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAACTGCTAAGAAATGTGTANNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE###########################EEEEEEEEEEEEEEEEEEEEE###############
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/4_f.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4_f.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,12 @@
+@NS500801:189:HWGFJBGX5:1:11101:7257:1118 1:N:0:GATCAG
+CCTAATAAAACTATAGAGCATTATCCCACCATGGTAGCAAATATGGCCCACAAAGGGATAAAAACTTCAATCACNC
++
+AA/AAAEE66EEEAEEEA/EEAEEE<EEEEEE/EEEAEEEEEEEEEEEEEEEEEE/<E/EAEEEAAEAEAEEEA#<
+@NS500801:189:HWGFJBGX5:1:11101:6563:1118 1:N:0:GATCAG
+CCAGCTTTTTCACACGAAGTTTGTGATTTCTGGCCTGGCGAAGAATGGTATTCCTGCGCATAGTCTTGGCGTAANG
++
+AAAAAEEEEEEAEE/EEEAEAEEEEEEEEEEEEE<EEEEEEEAEEEEAEEEEEEEE/EEEEEEEEEA/AEA/EE#A
+@NS500801:189:HWGFJBGX5:1:11101:14965:1119 1:N:0:GATCAG
+CGATCTTGAGCATTTTCCAGGCCAGTTTTAGGAGCAAAGCCATTTTCAACTAATGGAGGACCTAGGAGCTCTTTNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/E6#E
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/4_r.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4_r.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,12 @@
+@NS500801:189:HWGFJBGX5:1:11101:7257:1118 2:N:0:GATCAG
+ATAAAATGTANTANNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAACCAGAATAACTGCATCNNNNNNNNNNNNNNN
++
+AAAAAE66AA#EE############################EEEEEE/<AE/EEE/AAEEE###############
+@NS500801:189:HWGFJBGX5:1:11101:6563:1118 2:N:0:GATCAG
+GAAGAAGAATNCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACCCTTACGCCAAGACTNNNNNNNNNNNNNNN
++
+AAAA/EE/EE#/A############################EEA/EEEEEEEE/EAE</EE###############
+@NS500801:189:HWGFJBGX5:1:11101:14965:1119 2:N:0:GATCAG
+GCCTTACTGGNATNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAACTGCTAAGAAATGTGTANNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE###########################EEEEEEEEEEEEEEEEEEEEE###############
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/cat_wrapper_out3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cat_wrapper_out3.bed	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,131 @@
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+
+chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-
+chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+
+chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-
+chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
+chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+
+chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-
+chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+
+chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-
+chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+
+chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+
+chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
+chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-
+chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+
+chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-
+chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+
+chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+
+chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-
+chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+
+chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-
+chr1	147984545	147984630	BC007833_cds_0_0_chr1_147984546_f	0	+
+chr1	148078400	148078582	AJ011123_cds_0_0_chr1_148078401_r	0	-
+chr1	148185136	148185276	NM_002796_cds_0_0_chr1_148185137_f	0	+
+chr10	55251623	55253124	AY029205_cds_0_0_chr10_55251624_r	0	-
+chr11	116124407	116124501	AK057832_cds_0_0_chr11_116124408_r	0	-
+chr11	116206508	116206563	NM_000040_cds_1_0_chr11_116206509_f	0	+
+chr11	116211733	116212337	BC005380_cds_0_0_chr11_116211734_r	0	-
+chr11	130745911	130745993	AY358331_cds_0_0_chr11_130745912_f	0	+
+chr12	38440094	38440321	NM_052885_cds_0_0_chr12_38440095_r	0	-
+chr12	38905200	38905351	AY792511_cds_0_0_chr12_38905201_f	0	+
+chr13	112381694	112381953	NM_207440_cds_1_0_chr13_112381695_f	0	+
+chr13	29680676	29680875	NM_032116_cds_0_0_chr13_29680677_r	0	-
+chr14	98521864	98521922	U88895_cds_0_0_chr14_98521865_f	0	+
+chr14	98710240	98712285	NM_022898_cds_0_0_chr14_98710241_r	0	-
+chr15	41486872	41487060	BX537418_cds_0_0_chr15_41486873_r	0	-
+chr15	41673708	41673857	AK223365_cds_0_0_chr15_41673709_f	0	+
+chr15	41679161	41679250	NM_153700_cds_0_0_chr15_41679162_r	0	-
+chr15	41773540	41773689	AK223365_cds_0_0_chr15_41773541_f	0	+
+chr16	142908	143003	NM_005332_cds_0_0_chr16_142909_f	0	+
+chr16	179197	179339	BC065198_cds_0_0_chr16_179198_r	0	-
+chr16	244413	244681	AK057165_cds_2_0_chr16_244414_f	0	+
+chr16	259268	259383	AB016929_cds_0_0_chr16_259269_r	0	-
+chr18	23786114	23786321	NM_001792_cds_0_0_chr18_23786115_r	0	-
+chr18	59406881	59407046	NM_012397_cds_1_0_chr18_59406882_f	0	+
+chr18	59455932	59456337	AB046400_cds_0_0_chr18_59455933_r	0	-
+chr18	59528407	59528575	AY792326_cds_0_0_chr18_59528408_f	0	+
+chr19	59068595	59069564	BC013995_cds_1_0_chr19_59068596_f	0	+
+chr19	59236026	59236146	NM_198481_cds_0_0_chr19_59236027_r	0	-
+chr19	59297998	59298008	NM_004542_cds_0_0_chr19_59297999_f	0	+
+chr19	59318205	59318718	AK128544_cds_3_0_chr19_59318206_r	0	-
+chr2	118288583	118288668	NM_006773_cds_0_0_chr2_118288584_f	0	+
+chr2	118390395	118390500	BC005078_cds_0_0_chr2_118390396_r	0	-
+chr2	220108689	220109267	AY125465_cds_0_0_chr2_220108690_f	0	+
+chr2	220229609	220230869	NM_024536_cds_0_0_chr2_220229610_r	0	-
+chr20	33330413	33330423	NM_181466_cds_0_0_chr20_33330414_r	0	-
+chr20	33485370	33486123	BC085019_cds_1_0_chr20_33485371_f	0	+
+chr20	33488491	33489122	NM_000557_cds_1_0_chr20_33488492_r	0	-
+chr20	33513606	33513792	AF022655_cds_1_0_chr20_33513607_f	0	+
+chr21	32687402	32687588	NM_032910_cds_0_0_chr21_32687403_f	0	+
+chr21	32869641	32870022	NM_018277_cds_3_0_chr21_32869642_r	0	-
+chr21	33321040	33322012	NM_005806_cds_1_0_chr21_33321041_f	0	+
+chr21	33728358	33728724	AK129657_cds_0_0_chr21_33728359_r	0	-
+chr22	30120223	30120265	NM_004147_cds_0_0_chr22_30120224_f	0	+
+chr22	30160419	30160661	BC032941_cds_0_0_chr22_30160420_r	0	-
+chr22	30228824	30228916	NM_001007467_cds_1_0_chr22_30228825_f	0	+
+chr22	30340151	30340376	CR456540_cds_0_0_chr22_30340152_r	0	-
+chr5	131311206	131311254	AF099740_cds_11_0_chr5_131311207_r	0	-
+chr5	131424298	131424460	NM_000588_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	BC035813_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	BC003096_cds_0_0_chr5_131621327_f	0	+
+chr6	108299600	108299744	NM_007214_cds_0_0_chr6_108299601_r	0	-
+chr6	108594662	108594687	NM_003269_cds_0_0_chr6_108594663_f	0	+
+chr6	108640045	108640151	NM_003795_cds_0_0_chr6_108640046_r	0	-
+chr6	108722976	108723115	NM_145315_cds_0_0_chr6_108722977_f	0	+
+chr7	113660517	113660685	AF467257_cds_1_0_chr7_113660518_f	0	+
+chr7	116512159	116512389	NM_003391_cds_0_0_chr7_116512160_r	0	-
+chr7	116714099	116714152	NM_000492_cds_0_0_chr7_116714100_f	0	+
+chr7	116945541	116945787	AF377960_cds_0_0_chr7_116945542_r	0	-
+chr8	118881131	118881317	NM_000127_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	BC051300_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	NM_014908_cds_0_0_chr9_128787520_r	0	-
+chr9	128789552	128789584	NM_015354_cds_0_0_chr9_128789553_f	0	+
+chr9	128850516	128850624	AB058751_cds_0_0_chr9_128850517_r	0	-
+chrX	122745047	122745924	NM_001167_cds_1_0_chrX_122745048_f	0	+
+chrX	152648964	152649196	NM_000425_cds_0_0_chrX_152648965_r	0	-
+chrX	152691446	152691471	AF101728_cds_0_0_chrX_152691447_f	0	+
+chrX	152694029	152694263	BC052303_cds_0_0_chrX_152694030_r	0	-
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/f.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/f.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,36 @@
+@NS500801:189:HWGFJBGX5:1:11101:3766:1118 1:N:0:ACAGTG
+ATCCCATACTGCTCAAAATAATCTCGTAGGTGATGTTCTTCAGTGTCTTCTTTAATACCACCAACAAAGATCTTNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE#E
+@NS500801:189:HWGFJBGX5:1:11101:25700:1118 1:N:0:ACAGTG
+GTGCCGTTGAATTTGCCGTGAGTGGAGTCATACTGGAACATGTAGACCATGTAGTTGAGGTCAATGAAGGGGTCNT
++
+AAAAAAAEAEEAEEEEAE/</EEEEAEEEEAAEEEEEEEEEEE6EE<6EEEEEEEEAEEE///EAEEEE<AEEE#E
+@NS500801:189:HWGFJBGX5:1:11101:24308:1119 1:N:0:ACAGTG
+CACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGGCGGTTCACCCCTCCTTAGGCAACCNG
++
+AAAAAEAAEE/EAA/AE//EE6/EEAEEEEE<EE<EEEEEEEEE6<E/////E/E//E</A<EEEE6E6EEEEE#A
+@NS500801:189:HWGFJBGX5:1:11101:15584:1117 1:N:0:TGACCA
+GTTGATTCATAAAATTGTTTTTAGGTAGCTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTAGAAGNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEA#E
+@NS500801:189:HWGFJBGX5:1:11101:26457:1117 1:N:0:TGACCA
+CTTTTACAGTAACTCCGGGCATCGTGCGGCCTCCGCGCTGCCAGCCAGGGGAAAGGGAACGACGGGGTTTCCCGNG
++
+/AAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEE6EEEEEEEEEEEEEEEEEEEAE#E
+@NS500801:189:HWGFJBGX5:1:11101:25352:1117 1:N:0:TGACCA
+GTCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCNG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEA#E
+@NS500801:189:HWGFJBGX5:1:11101:7257:1118 1:N:0:GATCAG
+CCTAATAAAACTATAGAGCATTATCCCACCATGGTAGCAAATATGGCCCACAAAGGGATAAAAACTTCAATCACNC
++
+AA/AAAEE66EEEAEEEA/EEAEEE<EEEEEE/EEEAEEEEEEEEEEEEEEEEEE/<E/EAEEEAAEAEAEEEA#<
+@NS500801:189:HWGFJBGX5:1:11101:6563:1118 1:N:0:GATCAG
+CCAGCTTTTTCACACGAAGTTTGTGATTTCTGGCCTGGCGAAGAATGGTATTCCTGCGCATAGTCTTGGCGTAANG
++
+AAAAAEEEEEEAEE/EEEAEAEEEEEEEEEEEEE<EEEEEEEAEEEEAEEEEEEEE/EEEEEEEEEA/AEA/EE#A
+@NS500801:189:HWGFJBGX5:1:11101:14965:1119 1:N:0:GATCAG
+CGATCTTGAGCATTTTCCAGGCCAGTTTTAGGAGCAAAGCCATTTTCAACTAATGGAGGACCTAGGAGCTCTTTNT
++
+AAAAAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/E6#E
diff -r 6f54dc6b37da -r 3a4694d4354f test-data/r.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/r.fastq	Wed Mar 20 07:17:16 2019 -0400
@@ -0,0 +1,36 @@
+@NS500801:189:HWGFJBGX5:1:11101:3766:1118 2:N:0:ACAGTG
+ACCACACCTTNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTGAAGTCATTTTTCCTTNNNNNNNNNNNNNNN
++
+/AAAAEEE6E#EE############################EEEEEEEEEEEEAEEEEEAE###############
+@NS500801:189:HWGFJBGX5:1:11101:25700:1118 2:N:0:ACAGTG
+GCCGCATCTTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAATGGTGAAGGTCGGTGTGNNNNNNNNNNNNNNN
++
+AAAAAEEEE6#E/############################/EEA/EE6/EEEEE6E/AEE###############
+@NS500801:189:HWGFJBGX5:1:11101:24308:1119 2:N:0:ACAGTG
+GGAGGATCGCNTGNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATGCCGATCGGGTGTCCGCNNNNNNNNNNNNNNN
++
+A//AA/EEEE#EE###########################/E//AAEAEE//EEEE<EA/E###############
+@NS500801:189:HWGFJBGX5:1:11101:15584:1117 2:N:0:TGACCA
+GTAAGAACAANCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACTAACTAGAAAACTTCNNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEE###############
+@NS500801:189:HWGFJBGX5:1:11101:26457:1117 2:N:0:TGACCA
+GCGAGACTCGNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTTCCCTTTCCCCTGGCTGNNNNNNNNNNNNNNN
++
+AAAAAEEEEE##E############################EEEE/EEEEEEEEEEEEAAE###############
+@NS500801:189:HWGFJBGX5:1:11101:25352:1117 2:N:0:TGACCA
+GGGGGACCACNAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTCGGAAACGGAGCAGGTCNNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEA###############
+@NS500801:189:HWGFJBGX5:1:11101:7257:1118 2:N:0:GATCAG
+ATAAAATGTANTANNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAACCAGAATAACTGCATCNNNNNNNNNNNNNNN
++
+AAAAAE66AA#EE############################EEEEEE/<AE/EEE/AAEEE###############
+@NS500801:189:HWGFJBGX5:1:11101:6563:1118 2:N:0:GATCAG
+GAAGAAGAATNCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACCCTTACGCCAAGACTNNNNNNNNNNNNNNN
++
+AAAA/EE/EE#/A############################EEA/EEEEEEEE/EAE</EE###############
+@NS500801:189:HWGFJBGX5:1:11101:14965:1119 2:N:0:GATCAG
+GCCTTACTGGNATNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAACTGCTAAGAAATGTGTANNNNNNNNNNNNNNN
++
+AAAAAEEEEE#EE###########################EEEEEEEEEEEEEEEEEEEEE###############