# HG changeset patch
# User iuc
# Date 1494343141 14400
# Node ID 24c5d43cb545ce9cc36e0f7b49f71f7986841cf8
# Parent  8cfc17e271327dada98f4342524bf3961e4343c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

diff -r 8cfc17e27132 -r 24c5d43cb545 macros.xml
--- a/macros.xml	Wed Nov 11 12:55:15 2015 -0500
+++ b/macros.xml	Tue May 09 11:19:01 2017 -0400
@@ -1,16 +1,17 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.2">samtools</requirement>
+            <requirement type="package" version="1.3.1">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
+    <token name="@TOOL_VERSION@">1.3.1</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
                 @misc{SAM_def,
                 title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+                url = {https://samtools.github.io/hts-specs/},}
             </citation>
             <citation type="doi">10.1093/bioinformatics/btp352</citation>
             <citation type="doi">10.1093/bioinformatics/btr076</citation>
@@ -41,7 +42,7 @@
         </citations>
     </xml>
     <xml name="version_command">
-        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
     </xml>
     <xml name="stdio">
         <stdio>
@@ -64,7 +65,5 @@
 5. Click **Save**
 
 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-
     </token>
-
 </macros>
diff -r 8cfc17e27132 -r 24c5d43cb545 samtools_stats.xml
--- a/samtools_stats.xml	Wed Nov 11 12:55:15 2015 -0500
+++ b/samtools_stats.xml	Tue May 09 11:19:01 2017 -0400
@@ -1,144 +1,171 @@
-<tool id="samtools_stats" name="Stats" version="2.0">
+<tool id="samtools_stats" name="Stats" version="2.0.1">
     <description>generate statistics for BAM dataset</description>
     <macros>
-    <import>macros.xml</import>
-  </macros>
-    <expand macro="requirements"></expand>
-    <expand macro="stdio"></expand>
-    <expand macro="version_command"></expand>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
     <command><![CDATA[
         #if $use_reference.use_ref_selector == "yes":
             #if $use_reference.reference_source.reference_source_selector == "history":
-               ln -s "${use_reference.reference_source.ref_file}" && samtools faidx `basename "${use_reference.reference_source.ref_file}"` && samtools stats
-            #else:
-                samtools stats
-            #end if
-        #else:
-            samtools stats
-        #end if
-        "${input_file}"
-        --coverage ${coverage_min},${coverage_max},${coverage_step}
-        ${remove_dups}
-        #if str( $filter_by_flags.filter_flags ) == "filter":
-            #if $filter_by_flags.require_flags:
-                --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
-            #end if
-            #if $filter_by_flags.exclude_flags:
-                --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
+               ln -s '${use_reference.reference_source.ref_file}' &&
+               samtools faidx `basename '${use_reference.reference_source.ref_file}'` &&
             #end if
         #end if
-        --GC-depth ${gc_depth}
-        --insert-size ${insert_size}
+
+        samtools stats
+            '${input_file}'
+            --coverage ${coverage_min},${coverage_max},${coverage_step}
+            ${remove_dups}
 
-        ## The code below is commented out because using -I/--id options causes the following exception
-        ## Samtools-htslib: init_group_id() header parsing not yet implemented
+            #if str( $filter_by_flags.filter_flags ) == "filter":
+                #if $filter_by_flags.require_flags:
+                    --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
+                #end if
+                #if $filter_by_flags.exclude_flags:
+                    --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
+                #end if
+            #end if
 
-        ##if str($read_group) != "":
-        ##    -I "${read_group}"
-        ##end if
+            --GC-depth ${gc_depth}
+            --insert-size ${insert_size}
 
-        #if str($read_length) != "0":
-            --read-length "${read_length}"
-        #end if
-        --most-inserts ${most_inserts}
-        --trim-quality ${trim_quality}
-        #if $use_reference.use_ref_selector == "yes":
-            #if $use_reference.reference_source.reference_source_selector != "history":
-                --ref-seq "${use_reference.reference_source.ref_file.fields.path}"
-            #else:
-                --ref-seq "${use_reference.reference_source.ref_file}"
+            ## The code below is commented out because using -I/--id options causes the following exception
+            ## Samtools-htslib: init_group_id() header parsing not yet implemented
+            ##if str($read_group) != "":
+            ##    -I "${read_group}"
+            ##end if
+
+            #if str($read_length):
+                --read-length ${read_length}
             #end if
-        #end if
-        > "${output}"
+
+            --most-inserts ${most_inserts}
+            --trim-quality ${trim_quality}
+
+            #if $use_reference.use_ref_selector == "yes":
+                #if $use_reference.reference_source.reference_source_selector != "history":
+                    --ref-seq '${use_reference.reference_source.ref_file.fields.path}'
+                #else:
+                    --ref-seq '${use_reference.reference_source.ref_file}'
+                #end if
+            #end if
+            > '${output}'
+
         #if $split_output.split_output_selector == "yes":
             #set outputs_to_split = str($split_output.generate_tables).split(',')
-            && mkdir split && echo ${split_output.generate_tables} &&
+            && mkdir split &&
+            echo ${split_output.generate_tables}
 
             #if 'sn' in $outputs_to_split:
-                echo "# Summary Numbers\n"  > "split/Summary numbers.tab" &&
-                grep -q ^SN  "${output}" ; if [ $? = 0 ] ; then grep ^SN  "${output}" | cut -f 2- >> "split/Summary numbers.tab"  ; fi &&
+                && echo "# Summary Numbers" > 'split/Summary numbers.tab' &&
+                echo "" >> 'split/Summary numbers.tab' &&
+                if grep -q ^SN '${output}'; then
+                    grep ^SN '${output}' | cut -f 2- >> 'split/Summary numbers.tab';
+                fi
             #end if
 
             #if 'ffq' in $outputs_to_split:
-                echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" &&
-                grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi &&
+                && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' &&
+                if grep -q ^FFQ '${output}'; then
+                    grep ^FFQ '${output}' | cut -f 2- >> 'split/First Fragment Qualities.tab';
+                fi
             #end if
 
             #if 'lfq' in $outputs_to_split:
-                echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" &&
-                grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi &&
+                && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' &&
+                if grep -q ^LFQ '${output}'; then
+                    grep ^LFQ '${output}' | cut -f 2- >> 'split/Last Fragment Qualities.tab';
+                fi
             #end if
 
             #if 'mpc' in $outputs_to_split:
-                echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" &&
-                grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi &&
+                && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' &&
+                if grep -q ^MPC '${output}'; then
+                    grep ^MPC '${output}' | cut -f 2- >> 'split/Mismatches per cycle.tab';
+                fi
             #end if
 
             #if 'gcf' in $outputs_to_split:
-                echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" &&
-                grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- >> "split/GC Content of first fragments.tab" ; fi &&
+                && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' &&
+                if grep -q ^GCF '${output}'; then
+                    grep ^GCF '${output}' | cut -f 2- >> 'split/GC Content of first fragments.tab';
+                fi
             #end if
 
             #if 'gcl' in $outputs_to_split:
-                echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" &&
-                grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- >> "split/GC Content of last fragments.tab" ; fi &&
+                && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' &&
+                if grep -q ^GCL '${output}'; then
+                    grep ^GCL '${output}' | cut -f 2- >> 'split/GC Content of last fragments.tab';
+                fi
             #end if
 
             #if 'gcc' in $outputs_to_split:
-                echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" &&
-                grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- >> "split/ACGT content per cycle.tab" ; fi &&
+                && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' &&
+                if grep -q ^GCC '${output}'; then
+                    grep ^GCC '${output}' | cut -f 2- >> 'split/ACGT content per cycle.tab';
+                fi
             #end if
 
             #if 'is' in $outputs_to_split:
-                echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" &&
-                grep -q ^IS  "${output}" ; if [ $? = 0 ] ; then grep ^IS  "${output}" | cut -f 2- >> "split/Insert sizes.tab"  ; fi &&
+                && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' &&
+                if grep -q ^IS '${output}'; then
+                    grep ^IS '${output}' | cut -f 2- >> 'split/Insert sizes.tab';
+                fi
             #end if
 
             #if 'rl' in $outputs_to_split:
-                echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" &&
-                grep -q ^RL  "${output}" ; if [ $? = 0 ] ; then grep ^RL  "${output}" | cut -f 2- >> "split/Read lengths.tab"  ; fi &&
+                && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' &&
+                if grep -q ^RL '${output}'; then
+                    grep ^RL '${output}' | cut -f 2- >> 'split/Read lengths.tab';
+                fi
             #end if
 
             #if 'id' in $outputs_to_split:
-                echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" &&
-                grep -q ^ID  "${output}" ; if [ $? = 0 ] ; then grep ^ID  "${output}" | cut -f 2- >> "split/Indel distribution.tab"  ; fi &&
+                && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' &&
+                if grep -q ^ID '${output}'; then
+                    grep ^ID '${output}' | cut -f 2- >> 'split/Indel distribution.tab';
+                fi
             #end if
 
             #if 'ic' in $outputs_to_split:
-                echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" >  "split/Indels per cycle.tab"  &&
-                grep -q ^IC  "${output}" ; if [ $? = 0 ] ; then grep ^IC  "${output}" | cut -f 2- >> "split/Indels per cycle.tab"  ; fi &&
+                && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' &&
+                if grep -q ^IC '${output}'; then
+                    grep ^IC '${output}' | cut -f 2- >> 'split/Indels per cycle.tab';
+                fi
             #end if
 
             #if 'cov' in $outputs_to_split:
-                echo "# Coverage distribution" > "split/Coverage distribution.tab" &&
-                grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- >> "split/Coverage distribution.tab" ; fi &&
+                && echo "# Coverage distribution" > 'split/Coverage distribution.tab' &&
+                if grep -q ^COV '${output}'; then
+                    grep ^COV '${output}' | cut -f 2- >> 'split/Coverage distribution.tab';
+                fi
             #end if
 
             #if 'gcd' in $outputs_to_split:
-                echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" &&
-                grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- >> "split/GC depth.tab" ; fi &&
+                && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' &&
+                if grep -q ^GCD '${output}'; then
+                    grep ^GCD '${output}' | cut -f 2- >> 'split/GC depth.tab';
+                fi
             #end if
-
-            ## Unix true command below
-
-            true
-
         #end if
         ]]></command>
     <inputs>
         <param name="input_file" type="data" format="sam,bam" label="BAM file" />
-        <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="minimum coverage value for --coverage option"/>
-        <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="maximum coverage value for --coverage option"/>
-        <param name="coverage_step" type="integer" value="1" label="Coverage step" help="step value for --coverage option"/>
-        <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" help="--remove-dups; default = False"/>
+        <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" />
+        <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" />
+        <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />
+        <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False"
+               label="Exclude reads marked as duplicates" />
         <conditional name="split_output">
-            <param name="split_output_selector" type="select" label="Output" help="Select between a single output or separate outputs for each statistics">
-                <option value="no" selected="True">a single summary file</option>
-                <option value="yes">separate datasets for each statistics</option>
+            <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics">
+                <option value="no" selected="True">One single summary file</option>
+                <option value="yes">Separate datasets for each statistic</option>
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Statistics to extract">
+                <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Desired output files">
                     <option value="sn">Summary numbers</option>
                     <option value="ffq">First Fragment Qualities</option>
                     <option value="lfq">Last Fragment Qualities</option>
@@ -156,12 +183,12 @@
             </when>
         </conditional>
         <conditional name="filter_by_flags">
-            <param name="filter_flags" type="select" label="Set filter by flags" help="-f and -F options">
+            <param name="filter_flags" type="select" label="Filter by SAM flags" help="More info on the flags: https://samtools.github.io/hts-specs/SAMv1.pdf">
                 <option value="nofilter" selected="True">Do not filter</option>
                 <option value="filter">Filter by flags to exclude or require</option>
             </param>
             <when value="filter">
-                <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require" help="-f">
+                <param name="require_flags" argument="-f" type="select" display="checkboxes" multiple="True" label="Require">
                     <option value="1">Read is paired</option>
                     <option value="2">Read is mapped in a proper pair</option>
                     <option value="4">The read is unmapped</option>
@@ -174,7 +201,7 @@
                     <option value="512">The read fails platform/vendor quality checks</option>
                     <option value="1024">The read is a PCR or optical duplicate</option>
                 </param>
-                <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude" help="-F">
+                <param name="exclude_flags" argument="-F" type="select" display="checkboxes" multiple="True" label="Exclude">
                     <option value="1">Read is paired</option>
                     <option value="2">Read is mapped in a proper pair</option>
                     <option value="4">The read is unmapped</option>
@@ -191,19 +218,18 @@
             <when value="nofilter" />
 
         </conditional>
-        <param name="gc_depth" type="float" value="20000" label="GC-depth bin size" help="--GC-depth; decreasing bin size increases memory requirement; default = 20000.0"/>
-        <param name="insert_size" type="integer" value="8000" label="Maximum insert size" help="--insert-size; default = 8000"/>
+        <param name="gc_depth" argument="--GC-depth" type="float" value="20000" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement" />
+        <param name="insert_size" argument="--insert-size" type="integer" value="8000" label="Maximum insert size" />
+        <!--
 
-        <!--
-            
             The -I option of samtools stats returns the following message in version 1.2:
 
             Samtools-htslib: init_group_id() header parsing not yet implemented
             Abort trap: 6
-    
+
             Because of this the section below is commented out until this stats bug is fixed
 
-            <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" > 
+            <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
                 <options>
                     <filter type="data_meta" ref="input_file" key="read_groups" />
                 </options>
@@ -211,12 +237,12 @@
 
         -->
 
-        <param name="read_length" type="integer" value="0" label="Minimum read length to generate statistics for" help="--read-length; default = no cutoff"/>
-        <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" help="--most-inserts; default = 0.99"/>
-        <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" help="--trim-quality; default = 0"/>
-        
+        <param name="read_length" argument="--read-length" type="integer" value="" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty"/>
+        <param name="most_inserts" argument="--most-inserts" type="float" value="0.99" label="Report only the main part of inserts" />
+        <param name="trim_quality" argument="--trim-quality" type="integer" value="0" label="BWA trim parameter" />
+
         <conditional name="use_reference">
-            <param name="use_ref_selector" type="select" label="Use reference sequence" help="--ref-seq; required for GC-depth and mismatches-per-cycle calculation">
+            <param name="use_ref_selector" argument="--ref-seq" type="select" label="Use reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation">
                 <option value="yes">Use reference</option>
                 <option selected="True" value="no">Do not use reference</option>
             </param>
@@ -228,8 +254,9 @@
                     </param>
                     <when value="cached">
                         <param name="ref_file" type="select" label="Using genome">
-                            <options from_data_table="fasta_indexes" />
-                            <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
+                            <options from_data_table="fasta_indexes">
+                                <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
+                            </options>
                         </param>
                     </when>
                     <when value="history">
@@ -243,7 +270,7 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="output" label="${tool.name} on ${on_string}">
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tab" ext="tabular" visible="true" directory="split" />
         </data>
     </outputs>
@@ -263,34 +290,17 @@
             <param name="split_output_selector" value="yes" />
             <param name="generate_tables" value="sn,mpc,gcc" />
             <output name="output" file="samtools_stats_out2.tab" lines_diff="4">
-                <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2/sn.tab" />
-                <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2/gcc.tab" />
-                <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2/mpc.tab" />
+                <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2__sn.tab" />
+                <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2__gcc.tab" />
+                <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2__mpc.tab" />
             </output>
         </test>
     </tests>
     <help><![CDATA[
 **What it does**
 
-This tool runs the ``samtools stats`` command. It has the following options::
-
-    -c, --coverage <int>,<int>,<int>    Coverage distribution min,max,step [1,1000,1]
-    -d, --remove-dups                   Exclude from statistics reads marked as duplicates
-    -f, --required-flag  <str|int>      Required flag, 0 for unset. See also `samtools flags` [0]
-    -F, --filtering-flag <str|int>      Filtering flag, 0 for unset. See also `samtools flags` [0]
-        --GC-depth <float>              the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]
-    -h, --help                          This help message
-    -i, --insert-size <int>             Maximum insert size [8000]
-    -I, --id <string>                   Include only listed read group or sample name
-    -l, --read-length <int>             Include in the statistics only reads with the given read length []
-    -m, --most-inserts <float>          Report only the main part of inserts [0.99]
-    -q, --trim-quality <int>            The BWA trimming parameter [0]
-    -r, --ref-seq <file>                Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy
-                                        will provide options for selecting a reference cached as this Galaxy instance or choosing
-                                        one from history.
-   
-
+This tool runs the ``samtools stats`` command.
     ]]></help>
-    <expand macro="citations"></expand>
+    <expand macro="citations"/>
 </tool>
 
diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out1.tab
--- a/test-data/samtools_stats_out1.tab	Wed Nov 11 12:55:15 2015 -0500
+++ b/test-data/samtools_stats_out1.tab	Tue May 09 11:19:01 2017 -0400
@@ -1,5 +1,6 @@
-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats
-# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat
+# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_2.dat /tmp/tmpO1aTrb/files/000/dataset_1.dat
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	1bd20fd8	58ad2167	29883386
@@ -836,258 +837,258 @@
 GCL	52.01	1
 GCL	52.51	0
 GCL	53.02	1
-# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%]
-GCC	1	21.50	29.50	33.50	15.50
-GCC	2	30.00	16.00	11.00	43.00
-GCC	3	33.00	25.00	9.00	33.00
-GCC	4	17.00	29.00	13.00	41.00
-GCC	5	37.00	22.00	12.00	29.00
-GCC	6	36.00	26.00	17.00	21.00
-GCC	7	29.50	13.50	31.50	25.50
-GCC	8	50.50	14.50	19.50	15.50
-GCC	9	17.00	33.00	18.00	32.00
-GCC	10	37.00	14.00	21.00	28.00
-GCC	11	20.50	14.50	29.50	35.50
-GCC	12	30.00	24.00	22.00	24.00
-GCC	13	27.00	15.00	21.00	37.00
-GCC	14	24.00	22.00	26.00	28.00
-GCC	15	25.50	20.50	24.50	29.50
-GCC	16	31.00	15.00	20.00	34.00
-GCC	17	28.00	25.00	14.00	33.00
-GCC	18	30.50	28.50	19.50	21.50
-GCC	19	29.00	26.00	21.00	24.00
-GCC	20	22.50	23.50	17.50	36.50
-GCC	21	35.50	17.50	19.50	27.50
-GCC	22	37.50	28.50	15.50	18.50
-GCC	23	31.00	19.00	13.00	37.00
-GCC	24	37.00	12.00	22.00	29.00
-GCC	25	35.50	22.50	17.50	24.50
-GCC	26	33.50	18.50	15.50	32.50
-GCC	27	34.50	14.50	25.50	25.50
-GCC	28	31.00	14.00	24.00	31.00
-GCC	29	30.00	27.00	24.00	19.00
-GCC	30	31.00	20.00	14.00	35.00
-GCC	31	33.50	29.50	13.50	23.50
-GCC	32	42.50	20.50	19.50	17.50
-GCC	33	25.50	23.50	14.50	36.50
-GCC	34	39.50	16.50	20.50	23.50
-GCC	35	32.50	23.50	21.50	22.50
-GCC	36	42.00	25.00	16.00	17.00
-GCC	37	38.00	17.00	19.00	26.00
-GCC	38	24.00	26.00	25.00	25.00
-GCC	39	22.50	41.50	18.50	17.50
-GCC	40	32.00	16.00	21.00	31.00
-GCC	41	33.00	28.00	19.00	20.00
-GCC	42	30.50	25.50	19.50	24.50
-GCC	43	35.00	29.00	15.00	21.00
-GCC	44	20.00	27.00	22.00	31.00
-GCC	45	40.50	21.50	21.50	16.50
-GCC	46	26.50	20.50	22.50	30.50
-GCC	47	38.50	29.50	16.50	15.50
-GCC	48	27.50	24.50	17.50	30.50
-GCC	49	28.50	32.50	10.50	28.50
-GCC	50	46.50	20.50	9.50	23.50
-GCC	51	34.50	28.50	13.50	23.50
-GCC	52	41.50	23.50	20.50	14.50
-GCC	53	20.00	28.00	26.00	26.00
-GCC	54	31.50	18.50	24.50	25.50
-GCC	55	30.50	22.50	16.50	30.50
-GCC	56	33.50	22.50	13.50	30.50
-GCC	57	23.00	24.00	23.00	30.00
-GCC	58	25.00	37.00	19.00	19.00
-GCC	59	34.00	23.00	24.00	19.00
-GCC	60	29.00	28.00	17.00	26.00
-GCC	61	25.50	23.50	24.50	26.50
-GCC	62	31.50	22.50	16.50	29.50
-GCC	63	27.50	28.50	25.50	18.50
-GCC	64	33.50	21.50	25.50	19.50
-GCC	65	35.50	19.50	18.50	26.50
-GCC	66	34.00	25.00	15.00	26.00
-GCC	67	37.00	23.00	19.00	21.00
-GCC	68	36.50	29.50	13.50	20.50
-GCC	69	38.50	19.50	20.50	21.50
-GCC	70	38.50	16.50	18.50	26.50
-GCC	71	25.50	38.50	21.50	14.50
-GCC	72	29.00	29.00	25.00	17.00
-GCC	73	32.50	20.50	21.50	25.50
-GCC	74	28.50	32.50	12.50	26.50
-GCC	75	41.50	12.50	18.50	27.50
-GCC	76	24.50	29.50	23.50	22.50
-GCC	77	36.00	21.00	18.00	25.00
-GCC	78	27.00	34.00	22.00	17.00
-GCC	79	21.50	26.50	25.50	26.50
-GCC	80	34.00	19.00	28.00	19.00
-GCC	81	17.00	26.00	26.00	31.00
-GCC	82	31.00	30.00	23.00	16.00
-GCC	83	31.50	26.50	12.50	29.50
-GCC	84	19.00	41.00	21.00	19.00
-GCC	85	37.50	24.50	16.50	21.50
-GCC	86	15.00	48.00	15.00	22.00
-GCC	87	41.00	16.00	18.00	25.00
-GCC	88	23.50	27.50	27.50	21.50
-GCC	89	26.50	27.50	26.50	19.50
-GCC	90	18.50	23.50	24.50	33.50
-GCC	91	27.00	32.00	22.00	19.00
-GCC	92	23.50	17.50	27.50	31.50
-GCC	93	25.50	37.50	15.50	21.50
-GCC	94	27.00	17.00	24.00	32.00
-GCC	95	26.50	37.50	14.50	21.50
-GCC	96	29.50	25.50	16.50	28.50
-GCC	97	29.00	31.00	21.00	19.00
-GCC	98	18.00	33.00	22.00	27.00
-GCC	99	24.50	33.50	24.50	17.50
-GCC	100	24.50	16.50	24.50	34.50
-GCC	101	25.00	40.00	19.00	16.00
-GCC	102	17.50	17.50	32.50	32.50
-GCC	103	31.00	26.00	16.00	27.00
-GCC	104	26.50	29.50	20.50	23.50
-GCC	105	34.00	33.00	21.00	12.00
-GCC	106	23.00	31.00	26.00	20.00
-GCC	107	17.50	35.50	23.50	23.50
-GCC	108	24.50	30.50	23.50	21.50
-GCC	109	17.00	31.00	22.00	30.00
-GCC	110	16.00	35.00	24.00	25.00
-GCC	111	24.00	32.00	23.00	21.00
-GCC	112	37.00	28.00	16.00	19.00
-GCC	113	19.50	22.50	32.50	25.50
-GCC	114	17.00	31.00	35.00	17.00
-GCC	115	29.50	24.50	23.50	22.50
-GCC	116	22.00	30.00	34.00	14.00
-GCC	117	27.00	23.00	19.00	31.00
-GCC	118	25.50	14.50	34.50	25.50
-GCC	119	22.50	34.50	20.50	22.50
-GCC	120	17.50	24.50	26.50	31.50
-GCC	121	27.50	33.50	22.50	16.50
-GCC	122	17.00	23.00	25.00	35.00
-GCC	123	23.50	46.50	11.50	18.50
-GCC	124	9.00	32.00	34.00	25.00
-GCC	125	24.00	27.00	19.00	30.00
-GCC	126	26.00	17.00	28.00	29.00
-GCC	127	26.50	16.50	21.50	35.50
-GCC	128	18.00	34.00	31.00	17.00
-GCC	129	25.50	25.50	27.50	21.50
-GCC	130	25.00	20.00	22.00	33.00
-GCC	131	17.50	39.50	24.50	18.50
-GCC	132	21.00	28.00	23.00	28.00
-GCC	133	13.50	31.50	35.50	19.50
-GCC	134	24.50	19.50	30.50	25.50
-GCC	135	16.50	23.50	30.50	29.50
-GCC	136	28.00	32.00	15.00	25.00
-GCC	137	22.50	21.50	30.50	25.50
-GCC	138	14.50	34.50	24.50	26.50
-GCC	139	20.50	29.50	24.50	25.50
-GCC	140	17.00	23.00	30.00	30.00
-GCC	141	20.50	23.50	25.50	30.50
-GCC	142	18.00	29.00	38.00	15.00
-GCC	143	22.00	24.00	27.00	27.00
-GCC	144	21.50	30.50	26.50	21.50
-GCC	145	22.00	21.00	29.00	28.00
-GCC	146	25.00	16.00	39.00	20.00
-GCC	147	26.50	22.50	30.50	20.50
-GCC	148	12.50	28.50	36.50	22.50
-GCC	149	26.50	23.50	23.50	26.50
-GCC	150	14.00	29.00	24.00	33.00
-GCC	151	19.50	30.50	32.50	17.50
-GCC	152	18.50	17.50	29.50	34.50
-GCC	153	22.50	22.50	31.50	23.50
-GCC	154	22.00	21.00	29.00	28.00
-GCC	155	21.00	26.00	19.00	34.00
-GCC	156	14.50	23.50	35.50	26.50
-GCC	157	22.00	31.00	23.00	24.00
-GCC	158	22.50	29.50	24.50	23.50
-GCC	159	17.50	12.50	46.50	23.50
-GCC	160	24.50	26.50	26.50	22.50
-GCC	161	13.00	23.00	45.00	19.00
-GCC	162	31.50	16.50	22.50	29.50
-GCC	163	19.50	21.50	35.50	23.50
-GCC	164	29.00	18.00	21.00	32.00
-GCC	165	14.50	17.50	35.50	32.50
-GCC	166	17.50	37.50	28.50	16.50
-GCC	167	16.50	21.50	31.50	30.50
-GCC	168	14.00	25.00	30.00	31.00
-GCC	169	18.50	20.50	23.50	37.50
-GCC	170	19.00	23.00	28.00	30.00
-GCC	171	20.00	28.00	33.00	19.00
-GCC	172	19.00	20.00	32.00	29.00
-GCC	173	24.50	16.50	33.50	25.50
-GCC	174	17.50	23.50	33.50	25.50
-GCC	175	33.50	17.50	35.50	13.50
-GCC	176	16.50	32.50	28.50	22.50
-GCC	177	19.00	22.00	27.00	32.00
-GCC	178	16.00	26.00	30.00	28.00
-GCC	179	18.00	18.00	22.00	42.00
-GCC	180	21.00	22.00	34.00	23.00
-GCC	181	20.50	19.50	35.50	24.50
-GCC	182	32.50	18.50	22.50	26.50
-GCC	183	24.50	13.50	28.50	33.50
-GCC	184	15.00	29.00	30.00	26.00
-GCC	185	15.00	32.00	33.00	20.00
-GCC	186	22.50	23.50	34.50	19.50
-GCC	187	19.00	14.00	40.00	27.00
-GCC	188	27.50	21.50	27.50	23.50
-GCC	189	17.00	22.00	34.00	27.00
-GCC	190	23.00	30.00	23.00	24.00
-GCC	191	25.00	22.00	28.00	25.00
-GCC	192	34.50	24.50	13.50	27.50
-GCC	193	18.50	25.50	25.50	30.50
-GCC	194	18.50	33.50	24.50	23.50
-GCC	195	16.00	26.00	23.00	35.00
-GCC	196	21.50	25.50	24.50	28.50
-GCC	197	20.00	21.00	23.00	36.00
-GCC	198	17.00	21.00	37.00	25.00
-GCC	199	20.50	18.50	25.50	35.50
-GCC	200	21.00	29.00	21.00	29.00
-GCC	201	27.00	21.00	23.00	29.00
-GCC	202	21.50	24.50	19.50	34.50
-GCC	203	21.50	24.50	26.50	27.50
-GCC	204	27.00	29.00	24.00	20.00
-GCC	205	19.50	21.50	22.50	36.50
-GCC	206	26.50	24.50	21.50	27.50
-GCC	207	22.50	21.50	19.50	36.50
-GCC	208	14.00	35.00	29.00	22.00
-GCC	209	16.00	23.00	12.00	49.00
-GCC	210	18.50	19.50	40.50	21.50
-GCC	211	26.00	20.00	22.00	32.00
-GCC	212	21.00	31.00	18.00	30.00
-GCC	213	24.00	15.00	31.00	30.00
-GCC	214	17.50	24.50	25.50	32.50
-GCC	215	26.00	24.00	23.00	27.00
-GCC	216	21.50	17.50	25.50	35.50
-GCC	217	26.00	29.00	17.00	28.00
-GCC	218	20.00	27.00	21.00	32.00
-GCC	219	17.00	21.00	21.00	41.00
-GCC	220	25.50	23.50	23.50	27.50
-GCC	221	21.50	23.50	20.50	34.50
-GCC	222	21.50	21.50	18.50	38.50
-GCC	223	20.00	27.00	28.00	25.00
-GCC	224	22.50	22.50	24.50	30.50
-GCC	225	14.50	35.50	30.50	19.50
-GCC	226	20.00	23.00	26.00	31.00
-GCC	227	20.50	24.50	23.50	31.50
-GCC	228	33.00	19.00	26.00	22.00
-GCC	229	22.50	24.50	18.50	34.50
-GCC	230	21.00	32.00	16.00	31.00
-GCC	231	23.00	28.00	30.00	19.00
-GCC	232	23.50	21.50	12.50	42.50
-GCC	233	21.00	27.00	25.00	27.00
-GCC	234	16.50	27.50	22.50	33.50
-GCC	235	20.00	15.00	28.00	37.00
-GCC	236	28.00	23.00	21.00	28.00
-GCC	237	20.50	19.50	22.50	37.50
-GCC	238	21.50	29.50	24.50	24.50
-GCC	239	20.00	8.00	17.00	55.00
-GCC	240	28.00	24.00	16.00	32.00
-GCC	241	22.50	22.50	16.50	38.50
-GCC	242	29.00	25.00	13.00	33.00
-GCC	243	22.50	15.50	23.50	38.50
-GCC	244	20.50	23.50	16.50	39.50
-GCC	245	28.00	23.00	19.00	30.00
-GCC	246	21.00	29.00	25.00	25.00
-GCC	247	32.00	14.00	13.00	41.00
-GCC	248	18.00	18.00	25.00	39.00
-GCC	249	25.00	23.00	21.00	31.00
-GCC	250	27.50	22.50	17.50	32.50
-GCC	251	13.50	20.50	36.50	29.50
+# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
+GCC	1	21.94	30.10	34.18	13.78	2.04	0.00
+GCC	2	30.00	16.00	11.00	43.00	0.00	0.00
+GCC	3	33.00	25.00	9.00	33.00	0.00	0.00
+GCC	4	17.00	29.00	13.00	41.00	0.00	0.00
+GCC	5	37.00	22.00	12.00	29.00	0.00	0.00
+GCC	6	36.00	26.00	17.00	21.00	0.00	0.00
+GCC	7	29.50	13.50	31.50	25.50	0.00	0.00
+GCC	8	50.50	14.50	19.50	15.50	0.00	0.00
+GCC	9	17.00	33.00	18.00	32.00	0.00	0.00
+GCC	10	37.00	14.00	21.00	28.00	0.00	0.00
+GCC	11	20.50	14.50	29.50	35.50	0.00	0.00
+GCC	12	30.00	24.00	22.00	24.00	0.00	0.00
+GCC	13	27.00	15.00	21.00	37.00	0.00	0.00
+GCC	14	24.24	22.22	26.26	27.27	1.01	0.00
+GCC	15	25.50	20.50	24.50	29.50	0.00	0.00
+GCC	16	31.00	15.00	20.00	34.00	0.00	0.00
+GCC	17	28.00	25.00	14.00	33.00	0.00	0.00
+GCC	18	30.50	28.50	19.50	21.50	0.00	0.00
+GCC	19	29.00	26.00	21.00	24.00	0.00	0.00
+GCC	20	22.50	23.50	17.50	36.50	0.00	0.00
+GCC	21	35.50	17.50	19.50	27.50	0.00	0.00
+GCC	22	37.50	28.50	15.50	18.50	0.00	0.00
+GCC	23	31.31	19.19	13.13	36.36	1.01	0.00
+GCC	24	37.00	12.00	22.00	29.00	0.00	0.00
+GCC	25	35.50	22.50	17.50	24.50	0.00	0.00
+GCC	26	33.50	18.50	15.50	32.50	0.00	0.00
+GCC	27	34.50	14.50	25.50	25.50	0.00	0.00
+GCC	28	31.00	14.00	24.00	31.00	0.00	0.00
+GCC	29	30.00	27.00	24.00	19.00	0.00	0.00
+GCC	30	31.00	20.00	14.00	35.00	0.00	0.00
+GCC	31	33.50	29.50	13.50	23.50	0.00	0.00
+GCC	32	42.50	20.50	19.50	17.50	0.00	0.00
+GCC	33	25.50	23.50	14.50	36.50	0.00	0.00
+GCC	34	39.50	16.50	20.50	23.50	0.00	0.00
+GCC	35	32.50	23.50	21.50	22.50	0.00	0.00
+GCC	36	42.00	25.00	16.00	17.00	0.00	0.00
+GCC	37	38.00	17.00	19.00	26.00	0.00	0.00
+GCC	38	24.00	26.00	25.00	25.00	0.00	0.00
+GCC	39	22.50	41.50	18.50	17.50	0.00	0.00
+GCC	40	32.00	16.00	21.00	31.00	0.00	0.00
+GCC	41	33.00	28.00	19.00	20.00	0.00	0.00
+GCC	42	30.50	25.50	19.50	24.50	0.00	0.00
+GCC	43	35.00	29.00	15.00	21.00	0.00	0.00
+GCC	44	20.00	27.00	22.00	31.00	0.00	0.00
+GCC	45	40.50	21.50	21.50	16.50	0.00	0.00
+GCC	46	26.50	20.50	22.50	30.50	0.00	0.00
+GCC	47	38.50	29.50	16.50	15.50	0.00	0.00
+GCC	48	27.50	24.50	17.50	30.50	0.00	0.00
+GCC	49	28.50	32.50	10.50	28.50	0.00	0.00
+GCC	50	46.50	20.50	9.50	23.50	0.00	0.00
+GCC	51	34.50	28.50	13.50	23.50	0.00	0.00
+GCC	52	41.50	23.50	20.50	14.50	0.00	0.00
+GCC	53	20.00	28.00	26.00	26.00	0.00	0.00
+GCC	54	31.50	18.50	24.50	25.50	0.00	0.00
+GCC	55	30.50	22.50	16.50	30.50	0.00	0.00
+GCC	56	33.50	22.50	13.50	30.50	0.00	0.00
+GCC	57	23.00	24.00	23.00	30.00	0.00	0.00
+GCC	58	25.00	37.00	19.00	19.00	0.00	0.00
+GCC	59	34.00	23.00	24.00	19.00	0.00	0.00
+GCC	60	29.00	28.00	17.00	26.00	0.00	0.00
+GCC	61	25.50	23.50	24.50	26.50	0.00	0.00
+GCC	62	31.50	22.50	16.50	29.50	0.00	0.00
+GCC	63	27.50	28.50	25.50	18.50	0.00	0.00
+GCC	64	33.50	21.50	25.50	19.50	0.00	0.00
+GCC	65	35.50	19.50	18.50	26.50	0.00	0.00
+GCC	66	34.00	25.00	15.00	26.00	0.00	0.00
+GCC	67	37.00	23.00	19.00	21.00	0.00	0.00
+GCC	68	36.50	29.50	13.50	20.50	0.00	0.00
+GCC	69	38.50	19.50	20.50	21.50	0.00	0.00
+GCC	70	38.50	16.50	18.50	26.50	0.00	0.00
+GCC	71	25.50	38.50	21.50	14.50	0.00	0.00
+GCC	72	29.00	29.00	25.00	17.00	0.00	0.00
+GCC	73	32.50	20.50	21.50	25.50	0.00	0.00
+GCC	74	28.50	32.50	12.50	26.50	0.00	0.00
+GCC	75	41.50	12.50	18.50	27.50	0.00	0.00
+GCC	76	24.50	29.50	23.50	22.50	0.00	0.00
+GCC	77	36.00	21.00	18.00	25.00	0.00	0.00
+GCC	78	27.00	34.00	22.00	17.00	0.00	0.00
+GCC	79	21.50	26.50	25.50	26.50	0.00	0.00
+GCC	80	34.00	19.00	28.00	19.00	0.00	0.00
+GCC	81	17.00	26.00	26.00	31.00	0.00	0.00
+GCC	82	31.00	30.00	23.00	16.00	0.00	0.00
+GCC	83	31.50	26.50	12.50	29.50	0.00	0.00
+GCC	84	19.00	41.00	21.00	19.00	0.00	0.00
+GCC	85	37.50	24.50	16.50	21.50	0.00	0.00
+GCC	86	15.00	48.00	15.00	22.00	0.00	0.00
+GCC	87	41.00	16.00	18.00	25.00	0.00	0.00
+GCC	88	23.50	27.50	27.50	21.50	0.00	0.00
+GCC	89	26.50	27.50	26.50	19.50	0.00	0.00
+GCC	90	18.50	23.50	24.50	33.50	0.00	0.00
+GCC	91	27.00	32.00	22.00	19.00	0.00	0.00
+GCC	92	23.50	17.50	27.50	31.50	0.00	0.00
+GCC	93	25.50	37.50	15.50	21.50	0.00	0.00
+GCC	94	27.00	17.00	24.00	32.00	0.00	0.00
+GCC	95	26.77	37.88	14.65	20.71	1.01	0.00
+GCC	96	29.50	25.50	16.50	28.50	0.00	0.00
+GCC	97	29.00	31.00	21.00	19.00	0.00	0.00
+GCC	98	18.18	33.33	22.22	26.26	1.01	0.00
+GCC	99	24.50	33.50	24.50	17.50	0.00	0.00
+GCC	100	24.50	16.50	24.50	34.50	0.00	0.00
+GCC	101	25.00	40.00	19.00	16.00	0.00	0.00
+GCC	102	17.50	17.50	32.50	32.50	0.00	0.00
+GCC	103	31.00	26.00	16.00	27.00	0.00	0.00
+GCC	104	26.50	29.50	20.50	23.50	0.00	0.00
+GCC	105	34.00	33.00	21.00	12.00	0.00	0.00
+GCC	106	23.00	31.00	26.00	20.00	0.00	0.00
+GCC	107	17.68	35.86	23.74	22.73	1.01	0.00
+GCC	108	24.75	30.81	23.74	20.71	1.01	0.00
+GCC	109	17.00	31.00	22.00	30.00	0.00	0.00
+GCC	110	16.16	35.35	24.24	24.24	1.01	0.00
+GCC	111	24.24	32.32	23.23	20.20	1.01	0.00
+GCC	112	37.37	28.28	16.16	18.18	1.01	0.00
+GCC	113	19.70	22.73	32.83	24.75	1.01	0.00
+GCC	114	17.00	31.00	35.00	17.00	0.00	0.00
+GCC	115	29.50	24.50	23.50	22.50	0.00	0.00
+GCC	116	22.00	30.00	34.00	14.00	0.00	0.00
+GCC	117	27.00	23.00	19.00	31.00	0.00	0.00
+GCC	118	25.50	14.50	34.50	25.50	0.00	0.00
+GCC	119	22.50	34.50	20.50	22.50	0.00	0.00
+GCC	120	17.50	24.50	26.50	31.50	0.00	0.00
+GCC	121	27.78	33.84	22.73	15.66	1.01	0.00
+GCC	122	17.00	23.00	25.00	35.00	0.00	0.00
+GCC	123	23.50	46.50	11.50	18.50	0.00	0.00
+GCC	124	9.00	32.00	34.00	25.00	0.00	0.00
+GCC	125	24.00	27.00	19.00	30.00	0.00	0.00
+GCC	126	26.00	17.00	28.00	29.00	0.00	0.00
+GCC	127	26.50	16.50	21.50	35.50	0.00	0.00
+GCC	128	18.00	34.00	31.00	17.00	0.00	0.00
+GCC	129	25.50	25.50	27.50	21.50	0.00	0.00
+GCC	130	25.00	20.00	22.00	33.00	0.00	0.00
+GCC	131	17.50	39.50	24.50	18.50	0.00	0.00
+GCC	132	21.00	28.00	23.00	28.00	0.00	0.00
+GCC	133	13.50	31.50	35.50	19.50	0.00	0.00
+GCC	134	24.50	19.50	30.50	25.50	0.00	0.00
+GCC	135	16.50	23.50	30.50	29.50	0.00	0.00
+GCC	136	28.00	32.00	15.00	25.00	0.00	0.00
+GCC	137	22.50	21.50	30.50	25.50	0.00	0.00
+GCC	138	14.50	34.50	24.50	26.50	0.00	0.00
+GCC	139	20.50	29.50	24.50	25.50	0.00	0.00
+GCC	140	17.00	23.00	30.00	30.00	0.00	0.00
+GCC	141	20.50	23.50	25.50	30.50	0.00	0.00
+GCC	142	18.00	29.00	38.00	15.00	0.00	0.00
+GCC	143	22.00	24.00	27.00	27.00	0.00	0.00
+GCC	144	21.50	30.50	26.50	21.50	0.00	0.00
+GCC	145	22.00	21.00	29.00	28.00	0.00	0.00
+GCC	146	25.00	16.00	39.00	20.00	0.00	0.00
+GCC	147	26.50	22.50	30.50	20.50	0.00	0.00
+GCC	148	12.50	28.50	36.50	22.50	0.00	0.00
+GCC	149	26.50	23.50	23.50	26.50	0.00	0.00
+GCC	150	14.00	29.00	24.00	33.00	0.00	0.00
+GCC	151	19.50	30.50	32.50	17.50	0.00	0.00
+GCC	152	18.50	17.50	29.50	34.50	0.00	0.00
+GCC	153	22.50	22.50	31.50	23.50	0.00	0.00
+GCC	154	22.00	21.00	29.00	28.00	0.00	0.00
+GCC	155	21.00	26.00	19.00	34.00	0.00	0.00
+GCC	156	14.50	23.50	35.50	26.50	0.00	0.00
+GCC	157	22.00	31.00	23.00	24.00	0.00	0.00
+GCC	158	22.50	29.50	24.50	23.50	0.00	0.00
+GCC	159	17.50	12.50	46.50	23.50	0.00	0.00
+GCC	160	24.50	26.50	26.50	22.50	0.00	0.00
+GCC	161	13.00	23.00	45.00	19.00	0.00	0.00
+GCC	162	31.50	16.50	22.50	29.50	0.00	0.00
+GCC	163	19.50	21.50	35.50	23.50	0.00	0.00
+GCC	164	29.00	18.00	21.00	32.00	0.00	0.00
+GCC	165	14.50	17.50	35.50	32.50	0.00	0.00
+GCC	166	17.50	37.50	28.50	16.50	0.00	0.00
+GCC	167	16.50	21.50	31.50	30.50	0.00	0.00
+GCC	168	14.00	25.00	30.00	31.00	0.00	0.00
+GCC	169	18.50	20.50	23.50	37.50	0.00	0.00
+GCC	170	19.00	23.00	28.00	30.00	0.00	0.00
+GCC	171	20.00	28.00	33.00	19.00	0.00	0.00
+GCC	172	19.00	20.00	32.00	29.00	0.00	0.00
+GCC	173	24.50	16.50	33.50	25.50	0.00	0.00
+GCC	174	17.50	23.50	33.50	25.50	0.00	0.00
+GCC	175	33.50	17.50	35.50	13.50	0.00	0.00
+GCC	176	16.50	32.50	28.50	22.50	0.00	0.00
+GCC	177	19.00	22.00	27.00	32.00	0.00	0.00
+GCC	178	16.00	26.00	30.00	28.00	0.00	0.00
+GCC	179	18.00	18.00	22.00	42.00	0.00	0.00
+GCC	180	21.00	22.00	34.00	23.00	0.00	0.00
+GCC	181	20.50	19.50	35.50	24.50	0.00	0.00
+GCC	182	32.50	18.50	22.50	26.50	0.00	0.00
+GCC	183	24.50	13.50	28.50	33.50	0.00	0.00
+GCC	184	15.00	29.00	30.00	26.00	0.00	0.00
+GCC	185	15.00	32.00	33.00	20.00	0.00	0.00
+GCC	186	22.50	23.50	34.50	19.50	0.00	0.00
+GCC	187	19.00	14.00	40.00	27.00	0.00	0.00
+GCC	188	27.50	21.50	27.50	23.50	0.00	0.00
+GCC	189	17.00	22.00	34.00	27.00	0.00	0.00
+GCC	190	23.00	30.00	23.00	24.00	0.00	0.00
+GCC	191	25.00	22.00	28.00	25.00	0.00	0.00
+GCC	192	34.50	24.50	13.50	27.50	0.00	0.00
+GCC	193	18.50	25.50	25.50	30.50	0.00	0.00
+GCC	194	18.50	33.50	24.50	23.50	0.00	0.00
+GCC	195	16.00	26.00	23.00	35.00	0.00	0.00
+GCC	196	21.50	25.50	24.50	28.50	0.00	0.00
+GCC	197	20.00	21.00	23.00	36.00	0.00	0.00
+GCC	198	17.00	21.00	37.00	25.00	0.00	0.00
+GCC	199	20.50	18.50	25.50	35.50	0.00	0.00
+GCC	200	21.00	29.00	21.00	29.00	0.00	0.00
+GCC	201	27.00	21.00	23.00	29.00	0.00	0.00
+GCC	202	21.50	24.50	19.50	34.50	0.00	0.00
+GCC	203	21.50	24.50	26.50	27.50	0.00	0.00
+GCC	204	27.00	29.00	24.00	20.00	0.00	0.00
+GCC	205	19.50	21.50	22.50	36.50	0.00	0.00
+GCC	206	26.50	24.50	21.50	27.50	0.00	0.00
+GCC	207	22.50	21.50	19.50	36.50	0.00	0.00
+GCC	208	14.00	35.00	29.00	22.00	0.00	0.00
+GCC	209	16.00	23.00	12.00	49.00	0.00	0.00
+GCC	210	18.50	19.50	40.50	21.50	0.00	0.00
+GCC	211	26.00	20.00	22.00	32.00	0.00	0.00
+GCC	212	21.00	31.00	18.00	30.00	0.00	0.00
+GCC	213	24.00	15.00	31.00	30.00	0.00	0.00
+GCC	214	17.50	24.50	25.50	32.50	0.00	0.00
+GCC	215	26.00	24.00	23.00	27.00	0.00	0.00
+GCC	216	21.50	17.50	25.50	35.50	0.00	0.00
+GCC	217	26.00	29.00	17.00	28.00	0.00	0.00
+GCC	218	20.00	27.00	21.00	32.00	0.00	0.00
+GCC	219	17.00	21.00	21.00	41.00	0.00	0.00
+GCC	220	25.50	23.50	23.50	27.50	0.00	0.00
+GCC	221	21.50	23.50	20.50	34.50	0.00	0.00
+GCC	222	21.50	21.50	18.50	38.50	0.00	0.00
+GCC	223	20.00	27.00	28.00	25.00	0.00	0.00
+GCC	224	22.50	22.50	24.50	30.50	0.00	0.00
+GCC	225	14.50	35.50	30.50	19.50	0.00	0.00
+GCC	226	20.00	23.00	26.00	31.00	0.00	0.00
+GCC	227	20.50	24.50	23.50	31.50	0.00	0.00
+GCC	228	33.00	19.00	26.00	22.00	0.00	0.00
+GCC	229	22.50	24.50	18.50	34.50	0.00	0.00
+GCC	230	21.00	32.00	16.00	31.00	0.00	0.00
+GCC	231	23.00	28.00	30.00	19.00	0.00	0.00
+GCC	232	23.50	21.50	12.50	42.50	0.00	0.00
+GCC	233	21.00	27.00	25.00	27.00	0.00	0.00
+GCC	234	16.50	27.50	22.50	33.50	0.00	0.00
+GCC	235	20.00	15.00	28.00	37.00	0.00	0.00
+GCC	236	28.00	23.00	21.00	28.00	0.00	0.00
+GCC	237	20.50	19.50	22.50	37.50	0.00	0.00
+GCC	238	21.50	29.50	24.50	24.50	0.00	0.00
+GCC	239	20.00	8.00	17.00	55.00	0.00	0.00
+GCC	240	28.00	24.00	16.00	32.00	0.00	0.00
+GCC	241	22.50	22.50	16.50	38.50	0.00	0.00
+GCC	242	29.00	25.00	13.00	33.00	0.00	0.00
+GCC	243	22.50	15.50	23.50	38.50	0.00	0.00
+GCC	244	20.50	23.50	16.50	39.50	0.00	0.00
+GCC	245	28.00	23.00	19.00	30.00	0.00	0.00
+GCC	246	21.00	29.00	25.00	25.00	0.00	0.00
+GCC	247	32.00	14.00	13.00	41.00	0.00	0.00
+GCC	248	18.00	18.00	25.00	39.00	0.00	0.00
+GCC	249	25.00	23.00	21.00	31.00	0.00	0.00
+GCC	250	27.50	22.50	17.50	32.50	0.00	0.00
+GCC	251	13.50	20.50	36.50	29.50	0.00	0.00
 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
 RL	251	200
diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2.tab
--- a/test-data/samtools_stats_out2.tab	Wed Nov 11 12:55:15 2015 -0500
+++ b/test-data/samtools_stats_out2.tab	Tue May 09 11:19:01 2017 -0400
@@ -1,5 +1,6 @@
-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats
-# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat
+# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_5.dat /tmp/tmpO1aTrb/files/000/dataset_4.dat
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	1bd20fd8	58ad2167	29883386
@@ -836,258 +837,258 @@
 GCL	52.01	1
 GCL	52.51	0
 GCL	53.02	1
-# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%]
-GCC	1	21.50	29.50	33.50	15.50
-GCC	2	30.00	16.00	11.00	43.00
-GCC	3	33.00	25.00	9.00	33.00
-GCC	4	17.00	29.00	13.00	41.00
-GCC	5	37.00	22.00	12.00	29.00
-GCC	6	36.00	26.00	17.00	21.00
-GCC	7	29.50	13.50	31.50	25.50
-GCC	8	50.50	14.50	19.50	15.50
-GCC	9	17.00	33.00	18.00	32.00
-GCC	10	37.00	14.00	21.00	28.00
-GCC	11	20.50	14.50	29.50	35.50
-GCC	12	30.00	24.00	22.00	24.00
-GCC	13	27.00	15.00	21.00	37.00
-GCC	14	24.00	22.00	26.00	28.00
-GCC	15	25.50	20.50	24.50	29.50
-GCC	16	31.00	15.00	20.00	34.00
-GCC	17	28.00	25.00	14.00	33.00
-GCC	18	30.50	28.50	19.50	21.50
-GCC	19	29.00	26.00	21.00	24.00
-GCC	20	22.50	23.50	17.50	36.50
-GCC	21	35.50	17.50	19.50	27.50
-GCC	22	37.50	28.50	15.50	18.50
-GCC	23	31.00	19.00	13.00	37.00
-GCC	24	37.00	12.00	22.00	29.00
-GCC	25	35.50	22.50	17.50	24.50
-GCC	26	33.50	18.50	15.50	32.50
-GCC	27	34.50	14.50	25.50	25.50
-GCC	28	31.00	14.00	24.00	31.00
-GCC	29	30.00	27.00	24.00	19.00
-GCC	30	31.00	20.00	14.00	35.00
-GCC	31	33.50	29.50	13.50	23.50
-GCC	32	42.50	20.50	19.50	17.50
-GCC	33	25.50	23.50	14.50	36.50
-GCC	34	39.50	16.50	20.50	23.50
-GCC	35	32.50	23.50	21.50	22.50
-GCC	36	42.00	25.00	16.00	17.00
-GCC	37	38.00	17.00	19.00	26.00
-GCC	38	24.00	26.00	25.00	25.00
-GCC	39	22.50	41.50	18.50	17.50
-GCC	40	32.00	16.00	21.00	31.00
-GCC	41	33.00	28.00	19.00	20.00
-GCC	42	30.50	25.50	19.50	24.50
-GCC	43	35.00	29.00	15.00	21.00
-GCC	44	20.00	27.00	22.00	31.00
-GCC	45	40.50	21.50	21.50	16.50
-GCC	46	26.50	20.50	22.50	30.50
-GCC	47	38.50	29.50	16.50	15.50
-GCC	48	27.50	24.50	17.50	30.50
-GCC	49	28.50	32.50	10.50	28.50
-GCC	50	46.50	20.50	9.50	23.50
-GCC	51	34.50	28.50	13.50	23.50
-GCC	52	41.50	23.50	20.50	14.50
-GCC	53	20.00	28.00	26.00	26.00
-GCC	54	31.50	18.50	24.50	25.50
-GCC	55	30.50	22.50	16.50	30.50
-GCC	56	33.50	22.50	13.50	30.50
-GCC	57	23.00	24.00	23.00	30.00
-GCC	58	25.00	37.00	19.00	19.00
-GCC	59	34.00	23.00	24.00	19.00
-GCC	60	29.00	28.00	17.00	26.00
-GCC	61	25.50	23.50	24.50	26.50
-GCC	62	31.50	22.50	16.50	29.50
-GCC	63	27.50	28.50	25.50	18.50
-GCC	64	33.50	21.50	25.50	19.50
-GCC	65	35.50	19.50	18.50	26.50
-GCC	66	34.00	25.00	15.00	26.00
-GCC	67	37.00	23.00	19.00	21.00
-GCC	68	36.50	29.50	13.50	20.50
-GCC	69	38.50	19.50	20.50	21.50
-GCC	70	38.50	16.50	18.50	26.50
-GCC	71	25.50	38.50	21.50	14.50
-GCC	72	29.00	29.00	25.00	17.00
-GCC	73	32.50	20.50	21.50	25.50
-GCC	74	28.50	32.50	12.50	26.50
-GCC	75	41.50	12.50	18.50	27.50
-GCC	76	24.50	29.50	23.50	22.50
-GCC	77	36.00	21.00	18.00	25.00
-GCC	78	27.00	34.00	22.00	17.00
-GCC	79	21.50	26.50	25.50	26.50
-GCC	80	34.00	19.00	28.00	19.00
-GCC	81	17.00	26.00	26.00	31.00
-GCC	82	31.00	30.00	23.00	16.00
-GCC	83	31.50	26.50	12.50	29.50
-GCC	84	19.00	41.00	21.00	19.00
-GCC	85	37.50	24.50	16.50	21.50
-GCC	86	15.00	48.00	15.00	22.00
-GCC	87	41.00	16.00	18.00	25.00
-GCC	88	23.50	27.50	27.50	21.50
-GCC	89	26.50	27.50	26.50	19.50
-GCC	90	18.50	23.50	24.50	33.50
-GCC	91	27.00	32.00	22.00	19.00
-GCC	92	23.50	17.50	27.50	31.50
-GCC	93	25.50	37.50	15.50	21.50
-GCC	94	27.00	17.00	24.00	32.00
-GCC	95	26.50	37.50	14.50	21.50
-GCC	96	29.50	25.50	16.50	28.50
-GCC	97	29.00	31.00	21.00	19.00
-GCC	98	18.00	33.00	22.00	27.00
-GCC	99	24.50	33.50	24.50	17.50
-GCC	100	24.50	16.50	24.50	34.50
-GCC	101	25.00	40.00	19.00	16.00
-GCC	102	17.50	17.50	32.50	32.50
-GCC	103	31.00	26.00	16.00	27.00
-GCC	104	26.50	29.50	20.50	23.50
-GCC	105	34.00	33.00	21.00	12.00
-GCC	106	23.00	31.00	26.00	20.00
-GCC	107	17.50	35.50	23.50	23.50
-GCC	108	24.50	30.50	23.50	21.50
-GCC	109	17.00	31.00	22.00	30.00
-GCC	110	16.00	35.00	24.00	25.00
-GCC	111	24.00	32.00	23.00	21.00
-GCC	112	37.00	28.00	16.00	19.00
-GCC	113	19.50	22.50	32.50	25.50
-GCC	114	17.00	31.00	35.00	17.00
-GCC	115	29.50	24.50	23.50	22.50
-GCC	116	22.00	30.00	34.00	14.00
-GCC	117	27.00	23.00	19.00	31.00
-GCC	118	25.50	14.50	34.50	25.50
-GCC	119	22.50	34.50	20.50	22.50
-GCC	120	17.50	24.50	26.50	31.50
-GCC	121	27.50	33.50	22.50	16.50
-GCC	122	17.00	23.00	25.00	35.00
-GCC	123	23.50	46.50	11.50	18.50
-GCC	124	9.00	32.00	34.00	25.00
-GCC	125	24.00	27.00	19.00	30.00
-GCC	126	26.00	17.00	28.00	29.00
-GCC	127	26.50	16.50	21.50	35.50
-GCC	128	18.00	34.00	31.00	17.00
-GCC	129	25.50	25.50	27.50	21.50
-GCC	130	25.00	20.00	22.00	33.00
-GCC	131	17.50	39.50	24.50	18.50
-GCC	132	21.00	28.00	23.00	28.00
-GCC	133	13.50	31.50	35.50	19.50
-GCC	134	24.50	19.50	30.50	25.50
-GCC	135	16.50	23.50	30.50	29.50
-GCC	136	28.00	32.00	15.00	25.00
-GCC	137	22.50	21.50	30.50	25.50
-GCC	138	14.50	34.50	24.50	26.50
-GCC	139	20.50	29.50	24.50	25.50
-GCC	140	17.00	23.00	30.00	30.00
-GCC	141	20.50	23.50	25.50	30.50
-GCC	142	18.00	29.00	38.00	15.00
-GCC	143	22.00	24.00	27.00	27.00
-GCC	144	21.50	30.50	26.50	21.50
-GCC	145	22.00	21.00	29.00	28.00
-GCC	146	25.00	16.00	39.00	20.00
-GCC	147	26.50	22.50	30.50	20.50
-GCC	148	12.50	28.50	36.50	22.50
-GCC	149	26.50	23.50	23.50	26.50
-GCC	150	14.00	29.00	24.00	33.00
-GCC	151	19.50	30.50	32.50	17.50
-GCC	152	18.50	17.50	29.50	34.50
-GCC	153	22.50	22.50	31.50	23.50
-GCC	154	22.00	21.00	29.00	28.00
-GCC	155	21.00	26.00	19.00	34.00
-GCC	156	14.50	23.50	35.50	26.50
-GCC	157	22.00	31.00	23.00	24.00
-GCC	158	22.50	29.50	24.50	23.50
-GCC	159	17.50	12.50	46.50	23.50
-GCC	160	24.50	26.50	26.50	22.50
-GCC	161	13.00	23.00	45.00	19.00
-GCC	162	31.50	16.50	22.50	29.50
-GCC	163	19.50	21.50	35.50	23.50
-GCC	164	29.00	18.00	21.00	32.00
-GCC	165	14.50	17.50	35.50	32.50
-GCC	166	17.50	37.50	28.50	16.50
-GCC	167	16.50	21.50	31.50	30.50
-GCC	168	14.00	25.00	30.00	31.00
-GCC	169	18.50	20.50	23.50	37.50
-GCC	170	19.00	23.00	28.00	30.00
-GCC	171	20.00	28.00	33.00	19.00
-GCC	172	19.00	20.00	32.00	29.00
-GCC	173	24.50	16.50	33.50	25.50
-GCC	174	17.50	23.50	33.50	25.50
-GCC	175	33.50	17.50	35.50	13.50
-GCC	176	16.50	32.50	28.50	22.50
-GCC	177	19.00	22.00	27.00	32.00
-GCC	178	16.00	26.00	30.00	28.00
-GCC	179	18.00	18.00	22.00	42.00
-GCC	180	21.00	22.00	34.00	23.00
-GCC	181	20.50	19.50	35.50	24.50
-GCC	182	32.50	18.50	22.50	26.50
-GCC	183	24.50	13.50	28.50	33.50
-GCC	184	15.00	29.00	30.00	26.00
-GCC	185	15.00	32.00	33.00	20.00
-GCC	186	22.50	23.50	34.50	19.50
-GCC	187	19.00	14.00	40.00	27.00
-GCC	188	27.50	21.50	27.50	23.50
-GCC	189	17.00	22.00	34.00	27.00
-GCC	190	23.00	30.00	23.00	24.00
-GCC	191	25.00	22.00	28.00	25.00
-GCC	192	34.50	24.50	13.50	27.50
-GCC	193	18.50	25.50	25.50	30.50
-GCC	194	18.50	33.50	24.50	23.50
-GCC	195	16.00	26.00	23.00	35.00
-GCC	196	21.50	25.50	24.50	28.50
-GCC	197	20.00	21.00	23.00	36.00
-GCC	198	17.00	21.00	37.00	25.00
-GCC	199	20.50	18.50	25.50	35.50
-GCC	200	21.00	29.00	21.00	29.00
-GCC	201	27.00	21.00	23.00	29.00
-GCC	202	21.50	24.50	19.50	34.50
-GCC	203	21.50	24.50	26.50	27.50
-GCC	204	27.00	29.00	24.00	20.00
-GCC	205	19.50	21.50	22.50	36.50
-GCC	206	26.50	24.50	21.50	27.50
-GCC	207	22.50	21.50	19.50	36.50
-GCC	208	14.00	35.00	29.00	22.00
-GCC	209	16.00	23.00	12.00	49.00
-GCC	210	18.50	19.50	40.50	21.50
-GCC	211	26.00	20.00	22.00	32.00
-GCC	212	21.00	31.00	18.00	30.00
-GCC	213	24.00	15.00	31.00	30.00
-GCC	214	17.50	24.50	25.50	32.50
-GCC	215	26.00	24.00	23.00	27.00
-GCC	216	21.50	17.50	25.50	35.50
-GCC	217	26.00	29.00	17.00	28.00
-GCC	218	20.00	27.00	21.00	32.00
-GCC	219	17.00	21.00	21.00	41.00
-GCC	220	25.50	23.50	23.50	27.50
-GCC	221	21.50	23.50	20.50	34.50
-GCC	222	21.50	21.50	18.50	38.50
-GCC	223	20.00	27.00	28.00	25.00
-GCC	224	22.50	22.50	24.50	30.50
-GCC	225	14.50	35.50	30.50	19.50
-GCC	226	20.00	23.00	26.00	31.00
-GCC	227	20.50	24.50	23.50	31.50
-GCC	228	33.00	19.00	26.00	22.00
-GCC	229	22.50	24.50	18.50	34.50
-GCC	230	21.00	32.00	16.00	31.00
-GCC	231	23.00	28.00	30.00	19.00
-GCC	232	23.50	21.50	12.50	42.50
-GCC	233	21.00	27.00	25.00	27.00
-GCC	234	16.50	27.50	22.50	33.50
-GCC	235	20.00	15.00	28.00	37.00
-GCC	236	28.00	23.00	21.00	28.00
-GCC	237	20.50	19.50	22.50	37.50
-GCC	238	21.50	29.50	24.50	24.50
-GCC	239	20.00	8.00	17.00	55.00
-GCC	240	28.00	24.00	16.00	32.00
-GCC	241	22.50	22.50	16.50	38.50
-GCC	242	29.00	25.00	13.00	33.00
-GCC	243	22.50	15.50	23.50	38.50
-GCC	244	20.50	23.50	16.50	39.50
-GCC	245	28.00	23.00	19.00	30.00
-GCC	246	21.00	29.00	25.00	25.00
-GCC	247	32.00	14.00	13.00	41.00
-GCC	248	18.00	18.00	25.00	39.00
-GCC	249	25.00	23.00	21.00	31.00
-GCC	250	27.50	22.50	17.50	32.50
-GCC	251	13.50	20.50	36.50	29.50
+# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
+GCC	1	21.94	30.10	34.18	13.78	2.04	0.00
+GCC	2	30.00	16.00	11.00	43.00	0.00	0.00
+GCC	3	33.00	25.00	9.00	33.00	0.00	0.00
+GCC	4	17.00	29.00	13.00	41.00	0.00	0.00
+GCC	5	37.00	22.00	12.00	29.00	0.00	0.00
+GCC	6	36.00	26.00	17.00	21.00	0.00	0.00
+GCC	7	29.50	13.50	31.50	25.50	0.00	0.00
+GCC	8	50.50	14.50	19.50	15.50	0.00	0.00
+GCC	9	17.00	33.00	18.00	32.00	0.00	0.00
+GCC	10	37.00	14.00	21.00	28.00	0.00	0.00
+GCC	11	20.50	14.50	29.50	35.50	0.00	0.00
+GCC	12	30.00	24.00	22.00	24.00	0.00	0.00
+GCC	13	27.00	15.00	21.00	37.00	0.00	0.00
+GCC	14	24.24	22.22	26.26	27.27	1.01	0.00
+GCC	15	25.50	20.50	24.50	29.50	0.00	0.00
+GCC	16	31.00	15.00	20.00	34.00	0.00	0.00
+GCC	17	28.00	25.00	14.00	33.00	0.00	0.00
+GCC	18	30.50	28.50	19.50	21.50	0.00	0.00
+GCC	19	29.00	26.00	21.00	24.00	0.00	0.00
+GCC	20	22.50	23.50	17.50	36.50	0.00	0.00
+GCC	21	35.50	17.50	19.50	27.50	0.00	0.00
+GCC	22	37.50	28.50	15.50	18.50	0.00	0.00
+GCC	23	31.31	19.19	13.13	36.36	1.01	0.00
+GCC	24	37.00	12.00	22.00	29.00	0.00	0.00
+GCC	25	35.50	22.50	17.50	24.50	0.00	0.00
+GCC	26	33.50	18.50	15.50	32.50	0.00	0.00
+GCC	27	34.50	14.50	25.50	25.50	0.00	0.00
+GCC	28	31.00	14.00	24.00	31.00	0.00	0.00
+GCC	29	30.00	27.00	24.00	19.00	0.00	0.00
+GCC	30	31.00	20.00	14.00	35.00	0.00	0.00
+GCC	31	33.50	29.50	13.50	23.50	0.00	0.00
+GCC	32	42.50	20.50	19.50	17.50	0.00	0.00
+GCC	33	25.50	23.50	14.50	36.50	0.00	0.00
+GCC	34	39.50	16.50	20.50	23.50	0.00	0.00
+GCC	35	32.50	23.50	21.50	22.50	0.00	0.00
+GCC	36	42.00	25.00	16.00	17.00	0.00	0.00
+GCC	37	38.00	17.00	19.00	26.00	0.00	0.00
+GCC	38	24.00	26.00	25.00	25.00	0.00	0.00
+GCC	39	22.50	41.50	18.50	17.50	0.00	0.00
+GCC	40	32.00	16.00	21.00	31.00	0.00	0.00
+GCC	41	33.00	28.00	19.00	20.00	0.00	0.00
+GCC	42	30.50	25.50	19.50	24.50	0.00	0.00
+GCC	43	35.00	29.00	15.00	21.00	0.00	0.00
+GCC	44	20.00	27.00	22.00	31.00	0.00	0.00
+GCC	45	40.50	21.50	21.50	16.50	0.00	0.00
+GCC	46	26.50	20.50	22.50	30.50	0.00	0.00
+GCC	47	38.50	29.50	16.50	15.50	0.00	0.00
+GCC	48	27.50	24.50	17.50	30.50	0.00	0.00
+GCC	49	28.50	32.50	10.50	28.50	0.00	0.00
+GCC	50	46.50	20.50	9.50	23.50	0.00	0.00
+GCC	51	34.50	28.50	13.50	23.50	0.00	0.00
+GCC	52	41.50	23.50	20.50	14.50	0.00	0.00
+GCC	53	20.00	28.00	26.00	26.00	0.00	0.00
+GCC	54	31.50	18.50	24.50	25.50	0.00	0.00
+GCC	55	30.50	22.50	16.50	30.50	0.00	0.00
+GCC	56	33.50	22.50	13.50	30.50	0.00	0.00
+GCC	57	23.00	24.00	23.00	30.00	0.00	0.00
+GCC	58	25.00	37.00	19.00	19.00	0.00	0.00
+GCC	59	34.00	23.00	24.00	19.00	0.00	0.00
+GCC	60	29.00	28.00	17.00	26.00	0.00	0.00
+GCC	61	25.50	23.50	24.50	26.50	0.00	0.00
+GCC	62	31.50	22.50	16.50	29.50	0.00	0.00
+GCC	63	27.50	28.50	25.50	18.50	0.00	0.00
+GCC	64	33.50	21.50	25.50	19.50	0.00	0.00
+GCC	65	35.50	19.50	18.50	26.50	0.00	0.00
+GCC	66	34.00	25.00	15.00	26.00	0.00	0.00
+GCC	67	37.00	23.00	19.00	21.00	0.00	0.00
+GCC	68	36.50	29.50	13.50	20.50	0.00	0.00
+GCC	69	38.50	19.50	20.50	21.50	0.00	0.00
+GCC	70	38.50	16.50	18.50	26.50	0.00	0.00
+GCC	71	25.50	38.50	21.50	14.50	0.00	0.00
+GCC	72	29.00	29.00	25.00	17.00	0.00	0.00
+GCC	73	32.50	20.50	21.50	25.50	0.00	0.00
+GCC	74	28.50	32.50	12.50	26.50	0.00	0.00
+GCC	75	41.50	12.50	18.50	27.50	0.00	0.00
+GCC	76	24.50	29.50	23.50	22.50	0.00	0.00
+GCC	77	36.00	21.00	18.00	25.00	0.00	0.00
+GCC	78	27.00	34.00	22.00	17.00	0.00	0.00
+GCC	79	21.50	26.50	25.50	26.50	0.00	0.00
+GCC	80	34.00	19.00	28.00	19.00	0.00	0.00
+GCC	81	17.00	26.00	26.00	31.00	0.00	0.00
+GCC	82	31.00	30.00	23.00	16.00	0.00	0.00
+GCC	83	31.50	26.50	12.50	29.50	0.00	0.00
+GCC	84	19.00	41.00	21.00	19.00	0.00	0.00
+GCC	85	37.50	24.50	16.50	21.50	0.00	0.00
+GCC	86	15.00	48.00	15.00	22.00	0.00	0.00
+GCC	87	41.00	16.00	18.00	25.00	0.00	0.00
+GCC	88	23.50	27.50	27.50	21.50	0.00	0.00
+GCC	89	26.50	27.50	26.50	19.50	0.00	0.00
+GCC	90	18.50	23.50	24.50	33.50	0.00	0.00
+GCC	91	27.00	32.00	22.00	19.00	0.00	0.00
+GCC	92	23.50	17.50	27.50	31.50	0.00	0.00
+GCC	93	25.50	37.50	15.50	21.50	0.00	0.00
+GCC	94	27.00	17.00	24.00	32.00	0.00	0.00
+GCC	95	26.77	37.88	14.65	20.71	1.01	0.00
+GCC	96	29.50	25.50	16.50	28.50	0.00	0.00
+GCC	97	29.00	31.00	21.00	19.00	0.00	0.00
+GCC	98	18.18	33.33	22.22	26.26	1.01	0.00
+GCC	99	24.50	33.50	24.50	17.50	0.00	0.00
+GCC	100	24.50	16.50	24.50	34.50	0.00	0.00
+GCC	101	25.00	40.00	19.00	16.00	0.00	0.00
+GCC	102	17.50	17.50	32.50	32.50	0.00	0.00
+GCC	103	31.00	26.00	16.00	27.00	0.00	0.00
+GCC	104	26.50	29.50	20.50	23.50	0.00	0.00
+GCC	105	34.00	33.00	21.00	12.00	0.00	0.00
+GCC	106	23.00	31.00	26.00	20.00	0.00	0.00
+GCC	107	17.68	35.86	23.74	22.73	1.01	0.00
+GCC	108	24.75	30.81	23.74	20.71	1.01	0.00
+GCC	109	17.00	31.00	22.00	30.00	0.00	0.00
+GCC	110	16.16	35.35	24.24	24.24	1.01	0.00
+GCC	111	24.24	32.32	23.23	20.20	1.01	0.00
+GCC	112	37.37	28.28	16.16	18.18	1.01	0.00
+GCC	113	19.70	22.73	32.83	24.75	1.01	0.00
+GCC	114	17.00	31.00	35.00	17.00	0.00	0.00
+GCC	115	29.50	24.50	23.50	22.50	0.00	0.00
+GCC	116	22.00	30.00	34.00	14.00	0.00	0.00
+GCC	117	27.00	23.00	19.00	31.00	0.00	0.00
+GCC	118	25.50	14.50	34.50	25.50	0.00	0.00
+GCC	119	22.50	34.50	20.50	22.50	0.00	0.00
+GCC	120	17.50	24.50	26.50	31.50	0.00	0.00
+GCC	121	27.78	33.84	22.73	15.66	1.01	0.00
+GCC	122	17.00	23.00	25.00	35.00	0.00	0.00
+GCC	123	23.50	46.50	11.50	18.50	0.00	0.00
+GCC	124	9.00	32.00	34.00	25.00	0.00	0.00
+GCC	125	24.00	27.00	19.00	30.00	0.00	0.00
+GCC	126	26.00	17.00	28.00	29.00	0.00	0.00
+GCC	127	26.50	16.50	21.50	35.50	0.00	0.00
+GCC	128	18.00	34.00	31.00	17.00	0.00	0.00
+GCC	129	25.50	25.50	27.50	21.50	0.00	0.00
+GCC	130	25.00	20.00	22.00	33.00	0.00	0.00
+GCC	131	17.50	39.50	24.50	18.50	0.00	0.00
+GCC	132	21.00	28.00	23.00	28.00	0.00	0.00
+GCC	133	13.50	31.50	35.50	19.50	0.00	0.00
+GCC	134	24.50	19.50	30.50	25.50	0.00	0.00
+GCC	135	16.50	23.50	30.50	29.50	0.00	0.00
+GCC	136	28.00	32.00	15.00	25.00	0.00	0.00
+GCC	137	22.50	21.50	30.50	25.50	0.00	0.00
+GCC	138	14.50	34.50	24.50	26.50	0.00	0.00
+GCC	139	20.50	29.50	24.50	25.50	0.00	0.00
+GCC	140	17.00	23.00	30.00	30.00	0.00	0.00
+GCC	141	20.50	23.50	25.50	30.50	0.00	0.00
+GCC	142	18.00	29.00	38.00	15.00	0.00	0.00
+GCC	143	22.00	24.00	27.00	27.00	0.00	0.00
+GCC	144	21.50	30.50	26.50	21.50	0.00	0.00
+GCC	145	22.00	21.00	29.00	28.00	0.00	0.00
+GCC	146	25.00	16.00	39.00	20.00	0.00	0.00
+GCC	147	26.50	22.50	30.50	20.50	0.00	0.00
+GCC	148	12.50	28.50	36.50	22.50	0.00	0.00
+GCC	149	26.50	23.50	23.50	26.50	0.00	0.00
+GCC	150	14.00	29.00	24.00	33.00	0.00	0.00
+GCC	151	19.50	30.50	32.50	17.50	0.00	0.00
+GCC	152	18.50	17.50	29.50	34.50	0.00	0.00
+GCC	153	22.50	22.50	31.50	23.50	0.00	0.00
+GCC	154	22.00	21.00	29.00	28.00	0.00	0.00
+GCC	155	21.00	26.00	19.00	34.00	0.00	0.00
+GCC	156	14.50	23.50	35.50	26.50	0.00	0.00
+GCC	157	22.00	31.00	23.00	24.00	0.00	0.00
+GCC	158	22.50	29.50	24.50	23.50	0.00	0.00
+GCC	159	17.50	12.50	46.50	23.50	0.00	0.00
+GCC	160	24.50	26.50	26.50	22.50	0.00	0.00
+GCC	161	13.00	23.00	45.00	19.00	0.00	0.00
+GCC	162	31.50	16.50	22.50	29.50	0.00	0.00
+GCC	163	19.50	21.50	35.50	23.50	0.00	0.00
+GCC	164	29.00	18.00	21.00	32.00	0.00	0.00
+GCC	165	14.50	17.50	35.50	32.50	0.00	0.00
+GCC	166	17.50	37.50	28.50	16.50	0.00	0.00
+GCC	167	16.50	21.50	31.50	30.50	0.00	0.00
+GCC	168	14.00	25.00	30.00	31.00	0.00	0.00
+GCC	169	18.50	20.50	23.50	37.50	0.00	0.00
+GCC	170	19.00	23.00	28.00	30.00	0.00	0.00
+GCC	171	20.00	28.00	33.00	19.00	0.00	0.00
+GCC	172	19.00	20.00	32.00	29.00	0.00	0.00
+GCC	173	24.50	16.50	33.50	25.50	0.00	0.00
+GCC	174	17.50	23.50	33.50	25.50	0.00	0.00
+GCC	175	33.50	17.50	35.50	13.50	0.00	0.00
+GCC	176	16.50	32.50	28.50	22.50	0.00	0.00
+GCC	177	19.00	22.00	27.00	32.00	0.00	0.00
+GCC	178	16.00	26.00	30.00	28.00	0.00	0.00
+GCC	179	18.00	18.00	22.00	42.00	0.00	0.00
+GCC	180	21.00	22.00	34.00	23.00	0.00	0.00
+GCC	181	20.50	19.50	35.50	24.50	0.00	0.00
+GCC	182	32.50	18.50	22.50	26.50	0.00	0.00
+GCC	183	24.50	13.50	28.50	33.50	0.00	0.00
+GCC	184	15.00	29.00	30.00	26.00	0.00	0.00
+GCC	185	15.00	32.00	33.00	20.00	0.00	0.00
+GCC	186	22.50	23.50	34.50	19.50	0.00	0.00
+GCC	187	19.00	14.00	40.00	27.00	0.00	0.00
+GCC	188	27.50	21.50	27.50	23.50	0.00	0.00
+GCC	189	17.00	22.00	34.00	27.00	0.00	0.00
+GCC	190	23.00	30.00	23.00	24.00	0.00	0.00
+GCC	191	25.00	22.00	28.00	25.00	0.00	0.00
+GCC	192	34.50	24.50	13.50	27.50	0.00	0.00
+GCC	193	18.50	25.50	25.50	30.50	0.00	0.00
+GCC	194	18.50	33.50	24.50	23.50	0.00	0.00
+GCC	195	16.00	26.00	23.00	35.00	0.00	0.00
+GCC	196	21.50	25.50	24.50	28.50	0.00	0.00
+GCC	197	20.00	21.00	23.00	36.00	0.00	0.00
+GCC	198	17.00	21.00	37.00	25.00	0.00	0.00
+GCC	199	20.50	18.50	25.50	35.50	0.00	0.00
+GCC	200	21.00	29.00	21.00	29.00	0.00	0.00
+GCC	201	27.00	21.00	23.00	29.00	0.00	0.00
+GCC	202	21.50	24.50	19.50	34.50	0.00	0.00
+GCC	203	21.50	24.50	26.50	27.50	0.00	0.00
+GCC	204	27.00	29.00	24.00	20.00	0.00	0.00
+GCC	205	19.50	21.50	22.50	36.50	0.00	0.00
+GCC	206	26.50	24.50	21.50	27.50	0.00	0.00
+GCC	207	22.50	21.50	19.50	36.50	0.00	0.00
+GCC	208	14.00	35.00	29.00	22.00	0.00	0.00
+GCC	209	16.00	23.00	12.00	49.00	0.00	0.00
+GCC	210	18.50	19.50	40.50	21.50	0.00	0.00
+GCC	211	26.00	20.00	22.00	32.00	0.00	0.00
+GCC	212	21.00	31.00	18.00	30.00	0.00	0.00
+GCC	213	24.00	15.00	31.00	30.00	0.00	0.00
+GCC	214	17.50	24.50	25.50	32.50	0.00	0.00
+GCC	215	26.00	24.00	23.00	27.00	0.00	0.00
+GCC	216	21.50	17.50	25.50	35.50	0.00	0.00
+GCC	217	26.00	29.00	17.00	28.00	0.00	0.00
+GCC	218	20.00	27.00	21.00	32.00	0.00	0.00
+GCC	219	17.00	21.00	21.00	41.00	0.00	0.00
+GCC	220	25.50	23.50	23.50	27.50	0.00	0.00
+GCC	221	21.50	23.50	20.50	34.50	0.00	0.00
+GCC	222	21.50	21.50	18.50	38.50	0.00	0.00
+GCC	223	20.00	27.00	28.00	25.00	0.00	0.00
+GCC	224	22.50	22.50	24.50	30.50	0.00	0.00
+GCC	225	14.50	35.50	30.50	19.50	0.00	0.00
+GCC	226	20.00	23.00	26.00	31.00	0.00	0.00
+GCC	227	20.50	24.50	23.50	31.50	0.00	0.00
+GCC	228	33.00	19.00	26.00	22.00	0.00	0.00
+GCC	229	22.50	24.50	18.50	34.50	0.00	0.00
+GCC	230	21.00	32.00	16.00	31.00	0.00	0.00
+GCC	231	23.00	28.00	30.00	19.00	0.00	0.00
+GCC	232	23.50	21.50	12.50	42.50	0.00	0.00
+GCC	233	21.00	27.00	25.00	27.00	0.00	0.00
+GCC	234	16.50	27.50	22.50	33.50	0.00	0.00
+GCC	235	20.00	15.00	28.00	37.00	0.00	0.00
+GCC	236	28.00	23.00	21.00	28.00	0.00	0.00
+GCC	237	20.50	19.50	22.50	37.50	0.00	0.00
+GCC	238	21.50	29.50	24.50	24.50	0.00	0.00
+GCC	239	20.00	8.00	17.00	55.00	0.00	0.00
+GCC	240	28.00	24.00	16.00	32.00	0.00	0.00
+GCC	241	22.50	22.50	16.50	38.50	0.00	0.00
+GCC	242	29.00	25.00	13.00	33.00	0.00	0.00
+GCC	243	22.50	15.50	23.50	38.50	0.00	0.00
+GCC	244	20.50	23.50	16.50	39.50	0.00	0.00
+GCC	245	28.00	23.00	19.00	30.00	0.00	0.00
+GCC	246	21.00	29.00	25.00	25.00	0.00	0.00
+GCC	247	32.00	14.00	13.00	41.00	0.00	0.00
+GCC	248	18.00	18.00	25.00	39.00	0.00	0.00
+GCC	249	25.00	23.00	21.00	31.00	0.00	0.00
+GCC	250	27.50	22.50	17.50	32.50	0.00	0.00
+GCC	251	13.50	20.50	36.50	29.50	0.00	0.00
 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
 RL	251	200
diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2/gcc.tab
--- a/test-data/samtools_stats_out2/gcc.tab	Wed Nov 11 12:55:15 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,252 +0,0 @@
-# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)
-1	21.50	29.50	33.50	15.50
-2	30.00	16.00	11.00	43.00
-3	33.00	25.00	9.00	33.00
-4	17.00	29.00	13.00	41.00
-5	37.00	22.00	12.00	29.00
-6	36.00	26.00	17.00	21.00
-7	29.50	13.50	31.50	25.50
-8	50.50	14.50	19.50	15.50
-9	17.00	33.00	18.00	32.00
-10	37.00	14.00	21.00	28.00
-11	20.50	14.50	29.50	35.50
-12	30.00	24.00	22.00	24.00
-13	27.00	15.00	21.00	37.00
-14	24.00	22.00	26.00	28.00
-15	25.50	20.50	24.50	29.50
-16	31.00	15.00	20.00	34.00
-17	28.00	25.00	14.00	33.00
-18	30.50	28.50	19.50	21.50
-19	29.00	26.00	21.00	24.00
-20	22.50	23.50	17.50	36.50
-21	35.50	17.50	19.50	27.50
-22	37.50	28.50	15.50	18.50
-23	31.00	19.00	13.00	37.00
-24	37.00	12.00	22.00	29.00
-25	35.50	22.50	17.50	24.50
-26	33.50	18.50	15.50	32.50
-27	34.50	14.50	25.50	25.50
-28	31.00	14.00	24.00	31.00
-29	30.00	27.00	24.00	19.00
-30	31.00	20.00	14.00	35.00
-31	33.50	29.50	13.50	23.50
-32	42.50	20.50	19.50	17.50
-33	25.50	23.50	14.50	36.50
-34	39.50	16.50	20.50	23.50
-35	32.50	23.50	21.50	22.50
-36	42.00	25.00	16.00	17.00
-37	38.00	17.00	19.00	26.00
-38	24.00	26.00	25.00	25.00
-39	22.50	41.50	18.50	17.50
-40	32.00	16.00	21.00	31.00
-41	33.00	28.00	19.00	20.00
-42	30.50	25.50	19.50	24.50
-43	35.00	29.00	15.00	21.00
-44	20.00	27.00	22.00	31.00
-45	40.50	21.50	21.50	16.50
-46	26.50	20.50	22.50	30.50
-47	38.50	29.50	16.50	15.50
-48	27.50	24.50	17.50	30.50
-49	28.50	32.50	10.50	28.50
-50	46.50	20.50	9.50	23.50
-51	34.50	28.50	13.50	23.50
-52	41.50	23.50	20.50	14.50
-53	20.00	28.00	26.00	26.00
-54	31.50	18.50	24.50	25.50
-55	30.50	22.50	16.50	30.50
-56	33.50	22.50	13.50	30.50
-57	23.00	24.00	23.00	30.00
-58	25.00	37.00	19.00	19.00
-59	34.00	23.00	24.00	19.00
-60	29.00	28.00	17.00	26.00
-61	25.50	23.50	24.50	26.50
-62	31.50	22.50	16.50	29.50
-63	27.50	28.50	25.50	18.50
-64	33.50	21.50	25.50	19.50
-65	35.50	19.50	18.50	26.50
-66	34.00	25.00	15.00	26.00
-67	37.00	23.00	19.00	21.00
-68	36.50	29.50	13.50	20.50
-69	38.50	19.50	20.50	21.50
-70	38.50	16.50	18.50	26.50
-71	25.50	38.50	21.50	14.50
-72	29.00	29.00	25.00	17.00
-73	32.50	20.50	21.50	25.50
-74	28.50	32.50	12.50	26.50
-75	41.50	12.50	18.50	27.50
-76	24.50	29.50	23.50	22.50
-77	36.00	21.00	18.00	25.00
-78	27.00	34.00	22.00	17.00
-79	21.50	26.50	25.50	26.50
-80	34.00	19.00	28.00	19.00
-81	17.00	26.00	26.00	31.00
-82	31.00	30.00	23.00	16.00
-83	31.50	26.50	12.50	29.50
-84	19.00	41.00	21.00	19.00
-85	37.50	24.50	16.50	21.50
-86	15.00	48.00	15.00	22.00
-87	41.00	16.00	18.00	25.00
-88	23.50	27.50	27.50	21.50
-89	26.50	27.50	26.50	19.50
-90	18.50	23.50	24.50	33.50
-91	27.00	32.00	22.00	19.00
-92	23.50	17.50	27.50	31.50
-93	25.50	37.50	15.50	21.50
-94	27.00	17.00	24.00	32.00
-95	26.50	37.50	14.50	21.50
-96	29.50	25.50	16.50	28.50
-97	29.00	31.00	21.00	19.00
-98	18.00	33.00	22.00	27.00
-99	24.50	33.50	24.50	17.50
-100	24.50	16.50	24.50	34.50
-101	25.00	40.00	19.00	16.00
-102	17.50	17.50	32.50	32.50
-103	31.00	26.00	16.00	27.00
-104	26.50	29.50	20.50	23.50
-105	34.00	33.00	21.00	12.00
-106	23.00	31.00	26.00	20.00
-107	17.50	35.50	23.50	23.50
-108	24.50	30.50	23.50	21.50
-109	17.00	31.00	22.00	30.00
-110	16.00	35.00	24.00	25.00
-111	24.00	32.00	23.00	21.00
-112	37.00	28.00	16.00	19.00
-113	19.50	22.50	32.50	25.50
-114	17.00	31.00	35.00	17.00
-115	29.50	24.50	23.50	22.50
-116	22.00	30.00	34.00	14.00
-117	27.00	23.00	19.00	31.00
-118	25.50	14.50	34.50	25.50
-119	22.50	34.50	20.50	22.50
-120	17.50	24.50	26.50	31.50
-121	27.50	33.50	22.50	16.50
-122	17.00	23.00	25.00	35.00
-123	23.50	46.50	11.50	18.50
-124	9.00	32.00	34.00	25.00
-125	24.00	27.00	19.00	30.00
-126	26.00	17.00	28.00	29.00
-127	26.50	16.50	21.50	35.50
-128	18.00	34.00	31.00	17.00
-129	25.50	25.50	27.50	21.50
-130	25.00	20.00	22.00	33.00
-131	17.50	39.50	24.50	18.50
-132	21.00	28.00	23.00	28.00
-133	13.50	31.50	35.50	19.50
-134	24.50	19.50	30.50	25.50
-135	16.50	23.50	30.50	29.50
-136	28.00	32.00	15.00	25.00
-137	22.50	21.50	30.50	25.50
-138	14.50	34.50	24.50	26.50
-139	20.50	29.50	24.50	25.50
-140	17.00	23.00	30.00	30.00
-141	20.50	23.50	25.50	30.50
-142	18.00	29.00	38.00	15.00
-143	22.00	24.00	27.00	27.00
-144	21.50	30.50	26.50	21.50
-145	22.00	21.00	29.00	28.00
-146	25.00	16.00	39.00	20.00
-147	26.50	22.50	30.50	20.50
-148	12.50	28.50	36.50	22.50
-149	26.50	23.50	23.50	26.50
-150	14.00	29.00	24.00	33.00
-151	19.50	30.50	32.50	17.50
-152	18.50	17.50	29.50	34.50
-153	22.50	22.50	31.50	23.50
-154	22.00	21.00	29.00	28.00
-155	21.00	26.00	19.00	34.00
-156	14.50	23.50	35.50	26.50
-157	22.00	31.00	23.00	24.00
-158	22.50	29.50	24.50	23.50
-159	17.50	12.50	46.50	23.50
-160	24.50	26.50	26.50	22.50
-161	13.00	23.00	45.00	19.00
-162	31.50	16.50	22.50	29.50
-163	19.50	21.50	35.50	23.50
-164	29.00	18.00	21.00	32.00
-165	14.50	17.50	35.50	32.50
-166	17.50	37.50	28.50	16.50
-167	16.50	21.50	31.50	30.50
-168	14.00	25.00	30.00	31.00
-169	18.50	20.50	23.50	37.50
-170	19.00	23.00	28.00	30.00
-171	20.00	28.00	33.00	19.00
-172	19.00	20.00	32.00	29.00
-173	24.50	16.50	33.50	25.50
-174	17.50	23.50	33.50	25.50
-175	33.50	17.50	35.50	13.50
-176	16.50	32.50	28.50	22.50
-177	19.00	22.00	27.00	32.00
-178	16.00	26.00	30.00	28.00
-179	18.00	18.00	22.00	42.00
-180	21.00	22.00	34.00	23.00
-181	20.50	19.50	35.50	24.50
-182	32.50	18.50	22.50	26.50
-183	24.50	13.50	28.50	33.50
-184	15.00	29.00	30.00	26.00
-185	15.00	32.00	33.00	20.00
-186	22.50	23.50	34.50	19.50
-187	19.00	14.00	40.00	27.00
-188	27.50	21.50	27.50	23.50
-189	17.00	22.00	34.00	27.00
-190	23.00	30.00	23.00	24.00
-191	25.00	22.00	28.00	25.00
-192	34.50	24.50	13.50	27.50
-193	18.50	25.50	25.50	30.50
-194	18.50	33.50	24.50	23.50
-195	16.00	26.00	23.00	35.00
-196	21.50	25.50	24.50	28.50
-197	20.00	21.00	23.00	36.00
-198	17.00	21.00	37.00	25.00
-199	20.50	18.50	25.50	35.50
-200	21.00	29.00	21.00	29.00
-201	27.00	21.00	23.00	29.00
-202	21.50	24.50	19.50	34.50
-203	21.50	24.50	26.50	27.50
-204	27.00	29.00	24.00	20.00
-205	19.50	21.50	22.50	36.50
-206	26.50	24.50	21.50	27.50
-207	22.50	21.50	19.50	36.50
-208	14.00	35.00	29.00	22.00
-209	16.00	23.00	12.00	49.00
-210	18.50	19.50	40.50	21.50
-211	26.00	20.00	22.00	32.00
-212	21.00	31.00	18.00	30.00
-213	24.00	15.00	31.00	30.00
-214	17.50	24.50	25.50	32.50
-215	26.00	24.00	23.00	27.00
-216	21.50	17.50	25.50	35.50
-217	26.00	29.00	17.00	28.00
-218	20.00	27.00	21.00	32.00
-219	17.00	21.00	21.00	41.00
-220	25.50	23.50	23.50	27.50
-221	21.50	23.50	20.50	34.50
-222	21.50	21.50	18.50	38.50
-223	20.00	27.00	28.00	25.00
-224	22.50	22.50	24.50	30.50
-225	14.50	35.50	30.50	19.50
-226	20.00	23.00	26.00	31.00
-227	20.50	24.50	23.50	31.50
-228	33.00	19.00	26.00	22.00
-229	22.50	24.50	18.50	34.50
-230	21.00	32.00	16.00	31.00
-231	23.00	28.00	30.00	19.00
-232	23.50	21.50	12.50	42.50
-233	21.00	27.00	25.00	27.00
-234	16.50	27.50	22.50	33.50
-235	20.00	15.00	28.00	37.00
-236	28.00	23.00	21.00	28.00
-237	20.50	19.50	22.50	37.50
-238	21.50	29.50	24.50	24.50
-239	20.00	8.00	17.00	55.00
-240	28.00	24.00	16.00	32.00
-241	22.50	22.50	16.50	38.50
-242	29.00	25.00	13.00	33.00
-243	22.50	15.50	23.50	38.50
-244	20.50	23.50	16.50	39.50
-245	28.00	23.00	19.00	30.00
-246	21.00	29.00	25.00	25.00
-247	32.00	14.00	13.00	41.00
-248	18.00	18.00	25.00	39.00
-249	25.00	23.00	21.00	31.00
-250	27.50	22.50	17.50	32.50
-251	13.50	20.50	36.50	29.50
diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2/mpc.tab
--- a/test-data/samtools_stats_out2/mpc.tab	Wed Nov 11 12:55:15 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,253 +0,0 @@
-# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches
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-231	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-232	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-233	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-234	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-235	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-238	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-239	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
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-241	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-242	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
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-244	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-245	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-246	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-247	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0
-248	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	3	2	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	2	0	0	0	3	0	0	0
-249	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	2	0	5	0	0	0	0	0	0	2	0	0	0	0	0	0	0
-250	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	2	0	0	0	2	0	0	0
-251	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	2	2	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	2	0	0	0	0	3	0	0	0
-252	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2/sn.tab
--- a/test-data/samtools_stats_out2/sn.tab	Wed Nov 11 12:55:15 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-# Summary Numbers
-
-raw total sequences:	200
-filtered sequences:	0
-sequences:	200
-is sorted:	1
-1st fragments:	100
-last fragments:	100
-reads mapped:	25
-reads mapped and paired:	0	# paired-end technology bit set + both mates mapped
-reads unmapped:	175
-reads properly paired:	0	# proper-pair bit set
-reads paired:	200	# paired-end technology bit set
-reads duplicated:	0	# PCR or optical duplicate bit set
-reads MQ0:	6	# mapped and MQ=0
-reads QC failed:	0
-non-primary alignments:	0
-total length:	50200	# ignores clipping
-bases mapped:	6275	# ignores clipping
-bases mapped (cigar):	6275	# more accurate
-bases trimmed:	0
-bases duplicated:	0
-mismatches:	591	# from NM fields
-error rate:	9.418327e-02	# mismatches / bases mapped (cigar)
-average length:	251
-maximum length:	251
-average quality:	34.7
-insert size average:	0.0
-insert size standard deviation:	0.0
-inward oriented pairs:	0
-outward oriented pairs:	0
-pairs with other orientation:	0
-pairs on different chromosomes:	0
diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2__gcc.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out2__gcc.tab	Tue May 09 11:19:01 2017 -0400
@@ -0,0 +1,252 @@
+# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)
+1	21.94	30.10	34.18	13.78	2.04	0.00
+2	30.00	16.00	11.00	43.00	0.00	0.00
+3	33.00	25.00	9.00	33.00	0.00	0.00
+4	17.00	29.00	13.00	41.00	0.00	0.00
+5	37.00	22.00	12.00	29.00	0.00	0.00
+6	36.00	26.00	17.00	21.00	0.00	0.00
+7	29.50	13.50	31.50	25.50	0.00	0.00
+8	50.50	14.50	19.50	15.50	0.00	0.00
+9	17.00	33.00	18.00	32.00	0.00	0.00
+10	37.00	14.00	21.00	28.00	0.00	0.00
+11	20.50	14.50	29.50	35.50	0.00	0.00
+12	30.00	24.00	22.00	24.00	0.00	0.00
+13	27.00	15.00	21.00	37.00	0.00	0.00
+14	24.24	22.22	26.26	27.27	1.01	0.00
+15	25.50	20.50	24.50	29.50	0.00	0.00
+16	31.00	15.00	20.00	34.00	0.00	0.00
+17	28.00	25.00	14.00	33.00	0.00	0.00
+18	30.50	28.50	19.50	21.50	0.00	0.00
+19	29.00	26.00	21.00	24.00	0.00	0.00
+20	22.50	23.50	17.50	36.50	0.00	0.00
+21	35.50	17.50	19.50	27.50	0.00	0.00
+22	37.50	28.50	15.50	18.50	0.00	0.00
+23	31.31	19.19	13.13	36.36	1.01	0.00
+24	37.00	12.00	22.00	29.00	0.00	0.00
+25	35.50	22.50	17.50	24.50	0.00	0.00
+26	33.50	18.50	15.50	32.50	0.00	0.00
+27	34.50	14.50	25.50	25.50	0.00	0.00
+28	31.00	14.00	24.00	31.00	0.00	0.00
+29	30.00	27.00	24.00	19.00	0.00	0.00
+30	31.00	20.00	14.00	35.00	0.00	0.00
+31	33.50	29.50	13.50	23.50	0.00	0.00
+32	42.50	20.50	19.50	17.50	0.00	0.00
+33	25.50	23.50	14.50	36.50	0.00	0.00
+34	39.50	16.50	20.50	23.50	0.00	0.00
+35	32.50	23.50	21.50	22.50	0.00	0.00
+36	42.00	25.00	16.00	17.00	0.00	0.00
+37	38.00	17.00	19.00	26.00	0.00	0.00
+38	24.00	26.00	25.00	25.00	0.00	0.00
+39	22.50	41.50	18.50	17.50	0.00	0.00
+40	32.00	16.00	21.00	31.00	0.00	0.00
+41	33.00	28.00	19.00	20.00	0.00	0.00
+42	30.50	25.50	19.50	24.50	0.00	0.00
+43	35.00	29.00	15.00	21.00	0.00	0.00
+44	20.00	27.00	22.00	31.00	0.00	0.00
+45	40.50	21.50	21.50	16.50	0.00	0.00
+46	26.50	20.50	22.50	30.50	0.00	0.00
+47	38.50	29.50	16.50	15.50	0.00	0.00
+48	27.50	24.50	17.50	30.50	0.00	0.00
+49	28.50	32.50	10.50	28.50	0.00	0.00
+50	46.50	20.50	9.50	23.50	0.00	0.00
+51	34.50	28.50	13.50	23.50	0.00	0.00
+52	41.50	23.50	20.50	14.50	0.00	0.00
+53	20.00	28.00	26.00	26.00	0.00	0.00
+54	31.50	18.50	24.50	25.50	0.00	0.00
+55	30.50	22.50	16.50	30.50	0.00	0.00
+56	33.50	22.50	13.50	30.50	0.00	0.00
+57	23.00	24.00	23.00	30.00	0.00	0.00
+58	25.00	37.00	19.00	19.00	0.00	0.00
+59	34.00	23.00	24.00	19.00	0.00	0.00
+60	29.00	28.00	17.00	26.00	0.00	0.00
+61	25.50	23.50	24.50	26.50	0.00	0.00
+62	31.50	22.50	16.50	29.50	0.00	0.00
+63	27.50	28.50	25.50	18.50	0.00	0.00
+64	33.50	21.50	25.50	19.50	0.00	0.00
+65	35.50	19.50	18.50	26.50	0.00	0.00
+66	34.00	25.00	15.00	26.00	0.00	0.00
+67	37.00	23.00	19.00	21.00	0.00	0.00
+68	36.50	29.50	13.50	20.50	0.00	0.00
+69	38.50	19.50	20.50	21.50	0.00	0.00
+70	38.50	16.50	18.50	26.50	0.00	0.00
+71	25.50	38.50	21.50	14.50	0.00	0.00
+72	29.00	29.00	25.00	17.00	0.00	0.00
+73	32.50	20.50	21.50	25.50	0.00	0.00
+74	28.50	32.50	12.50	26.50	0.00	0.00
+75	41.50	12.50	18.50	27.50	0.00	0.00
+76	24.50	29.50	23.50	22.50	0.00	0.00
+77	36.00	21.00	18.00	25.00	0.00	0.00
+78	27.00	34.00	22.00	17.00	0.00	0.00
+79	21.50	26.50	25.50	26.50	0.00	0.00
+80	34.00	19.00	28.00	19.00	0.00	0.00
+81	17.00	26.00	26.00	31.00	0.00	0.00
+82	31.00	30.00	23.00	16.00	0.00	0.00
+83	31.50	26.50	12.50	29.50	0.00	0.00
+84	19.00	41.00	21.00	19.00	0.00	0.00
+85	37.50	24.50	16.50	21.50	0.00	0.00
+86	15.00	48.00	15.00	22.00	0.00	0.00
+87	41.00	16.00	18.00	25.00	0.00	0.00
+88	23.50	27.50	27.50	21.50	0.00	0.00
+89	26.50	27.50	26.50	19.50	0.00	0.00
+90	18.50	23.50	24.50	33.50	0.00	0.00
+91	27.00	32.00	22.00	19.00	0.00	0.00
+92	23.50	17.50	27.50	31.50	0.00	0.00
+93	25.50	37.50	15.50	21.50	0.00	0.00
+94	27.00	17.00	24.00	32.00	0.00	0.00
+95	26.77	37.88	14.65	20.71	1.01	0.00
+96	29.50	25.50	16.50	28.50	0.00	0.00
+97	29.00	31.00	21.00	19.00	0.00	0.00
+98	18.18	33.33	22.22	26.26	1.01	0.00
+99	24.50	33.50	24.50	17.50	0.00	0.00
+100	24.50	16.50	24.50	34.50	0.00	0.00
+101	25.00	40.00	19.00	16.00	0.00	0.00
+102	17.50	17.50	32.50	32.50	0.00	0.00
+103	31.00	26.00	16.00	27.00	0.00	0.00
+104	26.50	29.50	20.50	23.50	0.00	0.00
+105	34.00	33.00	21.00	12.00	0.00	0.00
+106	23.00	31.00	26.00	20.00	0.00	0.00
+107	17.68	35.86	23.74	22.73	1.01	0.00
+108	24.75	30.81	23.74	20.71	1.01	0.00
+109	17.00	31.00	22.00	30.00	0.00	0.00
+110	16.16	35.35	24.24	24.24	1.01	0.00
+111	24.24	32.32	23.23	20.20	1.01	0.00
+112	37.37	28.28	16.16	18.18	1.01	0.00
+113	19.70	22.73	32.83	24.75	1.01	0.00
+114	17.00	31.00	35.00	17.00	0.00	0.00
+115	29.50	24.50	23.50	22.50	0.00	0.00
+116	22.00	30.00	34.00	14.00	0.00	0.00
+117	27.00	23.00	19.00	31.00	0.00	0.00
+118	25.50	14.50	34.50	25.50	0.00	0.00
+119	22.50	34.50	20.50	22.50	0.00	0.00
+120	17.50	24.50	26.50	31.50	0.00	0.00
+121	27.78	33.84	22.73	15.66	1.01	0.00
+122	17.00	23.00	25.00	35.00	0.00	0.00
+123	23.50	46.50	11.50	18.50	0.00	0.00
+124	9.00	32.00	34.00	25.00	0.00	0.00
+125	24.00	27.00	19.00	30.00	0.00	0.00
+126	26.00	17.00	28.00	29.00	0.00	0.00
+127	26.50	16.50	21.50	35.50	0.00	0.00
+128	18.00	34.00	31.00	17.00	0.00	0.00
+129	25.50	25.50	27.50	21.50	0.00	0.00
+130	25.00	20.00	22.00	33.00	0.00	0.00
+131	17.50	39.50	24.50	18.50	0.00	0.00
+132	21.00	28.00	23.00	28.00	0.00	0.00
+133	13.50	31.50	35.50	19.50	0.00	0.00
+134	24.50	19.50	30.50	25.50	0.00	0.00
+135	16.50	23.50	30.50	29.50	0.00	0.00
+136	28.00	32.00	15.00	25.00	0.00	0.00
+137	22.50	21.50	30.50	25.50	0.00	0.00
+138	14.50	34.50	24.50	26.50	0.00	0.00
+139	20.50	29.50	24.50	25.50	0.00	0.00
+140	17.00	23.00	30.00	30.00	0.00	0.00
+141	20.50	23.50	25.50	30.50	0.00	0.00
+142	18.00	29.00	38.00	15.00	0.00	0.00
+143	22.00	24.00	27.00	27.00	0.00	0.00
+144	21.50	30.50	26.50	21.50	0.00	0.00
+145	22.00	21.00	29.00	28.00	0.00	0.00
+146	25.00	16.00	39.00	20.00	0.00	0.00
+147	26.50	22.50	30.50	20.50	0.00	0.00
+148	12.50	28.50	36.50	22.50	0.00	0.00
+149	26.50	23.50	23.50	26.50	0.00	0.00
+150	14.00	29.00	24.00	33.00	0.00	0.00
+151	19.50	30.50	32.50	17.50	0.00	0.00
+152	18.50	17.50	29.50	34.50	0.00	0.00
+153	22.50	22.50	31.50	23.50	0.00	0.00
+154	22.00	21.00	29.00	28.00	0.00	0.00
+155	21.00	26.00	19.00	34.00	0.00	0.00
+156	14.50	23.50	35.50	26.50	0.00	0.00
+157	22.00	31.00	23.00	24.00	0.00	0.00
+158	22.50	29.50	24.50	23.50	0.00	0.00
+159	17.50	12.50	46.50	23.50	0.00	0.00
+160	24.50	26.50	26.50	22.50	0.00	0.00
+161	13.00	23.00	45.00	19.00	0.00	0.00
+162	31.50	16.50	22.50	29.50	0.00	0.00
+163	19.50	21.50	35.50	23.50	0.00	0.00
+164	29.00	18.00	21.00	32.00	0.00	0.00
+165	14.50	17.50	35.50	32.50	0.00	0.00
+166	17.50	37.50	28.50	16.50	0.00	0.00
+167	16.50	21.50	31.50	30.50	0.00	0.00
+168	14.00	25.00	30.00	31.00	0.00	0.00
+169	18.50	20.50	23.50	37.50	0.00	0.00
+170	19.00	23.00	28.00	30.00	0.00	0.00
+171	20.00	28.00	33.00	19.00	0.00	0.00
+172	19.00	20.00	32.00	29.00	0.00	0.00
+173	24.50	16.50	33.50	25.50	0.00	0.00
+174	17.50	23.50	33.50	25.50	0.00	0.00
+175	33.50	17.50	35.50	13.50	0.00	0.00
+176	16.50	32.50	28.50	22.50	0.00	0.00
+177	19.00	22.00	27.00	32.00	0.00	0.00
+178	16.00	26.00	30.00	28.00	0.00	0.00
+179	18.00	18.00	22.00	42.00	0.00	0.00
+180	21.00	22.00	34.00	23.00	0.00	0.00
+181	20.50	19.50	35.50	24.50	0.00	0.00
+182	32.50	18.50	22.50	26.50	0.00	0.00
+183	24.50	13.50	28.50	33.50	0.00	0.00
+184	15.00	29.00	30.00	26.00	0.00	0.00
+185	15.00	32.00	33.00	20.00	0.00	0.00
+186	22.50	23.50	34.50	19.50	0.00	0.00
+187	19.00	14.00	40.00	27.00	0.00	0.00
+188	27.50	21.50	27.50	23.50	0.00	0.00
+189	17.00	22.00	34.00	27.00	0.00	0.00
+190	23.00	30.00	23.00	24.00	0.00	0.00
+191	25.00	22.00	28.00	25.00	0.00	0.00
+192	34.50	24.50	13.50	27.50	0.00	0.00
+193	18.50	25.50	25.50	30.50	0.00	0.00
+194	18.50	33.50	24.50	23.50	0.00	0.00
+195	16.00	26.00	23.00	35.00	0.00	0.00
+196	21.50	25.50	24.50	28.50	0.00	0.00
+197	20.00	21.00	23.00	36.00	0.00	0.00
+198	17.00	21.00	37.00	25.00	0.00	0.00
+199	20.50	18.50	25.50	35.50	0.00	0.00
+200	21.00	29.00	21.00	29.00	0.00	0.00
+201	27.00	21.00	23.00	29.00	0.00	0.00
+202	21.50	24.50	19.50	34.50	0.00	0.00
+203	21.50	24.50	26.50	27.50	0.00	0.00
+204	27.00	29.00	24.00	20.00	0.00	0.00
+205	19.50	21.50	22.50	36.50	0.00	0.00
+206	26.50	24.50	21.50	27.50	0.00	0.00
+207	22.50	21.50	19.50	36.50	0.00	0.00
+208	14.00	35.00	29.00	22.00	0.00	0.00
+209	16.00	23.00	12.00	49.00	0.00	0.00
+210	18.50	19.50	40.50	21.50	0.00	0.00
+211	26.00	20.00	22.00	32.00	0.00	0.00
+212	21.00	31.00	18.00	30.00	0.00	0.00
+213	24.00	15.00	31.00	30.00	0.00	0.00
+214	17.50	24.50	25.50	32.50	0.00	0.00
+215	26.00	24.00	23.00	27.00	0.00	0.00
+216	21.50	17.50	25.50	35.50	0.00	0.00
+217	26.00	29.00	17.00	28.00	0.00	0.00
+218	20.00	27.00	21.00	32.00	0.00	0.00
+219	17.00	21.00	21.00	41.00	0.00	0.00
+220	25.50	23.50	23.50	27.50	0.00	0.00
+221	21.50	23.50	20.50	34.50	0.00	0.00
+222	21.50	21.50	18.50	38.50	0.00	0.00
+223	20.00	27.00	28.00	25.00	0.00	0.00
+224	22.50	22.50	24.50	30.50	0.00	0.00
+225	14.50	35.50	30.50	19.50	0.00	0.00
+226	20.00	23.00	26.00	31.00	0.00	0.00
+227	20.50	24.50	23.50	31.50	0.00	0.00
+228	33.00	19.00	26.00	22.00	0.00	0.00
+229	22.50	24.50	18.50	34.50	0.00	0.00
+230	21.00	32.00	16.00	31.00	0.00	0.00
+231	23.00	28.00	30.00	19.00	0.00	0.00
+232	23.50	21.50	12.50	42.50	0.00	0.00
+233	21.00	27.00	25.00	27.00	0.00	0.00
+234	16.50	27.50	22.50	33.50	0.00	0.00
+235	20.00	15.00	28.00	37.00	0.00	0.00
+236	28.00	23.00	21.00	28.00	0.00	0.00
+237	20.50	19.50	22.50	37.50	0.00	0.00
+238	21.50	29.50	24.50	24.50	0.00	0.00
+239	20.00	8.00	17.00	55.00	0.00	0.00
+240	28.00	24.00	16.00	32.00	0.00	0.00
+241	22.50	22.50	16.50	38.50	0.00	0.00
+242	29.00	25.00	13.00	33.00	0.00	0.00
+243	22.50	15.50	23.50	38.50	0.00	0.00
+244	20.50	23.50	16.50	39.50	0.00	0.00
+245	28.00	23.00	19.00	30.00	0.00	0.00
+246	21.00	29.00	25.00	25.00	0.00	0.00
+247	32.00	14.00	13.00	41.00	0.00	0.00
+248	18.00	18.00	25.00	39.00	0.00	0.00
+249	25.00	23.00	21.00	31.00	0.00	0.00
+250	27.50	22.50	17.50	32.50	0.00	0.00
+251	13.50	20.50	36.50	29.50	0.00	0.00
diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2__mpc.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out2__mpc.tab	Tue May 09 11:19:01 2017 -0400
@@ -0,0 +1,253 @@
+# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches
+1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0
+2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0
+3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	0	0	0	0
+4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0
+5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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diff -r 8cfc17e27132 -r 24c5d43cb545 test-data/samtools_stats_out2__sn.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out2__sn.tab	Tue May 09 11:19:01 2017 -0400
@@ -0,0 +1,33 @@
+# Summary Numbers
+
+raw total sequences:	200
+filtered sequences:	0
+sequences:	200
+is sorted:	1
+1st fragments:	100
+last fragments:	100
+reads mapped:	25
+reads mapped and paired:	0	# paired-end technology bit set + both mates mapped
+reads unmapped:	175
+reads properly paired:	0	# proper-pair bit set
+reads paired:	200	# paired-end technology bit set
+reads duplicated:	0	# PCR or optical duplicate bit set
+reads MQ0:	6	# mapped and MQ=0
+reads QC failed:	0
+non-primary alignments:	0
+total length:	50200	# ignores clipping
+bases mapped:	6275	# ignores clipping
+bases mapped (cigar):	6275	# more accurate
+bases trimmed:	0
+bases duplicated:	0
+mismatches:	591	# from NM fields
+error rate:	9.418327e-02	# mismatches / bases mapped (cigar)
+average length:	251
+maximum length:	251
+average quality:	34.7
+insert size average:	0.0
+insert size standard deviation:	0.0
+inward oriented pairs:	0
+outward oriented pairs:	0
+pairs with other orientation:	0
+pairs on different chromosomes:	0
diff -r 8cfc17e27132 -r 24c5d43cb545 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:55:15 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>