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changeset 8:e28839a4b932 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:17:39 +0000
parents 145f6d74ff5e
children 1cc79f49b8d5
files macros.xml samtools_stats.xml test-data/1.stats.expected test-data/11.stats.expected test-data/11.stats.g4.expected test-data/12.2reads.nooverlap.expected test-data/12.2reads.overlap.expected test-data/12.3reads.nooverlap.expected test-data/12.3reads.overlap.expected test-data/2.stats.expected test-data/6.stats.expected test-data/samtools_stats_out1.tab test-data/samtools_stats_out1__sn.tab
diffstat 13 files changed, 1084 insertions(+), 92 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Oct 17 02:21:23 2019 -0400
+++ b/macros.xml	Tue Sep 28 16:17:39 2021 +0000
@@ -5,10 +5,16 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.9</token>
-    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
+    <token name="@TOOL_VERSION@">1.13</token>
+    <token name="@PROFILE@">20.05</token>
+    <token name="@FLAGS@"><![CDATA[
+        #set $flags = 0
+        #if $filter
+            #set $flags = sum(map(int, str($filter).split(',')))
+        #end if
+    ]]></token>
     <token name="@PREPARE_IDX@"><![CDATA[
-        ##prepare input and indices 
+        ##prepare input and indices
         ln -s '$input' infile &&
         #if $input.is_of_type('bam'):
             #if str( $input.metadata.bam_index ) != "None":
@@ -25,7 +31,7 @@
         #end if
     ]]></token>
     <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
-        ##prepare input and indices 
+        ##prepare input and indices
         #for $i, $bam in enumerate( $input_bams ):
             ln -s '$bam' '${i}' &&
             #if $bam.is_of_type('bam'):
@@ -63,6 +69,51 @@
             #set reffai=None
         #end if
     ]]></token>
+
+    <xml name="optional_reference">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="no">No</option>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="no"/>
+            <when value="history">
+                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                    </options>
+                    <validator  type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="mandatory_reference" token_help="" token_argument="">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="history">
+                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+
+
     <token name="@ADDTHREADS@"><![CDATA[
         ##compute the number of ADDITIONAL threads to be used by samtools (-@)
         addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
@@ -70,28 +121,28 @@
     <token name="@ADDMEMORY@"><![CDATA[
         ##compute the number of memory available to samtools sort (-m)
         ##use only 75% of available: https://github.com/samtools/samtools/issues/831
-        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
+        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
         ((addmemory=addmemory*75/100)) &&
     ]]></token>
     <xml name="seed_input">
-       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 
+       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
     </xml>
-    <xml name="flag_options">
-        <option value="1">read is paired</option>
-        <option value="2">read is mapped in a proper pair</option>
-        <option value="4">read is unmapped</option>
-        <option value="8">mate is unmapped</option>
-        <option value="16">read reverse strand</option>
-        <option value="32">mate reverse strand</option>
-        <option value="64">read is the first in a pair</option>
-        <option value="128">read is the second in a pair</option>
-        <option value="256">alignment or read is not primary</option>
-        <option value="512">read fails platform/vendor quality checks</option>
-        <option value="1024">read is a PCR or optical duplicate</option>
-        <option value="2048">supplementary alignment</option>
+    <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
+        <option value="1" selected="@S1@">Read is paired</option>
+        <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
+        <option value="4" selected="@S4@">Read is unmapped</option>
+        <option value="8" selected="@S8@">Mate is unmapped</option>
+        <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
+        <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
+        <option value="64" selected="@S64@">Read is the first in a pair</option>
+        <option value="128" selected="@S128@">Read is the second in a pair</option>
+        <option value="256" selected="@S256@">Alignment of the read is not primary</option>
+        <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
+        <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
+        <option value="2048" selected="@S2048@">Alignment is supplementary</option>
     </xml>
 
-    <!-- region specification macros and tokens for tools that allow the specification 
+    <!-- region specification macros and tokens for tools that allow the specification
          of region by bed file / space separated list of regions -->
     <token name="@REGIONS_FILE@"><![CDATA[
         #if $cond_region.select_region == 'tab':
--- a/samtools_stats.xml	Thu Oct 17 02:21:23 2019 -0400
+++ b/samtools_stats.xml	Tue Sep 28 16:17:39 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy2">
+<tool id="samtools_stats" name="Samtools stats" version="2.0.3" profile="@PROFILE@">
     <description>generate statistics for BAM dataset</description>
     <macros>
         <import>macros.xml</import>
@@ -16,16 +16,12 @@
             #end if
             ${remove_dups}
             #if str( $filter_by_flags.filter_flags ) == "filter":
-                #if $filter_by_flags.require_flags:
-                    #set $filter = $filter_by_flags.require_flags
-                    @FLAGS@
-                    --required-flag $flags
-                #end if
-                #if $filter_by_flags.exclude_flags:
-                    #set $filter = $filter_by_flags.exclude_flags
-                    @FLAGS@
-                    --filtering-flag $flags
-                #end if
+                #set $filter = $filter_by_flags.require_flags
+                @FLAGS@
+                --required-flag $flags
+                #set $filter = $filter_by_flags.exclude_flags
+                @FLAGS@
+                --filtering-flag $flags
             #end if
             #if str($gc_depth):
                 --GC-depth ${gc_depth}
@@ -33,12 +29,9 @@
             #if str($insert_size):
                 --insert-size ${insert_size}
             #end if
-            ## The code below is commented out because using -I/--id options causes 
-            ## in samtools up to 1.9 the following exception
-            ## Samtools-htslib: init_group_id() header parsing not yet implemented
-            ##if str($read_group) != "":
-            ##    -I "${read_group}"
-            ##end if
+            ## #if $read_group
+            ##    -I '$read_group'
+            ## #end if
             #if str($read_length):
                 --read-length ${read_length}
             #end if
@@ -63,7 +56,7 @@
             #if str($cov_threshold):
                 -g $cov_threshold
             #end if
-            -@ \$addthreads 
+            -@ \$addthreads
             infile
             @REGIONS_MANUAL@
             > '$output'
@@ -139,40 +132,19 @@
         <!-- TODO I would like to set the default values of float and int parameters as on the samtools stats help page, but then the tests don't work. Hence I leave the optional and give the defaults in the help -->
         <param name="gc_depth" argument="--GC-depth" type="float" optional="True" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement. default=2e4" />
         <param name="insert_size" argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" />
-        <!--
-            The -I option of samtools stats returns the following message up to version 1.9:
-            Samtools-htslib: init_group_id() header parsing not yet implemented
-            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" >
-                <options>
-                    <filter type="data_meta" ref="input" key="read_groups" />
-                </options>
-            </param>
-        -->
+        <!-- TOOD https://github.com/samtools/samtools/issues/1489 -->    
+        <param name="read_group" argument="--id" type="select" optional="true" label="Limit to a specific read group name" >
+            <options>
+                <filter type="data_meta" ref="input" key="read_groups" />
+            </options>
+        </param>
         <param name="read_length" argument="--read-length" type="integer" 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" optional="true" label="Report only the main part of inserts" help="default=0.99" />
         <param name="trim_quality" argument="--trim-quality" type="integer" optional="true" label="BWA trim parameter" help="default=0" />
 
-        <conditional name="addref_cond">
-            <param name="addref_select" type="select" label="Use a reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation">
-                <option value="no">No</option>
-                <option value="cached">Locally cached</option>
-                <option value="history">History</option>
-            </param>
-            <when value="no"/>
-            <when value="cached">
-                <param name="ref" type="select" label="Using genome">
-                    <options from_data_table="fasta_indexes">
-                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey" />
-                    </options>
-                </param>
-            </when>
-            <when value="history">
-                <param name="ref" type="data" format="fasta" label="Using file" />
-            </when>
-        </conditional>
+        <expand macro="optional_reference" argument="--ref-seq" help="Required for GC-depth and mismatches-per-cycle calculation"/>
         <!-- unfortunately -t takes tabular and not bed like view (otherwise a macro might have simplified this) -->
-        
+
         <expand macro="regions_macro"/>
 
         <param name="sparse" argument="-x/--sparse" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Suppress absence of insertions" help="Suppress outputting IS rows where there are no insertions."/>
@@ -198,7 +170,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="2" />
         </test>
         <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
         <test>
@@ -207,7 +179,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="2" />
         </test>
         <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
         <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
@@ -220,7 +192,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="2" />
         </test>
         <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
         <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
@@ -236,7 +208,7 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
             </conditional>
-            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->
 
@@ -251,7 +223,7 @@
                 <param name="regions_repeat_1|region" value="ref1:30-46"/>
                 <param name="regions_repeat_2|region" value="ref1:39-56"/>
             </conditional>
-            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="2" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
 -->
@@ -265,7 +237,7 @@
                 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
             </conditional>
             <param name="cov_threshold" value="4" />
-            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->
         <test>
@@ -280,7 +252,7 @@
                 <param name="regions_repeat_2|region" value="ref1:39-56"/>
             </conditional>
             <param name="cov_threshold" value="4" />
-            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="2" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->
         <test>
@@ -292,7 +264,7 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
             </conditional>
-            <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
         <test>
@@ -305,7 +277,7 @@
                 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
             </conditional>
             <param name="remove_overlaps" value="-p"/>
-            <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
         <test>
@@ -317,7 +289,7 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
             </conditional>
-            <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
         <test>
@@ -330,7 +302,7 @@
                 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
             </conditional>
             <param name="remove_overlaps" value="-p"/>
-            <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="3" />
+            <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
         <test>
@@ -357,6 +329,18 @@
                 <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" />
             </output_collection>
         </test>
+        <!-- test filtering by read group -->
+        <!-- <test>
+            <param name="input" value="11_target.sam" ftype="sam" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="no" />
+            </conditional>
+            <param name="read_group" value="grp1" />
+            <output name="output" file="11.stats.read_groups.expected" ftype="tabular" lines_diff="2" />
+            <assert_command>
+                <has_text text="-I 'grp1'"/>
+            </assert_command>
+        </test> -->
     </tests>
     <help><![CDATA[
 **What it does**
@@ -367,4 +351,3 @@
     ]]></help>
     <expand macro="citations"/>
 </tool>
-
--- a/test-data/1.stats.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/1.stats.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats --ref-seq reference.fa -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	1a1c1362	29c426ae	7bab45da
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	2
+SN	raw total sequences:	2	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	2
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	0	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	70	# ignores clipping
 SN	total first fragment length:	35	# ignores clipping
 SN	total last fragment length:	35	# ignores clipping
@@ -195,6 +199,42 @@
 GCC	33	50.00	0.00	0.00	50.00	0.00	0.00
 GCC	34	50.00	0.00	50.00	0.00	0.00	0.00
 GCC	35	0.00	0.00	50.00	50.00	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	0.00	50.00	0.00	50.00
+GCT	2	50.00	0.00	50.00	0.00
+GCT	3	0.00	0.00	50.00	50.00
+GCT	4	0.00	0.00	100.00	0.00
+GCT	5	0.00	0.00	50.00	50.00
+GCT	6	0.00	50.00	0.00	50.00
+GCT	7	0.00	0.00	50.00	50.00
+GCT	8	0.00	0.00	0.00	100.00
+GCT	9	0.00	50.00	50.00	0.00
+GCT	10	50.00	0.00	50.00	0.00
+GCT	11	50.00	0.00	0.00	50.00
+GCT	12	50.00	0.00	50.00	0.00
+GCT	13	50.00	0.00	50.00	0.00
+GCT	14	0.00	0.00	0.00	100.00
+GCT	15	100.00	0.00	0.00	0.00
+GCT	16	50.00	0.00	0.00	50.00
+GCT	17	0.00	0.00	50.00	50.00
+GCT	18	0.00	50.00	50.00	0.00
+GCT	19	0.00	100.00	0.00	0.00
+GCT	20	0.00	0.00	50.00	50.00
+GCT	21	0.00	0.00	100.00	0.00
+GCT	22	0.00	50.00	0.00	50.00
+GCT	23	50.00	0.00	0.00	50.00
+GCT	24	50.00	0.00	50.00	0.00
+GCT	25	50.00	0.00	50.00	0.00
+GCT	26	0.00	0.00	100.00	0.00
+GCT	27	50.00	0.00	0.00	50.00
+GCT	28	0.00	0.00	50.00	50.00
+GCT	29	0.00	50.00	0.00	50.00
+GCT	30	0.00	50.00	0.00	50.00
+GCT	31	0.00	50.00	50.00	0.00
+GCT	32	0.00	0.00	100.00	0.00
+GCT	33	100.00	0.00	0.00	0.00
+GCT	34	0.00	0.00	50.00	50.00
+GCT	35	50.00	0.00	50.00	0.00
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -231,6 +271,8 @@
 FBC	33	100.00	0.00	0.00	0.00	0.00	0.00
 FBC	34	0.00	0.00	100.00	0.00	0.00	0.00
 FBC	35	0.00	0.00	100.00	0.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	6	5	15	9	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	0.00	0.00	100.00	0.00	0.00	0.00
 LBC	2	0.00	0.00	0.00	100.00	0.00	0.00
@@ -267,6 +309,8 @@
 LBC	33	0.00	0.00	0.00	100.00	0.00	0.00
 LBC	34	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	35	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	11	10	5	9	0
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/11.stats.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/11.stats.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	cb2d2d82	bcd83869	62ec814e
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	26
+SN	raw total sequences:	26	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	26
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	1	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	260	# ignores clipping
 SN	total first fragment length:	140	# ignores clipping
 SN	total last fragment length:	120	# ignores clipping
@@ -89,6 +93,17 @@
 GCC	8	26.92	23.08	38.46	11.54	0.00	0.00
 GCC	9	23.08	26.92	26.92	23.08	0.00	0.00
 GCC	10	23.08	23.08	38.46	15.38	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	26.92	26.92	30.77	15.38
+GCT	2	7.69	38.46	26.92	26.92
+GCT	3	26.92	26.92	30.77	15.38
+GCT	4	11.54	34.62	26.92	26.92
+GCT	5	23.08	26.92	38.46	11.54
+GCT	6	11.54	34.62	23.08	30.77
+GCT	7	19.23	23.08	38.46	19.23
+GCT	8	11.54	38.46	23.08	26.92
+GCT	9	23.08	19.23	34.62	23.08
+GCT	10	11.54	34.62	26.92	26.92
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	21.43	42.86	21.43	14.29	0.00	0.00
 FBC	2	7.14	28.57	42.86	21.43	0.00	0.00
@@ -100,6 +115,8 @@
 FBC	8	21.43	28.57	28.57	21.43	0.00	0.00
 FBC	9	21.43	21.43	35.71	21.43	0.00	0.00
 FBC	10	14.29	28.57	35.71	21.43	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	24	43	45	28	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	16.67	41.67	8.33	33.33	0.00	0.00
 LBC	2	33.33	8.33	50.00	8.33	0.00	0.00
@@ -111,6 +128,19 @@
 LBC	8	33.33	16.67	50.00	0.00	0.00	0.00
 LBC	9	25.00	33.33	16.67	25.00	0.00	0.00
 LBC	10	33.33	16.67	41.67	8.33	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	30	33	36	21	0
+# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%]
+BCC1	1	50.00	0.00	0.00	50.00	0.00
+BCC1	2	0.00	50.00	50.00	0.00	0.00
+BCC1	3	0.00	50.00	50.00	0.00	0.00
+BCC1	4	50.00	0.00	0.00	50.00	0.00
+# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
+QTQ1	1
+QTQ1	2
+QTQ1	3
+QTQ1	4
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/11.stats.g4.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/11.stats.g4.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats -g 4 -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	cb2d2d82	bcd83869	62ec814e
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	26
+SN	raw total sequences:	26	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	26
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	1	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	260	# ignores clipping
 SN	total first fragment length:	140	# ignores clipping
 SN	total last fragment length:	120	# ignores clipping
@@ -89,6 +93,17 @@
 GCC	8	26.92	23.08	38.46	11.54	0.00	0.00
 GCC	9	23.08	26.92	26.92	23.08	0.00	0.00
 GCC	10	23.08	23.08	38.46	15.38	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	26.92	26.92	30.77	15.38
+GCT	2	7.69	38.46	26.92	26.92
+GCT	3	26.92	26.92	30.77	15.38
+GCT	4	11.54	34.62	26.92	26.92
+GCT	5	23.08	26.92	38.46	11.54
+GCT	6	11.54	34.62	23.08	30.77
+GCT	7	19.23	23.08	38.46	19.23
+GCT	8	11.54	38.46	23.08	26.92
+GCT	9	23.08	19.23	34.62	23.08
+GCT	10	11.54	34.62	26.92	26.92
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	21.43	42.86	21.43	14.29	0.00	0.00
 FBC	2	7.14	28.57	42.86	21.43	0.00	0.00
@@ -100,6 +115,8 @@
 FBC	8	21.43	28.57	28.57	21.43	0.00	0.00
 FBC	9	21.43	21.43	35.71	21.43	0.00	0.00
 FBC	10	14.29	28.57	35.71	21.43	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	24	43	45	28	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	16.67	41.67	8.33	33.33	0.00	0.00
 LBC	2	33.33	8.33	50.00	8.33	0.00	0.00
@@ -111,6 +128,19 @@
 LBC	8	33.33	16.67	50.00	0.00	0.00	0.00
 LBC	9	25.00	33.33	16.67	25.00	0.00	0.00
 LBC	10	33.33	16.67	41.67	8.33	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	30	33	36	21	0
+# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%]
+BCC1	1	50.00	0.00	0.00	50.00	0.00
+BCC1	2	0.00	50.00	50.00	0.00	0.00
+BCC1	3	0.00	50.00	50.00	0.00	0.00
+BCC1	4	50.00	0.00	0.00	50.00	0.00
+# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
+QTQ1	1
+QTQ1	2
+QTQ1	3
+QTQ1	4
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/12.2reads.nooverlap.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/12.2reads.nooverlap.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats -t /tmp/tmp0r5zs075/files/b/2/1/dataset_b2175431-044e-449d-8f60-1bfd33679b61.dat -p -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	5b31676a	b0edee94	471895da
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	2
+SN	raw total sequences:	2	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	2
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	0	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	200	# ignores clipping
 SN	total first fragment length:	100	# ignores clipping
 SN	total last fragment length:	100	# ignores clipping
@@ -353,6 +357,107 @@
 GCC	98	50.00	50.00	0.00	0.00	0.00	0.00
 GCC	99	50.00	50.00	0.00	0.00	0.00	0.00
 GCC	100	100.00	0.00	0.00	0.00	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	50.00	0.00	50.00	0.00
+GCT	2	0.00	50.00	50.00	0.00
+GCT	3	0.00	50.00	0.00	50.00
+GCT	4	0.00	50.00	50.00	0.00
+GCT	5	0.00	0.00	50.00	50.00
+GCT	6	0.00	0.00	50.00	50.00
+GCT	7	0.00	50.00	0.00	50.00
+GCT	8	0.00	0.00	50.00	50.00
+GCT	9	0.00	50.00	0.00	50.00
+GCT	10	50.00	0.00	50.00	0.00
+GCT	11	0.00	0.00	100.00	0.00
+GCT	12	50.00	0.00	0.00	50.00
+GCT	13	0.00	50.00	50.00	0.00
+GCT	14	50.00	0.00	0.00	50.00
+GCT	15	0.00	0.00	50.00	50.00
+GCT	16	0.00	50.00	50.00	0.00
+GCT	17	0.00	50.00	0.00	50.00
+GCT	18	100.00	0.00	0.00	0.00
+GCT	19	50.00	0.00	0.00	50.00
+GCT	20	0.00	50.00	50.00	0.00
+GCT	21	50.00	0.00	0.00	50.00
+GCT	22	0.00	50.00	0.00	50.00
+GCT	23	0.00	0.00	0.00	100.00
+GCT	24	0.00	50.00	50.00	0.00
+GCT	25	0.00	0.00	0.00	100.00
+GCT	26	0.00	0.00	50.00	50.00
+GCT	27	0.00	100.00	0.00	0.00
+GCT	28	0.00	0.00	0.00	100.00
+GCT	29	50.00	0.00	50.00	0.00
+GCT	30	0.00	50.00	0.00	50.00
+GCT	31	0.00	50.00	0.00	50.00
+GCT	32	0.00	0.00	50.00	50.00
+GCT	33	0.00	50.00	0.00	50.00
+GCT	34	50.00	0.00	0.00	50.00
+GCT	35	0.00	50.00	0.00	50.00
+GCT	36	0.00	100.00	0.00	0.00
+GCT	37	0.00	50.00	0.00	50.00
+GCT	38	50.00	50.00	0.00	0.00
+GCT	39	100.00	0.00	0.00	0.00
+GCT	40	0.00	0.00	100.00	0.00
+GCT	41	0.00	50.00	0.00	50.00
+GCT	42	50.00	50.00	0.00	0.00
+GCT	43	0.00	0.00	50.00	50.00
+GCT	44	50.00	0.00	50.00	0.00
+GCT	45	50.00	0.00	50.00	0.00
+GCT	46	50.00	0.00	50.00	0.00
+GCT	47	50.00	0.00	50.00	0.00
+GCT	48	0.00	50.00	50.00	0.00
+GCT	49	50.00	0.00	0.00	50.00
+GCT	50	0.00	0.00	50.00	50.00
+GCT	51	0.00	0.00	100.00	0.00
+GCT	52	50.00	0.00	50.00	0.00
+GCT	53	0.00	50.00	0.00	50.00
+GCT	54	50.00	0.00	50.00	0.00
+GCT	55	50.00	0.00	0.00	50.00
+GCT	56	0.00	50.00	50.00	0.00
+GCT	57	100.00	0.00	0.00	0.00
+GCT	58	50.00	0.00	50.00	0.00
+GCT	59	100.00	0.00	0.00	0.00
+GCT	60	50.00	0.00	50.00	0.00
+GCT	61	0.00	0.00	0.00	100.00
+GCT	62	0.00	50.00	50.00	0.00
+GCT	63	50.00	0.00	0.00	50.00
+GCT	64	0.00	0.00	100.00	0.00
+GCT	65	50.00	50.00	0.00	0.00
+GCT	66	0.00	50.00	0.00	50.00
+GCT	67	0.00	0.00	0.00	100.00
+GCT	68	0.00	50.00	0.00	50.00
+GCT	69	0.00	50.00	0.00	50.00
+GCT	70	50.00	0.00	0.00	50.00
+GCT	71	0.00	0.00	0.00	100.00
+GCT	72	0.00	50.00	0.00	50.00
+GCT	73	0.00	0.00	0.00	100.00
+GCT	74	0.00	50.00	0.00	50.00
+GCT	75	50.00	0.00	0.00	50.00
+GCT	76	0.00	50.00	0.00	50.00
+GCT	77	50.00	0.00	0.00	50.00
+GCT	78	50.00	0.00	0.00	50.00
+GCT	79	50.00	0.00	0.00	50.00
+GCT	80	50.00	0.00	0.00	50.00
+GCT	81	50.00	0.00	0.00	50.00
+GCT	82	50.00	0.00	0.00	50.00
+GCT	83	50.00	0.00	0.00	50.00
+GCT	84	50.00	0.00	0.00	50.00
+GCT	85	50.00	0.00	0.00	50.00
+GCT	86	50.00	0.00	0.00	50.00
+GCT	87	50.00	0.00	0.00	50.00
+GCT	88	50.00	0.00	0.00	50.00
+GCT	89	50.00	0.00	0.00	50.00
+GCT	90	50.00	0.00	0.00	50.00
+GCT	91	50.00	0.00	50.00	0.00
+GCT	92	50.00	0.00	50.00	0.00
+GCT	93	50.00	0.00	50.00	0.00
+GCT	94	50.00	0.00	0.00	50.00
+GCT	95	50.00	0.00	50.00	0.00
+GCT	96	50.00	0.00	50.00	0.00
+GCT	97	50.00	0.00	50.00	0.00
+GCT	98	50.00	0.00	50.00	0.00
+GCT	99	50.00	0.00	50.00	0.00
+GCT	100	50.00	0.00	0.00	50.00
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -454,6 +559,8 @@
 FBC	98	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	100	100.00	0.00	0.00	0.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	50	21	14	15	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	0.00	0.00	100.00	0.00	0.00	0.00
 LBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -555,6 +662,26 @@
 LBC	98	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	99	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	100	100.00	0.00	0.00	0.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	41	20	23	16	0
+# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%]
+BCC1	2	0.00	0.00	100.00	0.00	0.00
+BCC1	3	0.00	0.00	0.00	100.00	0.00
+BCC1	4	0.00	100.00	0.00	0.00	0.00
+BCC1	5	0.00	0.00	0.00	100.00	0.00
+BCC1	6	100.00	0.00	0.00	0.00	0.00
+BCC1	7	0.00	0.00	0.00	100.00	0.00
+BCC1	8	0.00	100.00	0.00	0.00	0.00
+# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
+QTQ1	1	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	0	0	0
+QTQ1	2	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
+QTQ1	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	1	0	0	0	0	0	0	0	0	0
+QTQ1	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	0	1	0	0
+QTQ1	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	1	0	0
+QTQ1	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	1
+QTQ1	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	1
+QTQ1	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	1	0	0
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/12.2reads.overlap.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/12.2reads.overlap.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats -t /tmp/tmp0r5zs075/files/2/a/2/dataset_2a2a3ee9-3133-4880-a37c-50b6354c9000.dat -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	5b31676a	b0edee94	471895da
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	2
+SN	raw total sequences:	2	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	2
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	0	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	200	# ignores clipping
 SN	total first fragment length:	100	# ignores clipping
 SN	total last fragment length:	100	# ignores clipping
@@ -353,6 +357,107 @@
 GCC	98	50.00	50.00	0.00	0.00	0.00	0.00
 GCC	99	50.00	50.00	0.00	0.00	0.00	0.00
 GCC	100	100.00	0.00	0.00	0.00	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	50.00	0.00	50.00	0.00
+GCT	2	0.00	50.00	50.00	0.00
+GCT	3	0.00	50.00	0.00	50.00
+GCT	4	0.00	50.00	50.00	0.00
+GCT	5	0.00	0.00	50.00	50.00
+GCT	6	0.00	0.00	50.00	50.00
+GCT	7	0.00	50.00	0.00	50.00
+GCT	8	0.00	0.00	50.00	50.00
+GCT	9	0.00	50.00	0.00	50.00
+GCT	10	50.00	0.00	50.00	0.00
+GCT	11	0.00	0.00	100.00	0.00
+GCT	12	50.00	0.00	0.00	50.00
+GCT	13	0.00	50.00	50.00	0.00
+GCT	14	50.00	0.00	0.00	50.00
+GCT	15	0.00	0.00	50.00	50.00
+GCT	16	0.00	50.00	50.00	0.00
+GCT	17	0.00	50.00	0.00	50.00
+GCT	18	100.00	0.00	0.00	0.00
+GCT	19	50.00	0.00	0.00	50.00
+GCT	20	0.00	50.00	50.00	0.00
+GCT	21	50.00	0.00	0.00	50.00
+GCT	22	0.00	50.00	0.00	50.00
+GCT	23	0.00	0.00	0.00	100.00
+GCT	24	0.00	50.00	50.00	0.00
+GCT	25	0.00	0.00	0.00	100.00
+GCT	26	0.00	0.00	50.00	50.00
+GCT	27	0.00	100.00	0.00	0.00
+GCT	28	0.00	0.00	0.00	100.00
+GCT	29	50.00	0.00	50.00	0.00
+GCT	30	0.00	50.00	0.00	50.00
+GCT	31	0.00	50.00	0.00	50.00
+GCT	32	0.00	0.00	50.00	50.00
+GCT	33	0.00	50.00	0.00	50.00
+GCT	34	50.00	0.00	0.00	50.00
+GCT	35	0.00	50.00	0.00	50.00
+GCT	36	0.00	100.00	0.00	0.00
+GCT	37	0.00	50.00	0.00	50.00
+GCT	38	50.00	50.00	0.00	0.00
+GCT	39	100.00	0.00	0.00	0.00
+GCT	40	0.00	0.00	100.00	0.00
+GCT	41	0.00	50.00	0.00	50.00
+GCT	42	50.00	50.00	0.00	0.00
+GCT	43	0.00	0.00	50.00	50.00
+GCT	44	50.00	0.00	50.00	0.00
+GCT	45	50.00	0.00	50.00	0.00
+GCT	46	50.00	0.00	50.00	0.00
+GCT	47	50.00	0.00	50.00	0.00
+GCT	48	0.00	50.00	50.00	0.00
+GCT	49	50.00	0.00	0.00	50.00
+GCT	50	0.00	0.00	50.00	50.00
+GCT	51	0.00	0.00	100.00	0.00
+GCT	52	50.00	0.00	50.00	0.00
+GCT	53	0.00	50.00	0.00	50.00
+GCT	54	50.00	0.00	50.00	0.00
+GCT	55	50.00	0.00	0.00	50.00
+GCT	56	0.00	50.00	50.00	0.00
+GCT	57	100.00	0.00	0.00	0.00
+GCT	58	50.00	0.00	50.00	0.00
+GCT	59	100.00	0.00	0.00	0.00
+GCT	60	50.00	0.00	50.00	0.00
+GCT	61	0.00	0.00	0.00	100.00
+GCT	62	0.00	50.00	50.00	0.00
+GCT	63	50.00	0.00	0.00	50.00
+GCT	64	0.00	0.00	100.00	0.00
+GCT	65	50.00	50.00	0.00	0.00
+GCT	66	0.00	50.00	0.00	50.00
+GCT	67	0.00	0.00	0.00	100.00
+GCT	68	0.00	50.00	0.00	50.00
+GCT	69	0.00	50.00	0.00	50.00
+GCT	70	50.00	0.00	0.00	50.00
+GCT	71	0.00	0.00	0.00	100.00
+GCT	72	0.00	50.00	0.00	50.00
+GCT	73	0.00	0.00	0.00	100.00
+GCT	74	0.00	50.00	0.00	50.00
+GCT	75	50.00	0.00	0.00	50.00
+GCT	76	0.00	50.00	0.00	50.00
+GCT	77	50.00	0.00	0.00	50.00
+GCT	78	50.00	0.00	0.00	50.00
+GCT	79	50.00	0.00	0.00	50.00
+GCT	80	50.00	0.00	0.00	50.00
+GCT	81	50.00	0.00	0.00	50.00
+GCT	82	50.00	0.00	0.00	50.00
+GCT	83	50.00	0.00	0.00	50.00
+GCT	84	50.00	0.00	0.00	50.00
+GCT	85	50.00	0.00	0.00	50.00
+GCT	86	50.00	0.00	0.00	50.00
+GCT	87	50.00	0.00	0.00	50.00
+GCT	88	50.00	0.00	0.00	50.00
+GCT	89	50.00	0.00	0.00	50.00
+GCT	90	50.00	0.00	0.00	50.00
+GCT	91	50.00	0.00	50.00	0.00
+GCT	92	50.00	0.00	50.00	0.00
+GCT	93	50.00	0.00	50.00	0.00
+GCT	94	50.00	0.00	0.00	50.00
+GCT	95	50.00	0.00	50.00	0.00
+GCT	96	50.00	0.00	50.00	0.00
+GCT	97	50.00	0.00	50.00	0.00
+GCT	98	50.00	0.00	50.00	0.00
+GCT	99	50.00	0.00	50.00	0.00
+GCT	100	50.00	0.00	0.00	50.00
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -454,6 +559,8 @@
 FBC	98	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	100	100.00	0.00	0.00	0.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	50	21	14	15	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	0.00	0.00	100.00	0.00	0.00	0.00
 LBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -555,6 +662,26 @@
 LBC	98	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	99	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	100	100.00	0.00	0.00	0.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	41	20	23	16	0
+# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%]
+BCC1	2	0.00	0.00	100.00	0.00	0.00
+BCC1	3	0.00	0.00	0.00	100.00	0.00
+BCC1	4	0.00	100.00	0.00	0.00	0.00
+BCC1	5	0.00	0.00	0.00	100.00	0.00
+BCC1	6	100.00	0.00	0.00	0.00	0.00
+BCC1	7	0.00	0.00	0.00	100.00	0.00
+BCC1	8	0.00	100.00	0.00	0.00	0.00
+# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
+QTQ1	1	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	0	0	0
+QTQ1	2	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
+QTQ1	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	1	0	0	0	0	0	0	0	0	0
+QTQ1	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	0	1	0	0
+QTQ1	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	1	0	0
+QTQ1	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	1
+QTQ1	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	1
+QTQ1	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	1	0	0
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/12.3reads.nooverlap.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/12.3reads.nooverlap.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats -t /tmp/tmp0r5zs075/files/1/3/0/dataset_13082855-efe1-437e-8a91-ff7d013770db.dat -p -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	09f8b87f	140798ec	2b989f07
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	3
+SN	raw total sequences:	3	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	3
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	0	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	300	# ignores clipping
 SN	total first fragment length:	100	# ignores clipping
 SN	total last fragment length:	200	# ignores clipping
@@ -355,6 +359,107 @@
 GCC	98	0.00	66.67	0.00	33.33	0.00	0.00
 GCC	99	0.00	100.00	0.00	0.00	0.00	0.00
 GCC	100	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	33.33	0.00	0.00	66.67
+GCT	2	0.00	33.33	33.33	33.33
+GCT	3	0.00	33.33	33.33	33.33
+GCT	4	33.33	66.67	0.00	0.00
+GCT	5	0.00	66.67	33.33	0.00
+GCT	6	33.33	0.00	0.00	66.67
+GCT	7	33.33	0.00	0.00	66.67
+GCT	8	0.00	33.33	33.33	33.33
+GCT	9	0.00	66.67	33.33	0.00
+GCT	10	33.33	33.33	0.00	33.33
+GCT	11	33.33	33.33	0.00	33.33
+GCT	12	0.00	33.33	33.33	33.33
+GCT	13	0.00	0.00	33.33	66.67
+GCT	14	0.00	66.67	33.33	0.00
+GCT	15	33.33	66.67	0.00	0.00
+GCT	16	33.33	0.00	0.00	66.67
+GCT	17	33.33	0.00	0.00	66.67
+GCT	18	0.00	33.33	33.33	33.33
+GCT	19	0.00	33.33	33.33	33.33
+GCT	20	0.00	66.67	33.33	0.00
+GCT	21	33.33	66.67	0.00	0.00
+GCT	22	33.33	0.00	0.00	66.67
+GCT	23	0.00	0.00	33.33	66.67
+GCT	24	0.00	33.33	33.33	33.33
+GCT	25	33.33	66.67	0.00	0.00
+GCT	26	33.33	33.33	0.00	33.33
+GCT	27	0.00	33.33	33.33	33.33
+GCT	28	0.00	33.33	33.33	33.33
+GCT	29	0.00	0.00	33.33	66.67
+GCT	30	33.33	66.67	0.00	0.00
+GCT	31	33.33	66.67	0.00	0.00
+GCT	32	33.33	0.00	0.00	66.67
+GCT	33	0.00	0.00	33.33	66.67
+GCT	34	0.00	33.33	33.33	33.33
+GCT	35	33.33	33.33	0.00	33.33
+GCT	36	0.00	66.67	33.33	0.00
+GCT	37	33.33	66.67	0.00	0.00
+GCT	38	33.33	0.00	0.00	66.67
+GCT	39	0.00	0.00	33.33	66.67
+GCT	40	0.00	33.33	33.33	33.33
+GCT	41	33.33	66.67	0.00	0.00
+GCT	42	33.33	33.33	0.00	33.33
+GCT	43	0.00	33.33	33.33	33.33
+GCT	44	0.00	33.33	33.33	33.33
+GCT	45	0.00	33.33	33.33	33.33
+GCT	46	33.33	66.67	0.00	0.00
+GCT	47	33.33	33.33	0.00	33.33
+GCT	48	33.33	0.00	0.00	66.67
+GCT	49	0.00	0.00	33.33	66.67
+GCT	50	0.00	66.67	33.33	0.00
+GCT	51	33.33	66.67	0.00	0.00
+GCT	52	0.00	66.67	33.33	0.00
+GCT	53	33.33	0.00	0.00	66.67
+GCT	54	33.33	0.00	0.00	66.67
+GCT	55	0.00	33.33	33.33	33.33
+GCT	56	0.00	66.67	33.33	0.00
+GCT	57	33.33	33.33	0.00	33.33
+GCT	58	33.33	33.33	0.00	33.33
+GCT	59	0.00	33.33	33.33	33.33
+GCT	60	0.00	0.00	33.33	66.67
+GCT	61	0.00	66.67	33.33	0.00
+GCT	62	33.33	66.67	0.00	0.00
+GCT	63	33.33	0.00	0.00	66.67
+GCT	64	33.33	0.00	0.00	66.67
+GCT	65	0.00	33.33	33.33	33.33
+GCT	66	0.00	33.33	33.33	33.33
+GCT	67	33.33	66.67	0.00	0.00
+GCT	68	0.00	66.67	33.33	0.00
+GCT	69	33.33	0.00	0.00	66.67
+GCT	70	33.33	0.00	0.00	66.67
+GCT	71	0.00	33.33	33.33	33.33
+GCT	72	0.00	66.67	33.33	0.00
+GCT	73	33.33	33.33	0.00	33.33
+GCT	74	33.33	33.33	0.00	33.33
+GCT	75	0.00	33.33	33.33	33.33
+GCT	76	0.00	0.00	33.33	66.67
+GCT	77	0.00	66.67	33.33	0.00
+GCT	78	33.33	66.67	0.00	0.00
+GCT	79	33.33	0.00	0.00	66.67
+GCT	80	33.33	0.00	0.00	66.67
+GCT	81	0.00	33.33	33.33	33.33
+GCT	82	0.00	66.67	33.33	0.00
+GCT	83	0.00	66.67	33.33	0.00
+GCT	84	33.33	33.33	0.00	33.33
+GCT	85	33.33	0.00	0.00	66.67
+GCT	86	0.00	0.00	33.33	66.67
+GCT	87	0.00	66.67	33.33	0.00
+GCT	88	33.33	66.67	0.00	0.00
+GCT	89	33.33	33.33	0.00	33.33
+GCT	90	0.00	0.00	33.33	66.67
+GCT	91	0.00	33.33	33.33	33.33
+GCT	92	0.00	66.67	33.33	0.00
+GCT	93	33.33	66.67	0.00	0.00
+GCT	94	33.33	33.33	0.00	33.33
+GCT	95	33.33	0.00	0.00	66.67
+GCT	96	0.00	33.33	33.33	33.33
+GCT	97	33.33	0.00	33.33	33.33
+GCT	98	33.33	66.67	0.00	0.00
+GCT	99	0.00	66.67	33.33	0.00
+GCT	100	33.33	0.00	0.00	66.67
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	100.00	0.00	0.00	0.00	0.00
@@ -456,6 +561,8 @@
 FBC	98	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	100	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	0	51	0	49	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 LBC	2	0.00	50.00	0.00	50.00	0.00	0.00
@@ -557,6 +664,26 @@
 LBC	98	0.00	100.00	0.00	0.00	0.00	0.00
 LBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 LBC	100	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	1	102	0	97	0
+# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%]
+BCC1	2	0.00	0.00	100.00	0.00	0.00
+BCC1	3	0.00	0.00	0.00	100.00	0.00
+BCC1	4	0.00	100.00	0.00	0.00	0.00
+BCC1	5	0.00	0.00	0.00	100.00	0.00
+BCC1	6	100.00	0.00	0.00	0.00	0.00
+BCC1	7	0.00	0.00	0.00	100.00	0.00
+BCC1	8	0.00	100.00	0.00	0.00	0.00
+# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
+QTQ1	1	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	0	0	0
+QTQ1	2	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
+QTQ1	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	1	0	0	0	0	0	0	0	0	0
+QTQ1	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	0	1	0	0
+QTQ1	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	1
+QTQ1	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	1
+QTQ1	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	1
+QTQ1	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	1	0	0
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/12.3reads.overlap.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/12.3reads.overlap.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats -t /tmp/tmp0r5zs075/files/6/5/e/dataset_65ea4e4d-a70d-4001-911d-9d81ff2829a6.dat -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	09f8b87f	140798ec	2b989f07
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	3
+SN	raw total sequences:	3	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	3
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	0	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	300	# ignores clipping
 SN	total first fragment length:	100	# ignores clipping
 SN	total last fragment length:	200	# ignores clipping
@@ -355,6 +359,107 @@
 GCC	98	0.00	66.67	0.00	33.33	0.00	0.00
 GCC	99	0.00	100.00	0.00	0.00	0.00	0.00
 GCC	100	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	33.33	0.00	0.00	66.67
+GCT	2	0.00	33.33	33.33	33.33
+GCT	3	0.00	33.33	33.33	33.33
+GCT	4	33.33	66.67	0.00	0.00
+GCT	5	0.00	66.67	33.33	0.00
+GCT	6	33.33	0.00	0.00	66.67
+GCT	7	33.33	0.00	0.00	66.67
+GCT	8	0.00	33.33	33.33	33.33
+GCT	9	0.00	66.67	33.33	0.00
+GCT	10	33.33	33.33	0.00	33.33
+GCT	11	33.33	33.33	0.00	33.33
+GCT	12	0.00	33.33	33.33	33.33
+GCT	13	0.00	0.00	33.33	66.67
+GCT	14	0.00	66.67	33.33	0.00
+GCT	15	33.33	66.67	0.00	0.00
+GCT	16	33.33	0.00	0.00	66.67
+GCT	17	33.33	0.00	0.00	66.67
+GCT	18	0.00	33.33	33.33	33.33
+GCT	19	0.00	33.33	33.33	33.33
+GCT	20	0.00	66.67	33.33	0.00
+GCT	21	33.33	66.67	0.00	0.00
+GCT	22	33.33	0.00	0.00	66.67
+GCT	23	0.00	0.00	33.33	66.67
+GCT	24	0.00	33.33	33.33	33.33
+GCT	25	33.33	66.67	0.00	0.00
+GCT	26	33.33	33.33	0.00	33.33
+GCT	27	0.00	33.33	33.33	33.33
+GCT	28	0.00	33.33	33.33	33.33
+GCT	29	0.00	0.00	33.33	66.67
+GCT	30	33.33	66.67	0.00	0.00
+GCT	31	33.33	66.67	0.00	0.00
+GCT	32	33.33	0.00	0.00	66.67
+GCT	33	0.00	0.00	33.33	66.67
+GCT	34	0.00	33.33	33.33	33.33
+GCT	35	33.33	33.33	0.00	33.33
+GCT	36	0.00	66.67	33.33	0.00
+GCT	37	33.33	66.67	0.00	0.00
+GCT	38	33.33	0.00	0.00	66.67
+GCT	39	0.00	0.00	33.33	66.67
+GCT	40	0.00	33.33	33.33	33.33
+GCT	41	33.33	66.67	0.00	0.00
+GCT	42	33.33	33.33	0.00	33.33
+GCT	43	0.00	33.33	33.33	33.33
+GCT	44	0.00	33.33	33.33	33.33
+GCT	45	0.00	33.33	33.33	33.33
+GCT	46	33.33	66.67	0.00	0.00
+GCT	47	33.33	33.33	0.00	33.33
+GCT	48	33.33	0.00	0.00	66.67
+GCT	49	0.00	0.00	33.33	66.67
+GCT	50	0.00	66.67	33.33	0.00
+GCT	51	33.33	66.67	0.00	0.00
+GCT	52	0.00	66.67	33.33	0.00
+GCT	53	33.33	0.00	0.00	66.67
+GCT	54	33.33	0.00	0.00	66.67
+GCT	55	0.00	33.33	33.33	33.33
+GCT	56	0.00	66.67	33.33	0.00
+GCT	57	33.33	33.33	0.00	33.33
+GCT	58	33.33	33.33	0.00	33.33
+GCT	59	0.00	33.33	33.33	33.33
+GCT	60	0.00	0.00	33.33	66.67
+GCT	61	0.00	66.67	33.33	0.00
+GCT	62	33.33	66.67	0.00	0.00
+GCT	63	33.33	0.00	0.00	66.67
+GCT	64	33.33	0.00	0.00	66.67
+GCT	65	0.00	33.33	33.33	33.33
+GCT	66	0.00	33.33	33.33	33.33
+GCT	67	33.33	66.67	0.00	0.00
+GCT	68	0.00	66.67	33.33	0.00
+GCT	69	33.33	0.00	0.00	66.67
+GCT	70	33.33	0.00	0.00	66.67
+GCT	71	0.00	33.33	33.33	33.33
+GCT	72	0.00	66.67	33.33	0.00
+GCT	73	33.33	33.33	0.00	33.33
+GCT	74	33.33	33.33	0.00	33.33
+GCT	75	0.00	33.33	33.33	33.33
+GCT	76	0.00	0.00	33.33	66.67
+GCT	77	0.00	66.67	33.33	0.00
+GCT	78	33.33	66.67	0.00	0.00
+GCT	79	33.33	0.00	0.00	66.67
+GCT	80	33.33	0.00	0.00	66.67
+GCT	81	0.00	33.33	33.33	33.33
+GCT	82	0.00	66.67	33.33	0.00
+GCT	83	0.00	66.67	33.33	0.00
+GCT	84	33.33	33.33	0.00	33.33
+GCT	85	33.33	0.00	0.00	66.67
+GCT	86	0.00	0.00	33.33	66.67
+GCT	87	0.00	66.67	33.33	0.00
+GCT	88	33.33	66.67	0.00	0.00
+GCT	89	33.33	33.33	0.00	33.33
+GCT	90	0.00	0.00	33.33	66.67
+GCT	91	0.00	33.33	33.33	33.33
+GCT	92	0.00	66.67	33.33	0.00
+GCT	93	33.33	66.67	0.00	0.00
+GCT	94	33.33	33.33	0.00	33.33
+GCT	95	33.33	0.00	0.00	66.67
+GCT	96	0.00	33.33	33.33	33.33
+GCT	97	33.33	0.00	33.33	33.33
+GCT	98	33.33	66.67	0.00	0.00
+GCT	99	0.00	66.67	33.33	0.00
+GCT	100	33.33	0.00	0.00	66.67
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	100.00	0.00	0.00	0.00	0.00
@@ -456,6 +561,8 @@
 FBC	98	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 FBC	100	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	0	51	0	49	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 LBC	2	0.00	50.00	0.00	50.00	0.00	0.00
@@ -557,6 +664,26 @@
 LBC	98	0.00	100.00	0.00	0.00	0.00	0.00
 LBC	99	0.00	100.00	0.00	0.00	0.00	0.00
 LBC	100	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	1	102	0	97	0
+# ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%]
+BCC1	2	0.00	0.00	100.00	0.00	0.00
+BCC1	3	0.00	0.00	0.00	100.00	0.00
+BCC1	4	0.00	100.00	0.00	0.00	0.00
+BCC1	5	0.00	0.00	0.00	100.00	0.00
+BCC1	6	100.00	0.00	0.00	0.00	0.00
+BCC1	7	0.00	0.00	0.00	100.00	0.00
+BCC1	8	0.00	100.00	0.00	0.00	0.00
+# Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
+QTQ1	1	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	0	0	0
+QTQ1	2	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
+QTQ1	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	1	0	0	0	0	0	0	0	0	0
+QTQ1	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	0	1	0	0
+QTQ1	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	1
+QTQ1	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	1
+QTQ1	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	1
+QTQ1	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	1	0	0
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/2.stats.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/2.stats.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats --ref-seq reference.fa -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	1a1c1362	29c426ae	7bab45da
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	2
+SN	raw total sequences:	2	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	2
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	0	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	70	# ignores clipping
 SN	total first fragment length:	35	# ignores clipping
 SN	total last fragment length:	35	# ignores clipping
@@ -195,6 +199,42 @@
 GCC	33	50.00	0.00	0.00	50.00	0.00	0.00
 GCC	34	50.00	0.00	50.00	0.00	0.00	0.00
 GCC	35	0.00	0.00	50.00	50.00	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	0.00	50.00	0.00	50.00
+GCT	2	50.00	0.00	50.00	0.00
+GCT	3	0.00	0.00	50.00	50.00
+GCT	4	0.00	0.00	100.00	0.00
+GCT	5	0.00	0.00	50.00	50.00
+GCT	6	0.00	50.00	0.00	50.00
+GCT	7	0.00	0.00	50.00	50.00
+GCT	8	0.00	0.00	0.00	100.00
+GCT	9	0.00	50.00	50.00	0.00
+GCT	10	50.00	0.00	50.00	0.00
+GCT	11	50.00	0.00	0.00	50.00
+GCT	12	50.00	0.00	50.00	0.00
+GCT	13	50.00	0.00	50.00	0.00
+GCT	14	0.00	0.00	0.00	100.00
+GCT	15	100.00	0.00	0.00	0.00
+GCT	16	50.00	0.00	0.00	50.00
+GCT	17	0.00	0.00	50.00	50.00
+GCT	18	0.00	50.00	50.00	0.00
+GCT	19	0.00	100.00	0.00	0.00
+GCT	20	0.00	0.00	50.00	50.00
+GCT	21	0.00	0.00	100.00	0.00
+GCT	22	0.00	50.00	0.00	50.00
+GCT	23	50.00	0.00	0.00	50.00
+GCT	24	50.00	0.00	50.00	0.00
+GCT	25	50.00	0.00	50.00	0.00
+GCT	26	0.00	0.00	100.00	0.00
+GCT	27	50.00	0.00	0.00	50.00
+GCT	28	0.00	0.00	50.00	50.00
+GCT	29	0.00	50.00	0.00	50.00
+GCT	30	0.00	50.00	0.00	50.00
+GCT	31	0.00	50.00	50.00	0.00
+GCT	32	0.00	0.00	100.00	0.00
+GCT	33	100.00	0.00	0.00	0.00
+GCT	34	0.00	0.00	50.00	50.00
+GCT	35	50.00	0.00	50.00	0.00
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -231,6 +271,8 @@
 FBC	33	100.00	0.00	0.00	0.00	0.00	0.00
 FBC	34	0.00	0.00	100.00	0.00	0.00	0.00
 FBC	35	0.00	0.00	100.00	0.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	6	5	15	9	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	0.00	0.00	100.00	0.00	0.00	0.00
 LBC	2	0.00	0.00	0.00	100.00	0.00	0.00
@@ -267,6 +309,8 @@
 LBC	33	0.00	0.00	0.00	100.00	0.00	0.00
 LBC	34	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	35	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	11	10	5	9	0
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/6.stats.expected	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/6.stats.expected	Tue Sep 28 16:17:39 2021 +0000
@@ -1,8 +1,11 @@
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
+# This file contains statistics for all reads.
+# The command line was:  stats --insert-size 0 --ref-seq reference.fa -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
 CHK	1a1c1362	32507d92	7bab45da
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	2
+SN	raw total sequences:	2	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	2
 SN	is sorted:	1
@@ -17,6 +20,7 @@
 SN	reads MQ0:	0	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	70	# ignores clipping
 SN	total first fragment length:	35	# ignores clipping
 SN	total last fragment length:	35	# ignores clipping
@@ -195,6 +199,42 @@
 GCC	33	0.00	0.00	50.00	50.00	0.00	0.00
 GCC	34	100.00	0.00	0.00	0.00	0.00	0.00
 GCC	35	0.00	0.00	50.00	50.00	0.00	0.00
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	0.00	50.00	0.00	50.00
+GCT	2	50.00	0.00	50.00	0.00
+GCT	3	0.00	0.00	50.00	50.00
+GCT	4	0.00	0.00	100.00	0.00
+GCT	5	0.00	0.00	50.00	50.00
+GCT	6	0.00	50.00	50.00	0.00
+GCT	7	0.00	0.00	0.00	100.00
+GCT	8	0.00	0.00	50.00	50.00
+GCT	9	0.00	0.00	50.00	50.00
+GCT	10	0.00	50.00	50.00	0.00
+GCT	11	100.00	0.00	0.00	0.00
+GCT	12	0.00	0.00	50.00	50.00
+GCT	13	100.00	0.00	0.00	0.00
+GCT	14	0.00	0.00	50.00	50.00
+GCT	15	50.00	0.00	0.00	50.00
+GCT	16	50.00	0.00	0.00	50.00
+GCT	17	50.00	0.00	50.00	0.00
+GCT	18	0.00	0.00	50.00	50.00
+GCT	19	0.00	100.00	0.00	0.00
+GCT	20	0.00	50.00	0.00	50.00
+GCT	21	0.00	0.00	100.00	0.00
+GCT	22	0.00	50.00	50.00	0.00
+GCT	23	50.00	0.00	0.00	50.00
+GCT	24	50.00	0.00	0.00	50.00
+GCT	25	50.00	0.00	50.00	0.00
+GCT	26	0.00	0.00	100.00	0.00
+GCT	27	0.00	0.00	50.00	50.00
+GCT	28	50.00	0.00	0.00	50.00
+GCT	29	0.00	50.00	50.00	0.00
+GCT	30	0.00	0.00	0.00	100.00
+GCT	31	0.00	50.00	50.00	0.00
+GCT	32	0.00	50.00	50.00	0.00
+GCT	33	50.00	0.00	50.00	0.00
+GCT	34	50.00	0.00	0.00	50.00
+GCT	35	50.00	0.00	50.00	0.00
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	0.00	0.00	0.00	100.00	0.00	0.00
 FBC	2	0.00	0.00	100.00	0.00	0.00	0.00
@@ -231,6 +271,8 @@
 FBC	33	0.00	0.00	100.00	0.00	0.00	0.00
 FBC	34	100.00	0.00	0.00	0.00	0.00	0.00
 FBC	35	0.00	0.00	100.00	0.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	6	5	15	9	0
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	0.00	0.00	100.00	0.00	0.00	0.00
 LBC	2	0.00	0.00	0.00	100.00	0.00	0.00
@@ -267,6 +309,8 @@
 LBC	33	0.00	0.00	0.00	100.00	0.00	0.00
 LBC	34	100.00	0.00	0.00	0.00	0.00	0.00
 LBC	35	0.00	0.00	0.00	100.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	11	10	5	9	0
 # 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
 IS	0	0	0	0	0
 IS	1	0	0	0	0
--- a/test-data/samtools_stats_out1.tab	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/samtools_stats_out1.tab	Tue Sep 28 16:17:39 2021 +0000
@@ -1,11 +1,11 @@
-# This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats
+# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats
 # This file contains statistics for all reads.
-# The command line was:  stats --ref-seq reference.fa infile
+# The command line was:  stats --ref-seq reference.fa -@ 0 infile
 # 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
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	200
+SN	raw total sequences:	200	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	200
 SN	is sorted:	1
@@ -20,6 +20,7 @@
 SN	reads MQ0:	6	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
+SN	supplementary alignments:	0
 SN	total length:	50200	# ignores clipping
 SN	total first fragment length:	25100	# ignores clipping
 SN	total last fragment length:	25100	# ignores clipping
@@ -1094,6 +1095,258 @@
 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
+# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
+GCT	1	22.45	32.65	31.63	13.27
+GCT	2	26.00	17.00	10.00	47.00
+GCT	3	34.00	25.00	9.00	32.00
+GCT	4	13.00	32.00	10.00	45.00
+GCT	5	37.00	24.00	10.00	29.00
+GCT	6	44.00	26.00	17.00	13.00
+GCT	7	28.00	13.00	32.00	27.00
+GCT	8	49.00	16.00	18.00	17.00
+GCT	9	19.00	35.00	16.00	30.00
+GCT	10	35.00	13.00	22.00	30.00
+GCT	11	18.00	15.00	29.00	38.00
+GCT	12	28.00	24.00	22.00	26.00
+GCT	13	29.00	17.00	19.00	35.00
+GCT	14	21.21	24.24	24.24	30.30
+GCT	15	23.00	20.00	25.00	32.00
+GCT	16	35.00	15.00	20.00	30.00
+GCT	17	29.00	26.00	13.00	32.00
+GCT	18	31.00	30.00	18.00	21.00
+GCT	19	30.00	26.00	21.00	23.00
+GCT	20	23.00	21.00	20.00	36.00
+GCT	21	36.00	18.00	19.00	27.00
+GCT	22	39.00	31.00	13.00	17.00
+GCT	23	30.30	21.21	11.11	37.37
+GCT	24	36.00	14.00	20.00	30.00
+GCT	25	38.00	23.00	17.00	22.00
+GCT	26	36.00	21.00	13.00	30.00
+GCT	27	32.00	18.00	22.00	28.00
+GCT	28	30.00	13.00	25.00	32.00
+GCT	29	30.00	28.00	23.00	19.00
+GCT	30	34.00	21.00	13.00	32.00
+GCT	31	33.00	29.00	14.00	24.00
+GCT	32	38.00	20.00	20.00	22.00
+GCT	33	27.00	23.00	15.00	35.00
+GCT	34	43.00	17.00	20.00	20.00
+GCT	35	35.00	23.00	22.00	20.00
+GCT	36	41.00	25.00	16.00	18.00
+GCT	37	38.00	18.00	18.00	26.00
+GCT	38	23.00	26.00	25.00	26.00
+GCT	39	22.00	41.00	19.00	18.00
+GCT	40	29.00	14.00	23.00	34.00
+GCT	41	29.00	27.00	20.00	24.00
+GCT	42	29.00	27.00	18.00	26.00
+GCT	43	38.00	28.00	16.00	18.00
+GCT	44	21.00	26.00	23.00	30.00
+GCT	45	38.00	25.00	18.00	19.00
+GCT	46	27.00	21.00	22.00	30.00
+GCT	47	40.00	28.00	18.00	14.00
+GCT	48	25.00	22.00	20.00	33.00
+GCT	49	26.00	33.00	10.00	31.00
+GCT	50	49.00	20.00	10.00	21.00
+GCT	51	29.00	29.00	13.00	29.00
+GCT	52	43.00	22.00	22.00	13.00
+GCT	53	19.00	27.00	27.00	27.00
+GCT	54	25.00	18.00	25.00	32.00
+GCT	55	32.00	22.00	17.00	29.00
+GCT	56	36.00	20.00	16.00	28.00
+GCT	57	28.00	24.00	23.00	25.00
+GCT	58	23.00	39.00	17.00	21.00
+GCT	59	33.00	21.00	26.00	20.00
+GCT	60	30.00	26.00	19.00	25.00
+GCT	61	23.00	23.00	25.00	29.00
+GCT	62	35.00	19.00	20.00	26.00
+GCT	63	26.00	25.00	29.00	20.00
+GCT	64	30.00	20.00	27.00	23.00
+GCT	65	38.00	17.00	21.00	24.00
+GCT	66	33.00	26.00	14.00	27.00
+GCT	67	35.00	21.00	21.00	23.00
+GCT	68	39.00	28.00	15.00	18.00
+GCT	69	38.00	18.00	22.00	22.00
+GCT	70	40.00	13.00	22.00	25.00
+GCT	71	29.00	41.00	19.00	11.00
+GCT	72	33.00	26.00	28.00	13.00
+GCT	73	31.00	18.00	24.00	27.00
+GCT	74	31.00	32.00	13.00	24.00
+GCT	75	46.00	10.00	21.00	23.00
+GCT	76	23.00	28.00	25.00	24.00
+GCT	77	35.00	20.00	19.00	26.00
+GCT	78	29.00	30.00	26.00	15.00
+GCT	79	24.00	25.00	27.00	24.00
+GCT	80	40.00	18.00	29.00	13.00
+GCT	81	18.00	26.00	26.00	30.00
+GCT	82	30.00	25.00	28.00	17.00
+GCT	83	36.00	25.00	14.00	25.00
+GCT	84	22.00	39.00	23.00	16.00
+GCT	85	42.00	20.00	21.00	17.00
+GCT	86	12.00	47.00	16.00	25.00
+GCT	87	45.00	15.00	19.00	21.00
+GCT	88	26.00	24.00	31.00	19.00
+GCT	89	26.00	25.00	29.00	20.00
+GCT	90	24.00	22.00	26.00	28.00
+GCT	91	29.00	30.00	24.00	17.00
+GCT	92	22.00	13.00	32.00	33.00
+GCT	93	29.00	40.00	13.00	18.00
+GCT	94	30.00	16.00	25.00	29.00
+GCT	95	31.31	35.35	17.17	16.16
+GCT	96	34.00	27.00	15.00	24.00
+GCT	97	32.00	27.00	25.00	16.00
+GCT	98	21.21	31.31	24.24	23.23
+GCT	99	27.00	37.00	21.00	15.00
+GCT	100	29.00	15.00	26.00	30.00
+GCT	101	27.00	34.00	25.00	14.00
+GCT	102	20.00	14.00	36.00	30.00
+GCT	103	32.00	26.00	16.00	26.00
+GCT	104	30.00	28.00	22.00	20.00
+GCT	105	35.00	35.00	19.00	11.00
+GCT	106	22.00	32.00	25.00	21.00
+GCT	107	19.19	33.33	26.26	21.21
+GCT	108	27.27	33.33	21.21	18.18
+GCT	109	19.00	29.00	24.00	28.00
+GCT	110	20.20	31.31	28.28	20.20
+GCT	111	25.25	33.33	22.22	19.19
+GCT	112	39.39	28.28	16.16	16.16
+GCT	113	21.21	24.24	31.31	23.23
+GCT	114	19.00	31.00	35.00	15.00
+GCT	115	32.00	23.00	25.00	20.00
+GCT	116	20.00	29.00	35.00	16.00
+GCT	117	31.00	21.00	21.00	27.00
+GCT	118	25.00	14.00	35.00	26.00
+GCT	119	21.00	31.00	24.00	24.00
+GCT	120	19.00	24.00	27.00	30.00
+GCT	121	24.24	36.36	20.20	19.19
+GCT	122	18.00	25.00	23.00	34.00
+GCT	123	25.00	48.00	10.00	17.00
+GCT	124	10.00	31.00	35.00	24.00
+GCT	125	27.00	24.00	22.00	27.00
+GCT	126	24.00	19.00	26.00	31.00
+GCT	127	26.00	16.00	22.00	36.00
+GCT	128	16.00	35.00	30.00	19.00
+GCT	129	24.00	27.00	26.00	23.00
+GCT	130	25.00	19.00	23.00	33.00
+GCT	131	17.00	40.00	24.00	19.00
+GCT	132	20.00	27.00	24.00	29.00
+GCT	133	15.00	34.00	33.00	18.00
+GCT	134	22.00	19.00	31.00	28.00
+GCT	135	17.00	28.00	26.00	29.00
+GCT	136	25.00	33.00	14.00	28.00
+GCT	137	21.00	22.00	30.00	27.00
+GCT	138	15.00	30.00	29.00	26.00
+GCT	139	19.00	32.00	22.00	27.00
+GCT	140	19.00	24.00	29.00	28.00
+GCT	141	21.00	24.00	25.00	30.00
+GCT	142	17.00	32.00	35.00	16.00
+GCT	143	23.00	23.00	28.00	26.00
+GCT	144	20.00	33.00	24.00	23.00
+GCT	145	20.00	26.00	24.00	30.00
+GCT	146	26.00	15.00	40.00	19.00
+GCT	147	23.00	23.00	30.00	24.00
+GCT	148	12.00	32.00	33.00	23.00
+GCT	149	27.00	24.00	23.00	26.00
+GCT	150	12.00	32.00	21.00	35.00
+GCT	151	22.00	29.00	34.00	15.00
+GCT	152	16.00	21.00	26.00	37.00
+GCT	153	24.00	20.00	34.00	22.00
+GCT	154	25.00	22.00	28.00	25.00
+GCT	155	21.00	28.00	17.00	34.00
+GCT	156	16.00	23.00	36.00	25.00
+GCT	157	23.00	34.00	20.00	23.00
+GCT	158	21.00	33.00	21.00	25.00
+GCT	159	19.00	15.00	44.00	22.00
+GCT	160	24.00	31.00	22.00	23.00
+GCT	161	13.00	28.00	40.00	19.00
+GCT	162	33.00	19.00	20.00	28.00
+GCT	163	23.00	26.00	31.00	20.00
+GCT	164	33.00	19.00	20.00	28.00
+GCT	165	13.00	16.00	37.00	34.00
+GCT	166	20.00	36.00	30.00	14.00
+GCT	167	17.00	28.00	25.00	30.00
+GCT	168	16.00	24.00	31.00	29.00
+GCT	169	21.00	23.00	21.00	35.00
+GCT	170	22.00	24.00	27.00	27.00
+GCT	171	23.00	30.00	31.00	16.00
+GCT	172	24.00	22.00	30.00	24.00
+GCT	173	24.00	17.00	33.00	26.00
+GCT	174	21.00	24.00	33.00	22.00
+GCT	175	34.00	19.00	34.00	13.00
+GCT	176	17.00	37.00	24.00	22.00
+GCT	177	24.00	24.00	25.00	27.00
+GCT	178	19.00	26.00	30.00	25.00
+GCT	179	24.00	20.00	20.00	36.00
+GCT	180	22.00	25.00	31.00	22.00
+GCT	181	21.00	17.00	38.00	24.00
+GCT	182	35.00	21.00	20.00	24.00
+GCT	183	28.00	15.00	27.00	30.00
+GCT	184	17.00	30.00	29.00	24.00
+GCT	185	16.00	32.00	33.00	19.00
+GCT	186	21.00	22.00	36.00	21.00
+GCT	187	24.00	13.00	41.00	22.00
+GCT	188	29.00	19.00	30.00	22.00
+GCT	189	19.00	23.00	33.00	25.00
+GCT	190	24.00	28.00	25.00	23.00
+GCT	191	28.00	21.00	29.00	22.00
+GCT	192	37.00	25.00	13.00	25.00
+GCT	193	18.00	26.00	25.00	31.00
+GCT	194	21.00	34.00	24.00	21.00
+GCT	195	16.00	28.00	21.00	35.00
+GCT	196	23.00	23.00	27.00	27.00
+GCT	197	18.00	20.00	24.00	38.00
+GCT	198	15.00	19.00	39.00	27.00
+GCT	199	23.00	17.00	27.00	33.00
+GCT	200	25.00	27.00	23.00	25.00
+GCT	201	26.00	19.00	25.00	30.00
+GCT	202	23.00	23.00	21.00	33.00
+GCT	203	21.00	19.00	32.00	28.00
+GCT	204	26.00	29.00	24.00	21.00
+GCT	205	16.00	23.00	21.00	40.00
+GCT	206	28.00	25.00	21.00	26.00
+GCT	207	22.00	22.00	19.00	37.00
+GCT	208	12.00	32.00	32.00	24.00
+GCT	209	18.00	20.00	15.00	47.00
+GCT	210	18.00	15.00	45.00	22.00
+GCT	211	28.00	14.00	28.00	30.00
+GCT	212	23.00	27.00	22.00	28.00
+GCT	213	22.00	12.00	34.00	32.00
+GCT	214	16.00	24.00	26.00	34.00
+GCT	215	28.00	22.00	25.00	25.00
+GCT	216	18.00	17.00	26.00	39.00
+GCT	217	27.00	30.00	16.00	27.00
+GCT	218	18.00	24.00	24.00	34.00
+GCT	219	19.00	18.00	24.00	39.00
+GCT	220	28.00	23.00	24.00	25.00
+GCT	221	20.00	24.00	20.00	36.00
+GCT	222	22.00	21.00	19.00	38.00
+GCT	223	19.00	22.00	33.00	26.00
+GCT	224	19.00	20.00	27.00	34.00
+GCT	225	14.00	32.00	34.00	20.00
+GCT	226	20.00	20.00	29.00	31.00
+GCT	227	17.00	22.00	26.00	35.00
+GCT	228	34.00	20.00	25.00	21.00
+GCT	229	22.00	27.00	16.00	35.00
+GCT	230	23.00	33.00	15.00	29.00
+GCT	231	20.00	27.00	31.00	22.00
+GCT	232	25.00	23.00	11.00	41.00
+GCT	233	22.00	25.00	27.00	26.00
+GCT	234	14.00	27.00	23.00	36.00
+GCT	235	17.00	11.00	32.00	40.00
+GCT	236	29.00	20.00	24.00	27.00
+GCT	237	16.00	19.00	23.00	42.00
+GCT	238	22.00	25.00	29.00	24.00
+GCT	239	18.00	8.00	17.00	57.00
+GCT	240	27.00	26.00	14.00	33.00
+GCT	241	21.00	22.00	17.00	40.00
+GCT	242	26.00	28.00	10.00	36.00
+GCT	243	25.00	15.00	24.00	36.00
+GCT	244	15.00	24.00	16.00	45.00
+GCT	245	24.00	23.00	19.00	34.00
+GCT	246	18.00	25.00	29.00	28.00
+GCT	247	30.00	13.00	14.00	43.00
+GCT	248	22.00	17.00	26.00	35.00
+GCT	249	25.00	22.00	22.00	31.00
+GCT	250	25.00	20.00	20.00	35.00
+GCT	251	13.00	17.00	40.00	30.00
 # ACGT content per cycle for first fragments. Use `grep ^FBC | 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 [%]
 FBC	1	21.43	27.55	36.73	14.29	2.04	0.00
 FBC	2	34.00	15.00	12.00	39.00	0.00	0.00
@@ -1346,6 +1599,8 @@
 FBC	249	25.00	24.00	20.00	31.00	0.00	0.00
 FBC	250	30.00	25.00	15.00	30.00	0.00	0.00
 FBC	251	14.00	24.00	33.00	29.00	0.00	0.00
+# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+FTC	6178	6247	5821	6841	13
 # ACGT content per cycle for last fragments. Use `grep ^LBC | 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 [%]
 LBC	1	22.45	32.65	31.63	13.27	2.04	0.00
 LBC	2	26.00	17.00	10.00	47.00	0.00	0.00
@@ -1598,6 +1853,8 @@
 LBC	249	25.00	22.00	22.00	31.00	0.00	0.00
 LBC	250	25.00	20.00	20.00	35.00	0.00	0.00
 LBC	251	13.00	17.00	40.00	30.00	0.00	0.00
+# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
+LTC	6413	6102	5966	6606	13
 # 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
--- a/test-data/samtools_stats_out1__sn.tab	Thu Oct 17 02:21:23 2019 -0400
+++ b/test-data/samtools_stats_out1__sn.tab	Tue Sep 28 16:17:39 2021 +0000
@@ -1,5 +1,5 @@
 # Summary Numbers. 
-raw total sequences:	200
+raw total sequences:	200	# excluding supplementary and secondary reads
 filtered sequences:	0
 sequences:	200
 is sorted:	1
@@ -14,6 +14,7 @@
 reads MQ0:	6	# mapped and MQ=0
 reads QC failed:	0
 non-primary alignments:	0
+supplementary alignments:	0
 total length:	50200	# ignores clipping
 total first fragment length:	25100	# ignores clipping
 total last fragment length:	25100	# ignores clipping