# HG changeset patch
# User iuc
# Date 1636648539 0
# Node ID d34c645ab63f2c32b6dc197c1e88aa03f45a0c6b
# Parent  9982e346abc4119145d7010211830955f3e6c92c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"

diff -r 9982e346abc4 -r d34c645ab63f macros.xml
--- a/macros.xml	Tue Oct 05 20:04:22 2021 +0000
+++ b/macros.xml	Thu Nov 11 16:35:39 2021 +0000
@@ -31,6 +31,25 @@
             </conditional>
         </actions>
     </macro>
+    <macro name="input_type_cond">
+        <conditional name="input_type_cond">
+            <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
+                <option value="single" selected="true">Single dataset</option>
+                <option value="pair">Dataset pair</option>
+                <option value="paired">List of dataset pairs</option>
+            </param>
+            <when value="single">
+                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
+            </when>
+            <when value="pair">
+                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
+                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
+            </when>
+            <when value="paired">
+                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
+            </when>
+        </conditional>
+    </macro>
     <macro name="reference_source_cond">
         <conditional name="ref_source_cond">
             <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
@@ -46,10 +65,24 @@
                 </param>
             </when>
             <when value="history">
-                <param name="reference" type="data" format="fasta" label="Using reference genome">
-                    <validator type="no_options" message="The current history does not include a fasta dataset"/>
+                <param name="reference" type="data" format="fasta" label="Using reference genome"/>
+            </when>
+        </conditional>
+    </macro>
+    <macro name="ktrim_cond">
+        <conditional name="ktrim_cond">
+            <param name="ktrim_select"  type="select" label="Trim reads to remove bases matching reference kmers?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param argument="ktrim"  type="select" label="Select trimming position">
+                    <option value="r">Trim to the right</option>
+                    <option value="l">Trim to the left</option>
                 </param>
-            </when>
+                <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/>
+             </when>
         </conditional>
     </macro>
     <xml name="citations">
diff -r 9982e346abc4 -r d34c645ab63f test-data/adapters.fa.gz
Binary file test-data/adapters.fa.gz has changed
diff -r 9982e346abc4 -r d34c645ab63f test-data/bduk_output_dump1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_output_dump1.fasta	Thu Nov 11 16:35:39 2021 +0000
@@ -0,0 +1,100 @@
+>116
+GAGATGGAACTGTAACTGGAGTTCCTT
+>7
+TGCCTAAGTGACTAGAGTTCAGACGTG
+>28
+TGAACTCCAGTCAAATTCCTTTATCTC
+>141
+GCATACGAGATGTATAGGTGACTGGAG
+>3
+GTTCAGCAGGAATACCGAGACCGATCT
+>126
+GGTAGCATCTCGTATGCCGTCTTCTGC
+>123
+GCCAAGGAACTCCAGTCACGTTTCGAT
+>126
+ATACGAGATGCTAACGTGACTGGAGTT
+>18
+CCGTATCTCGTATACCGTCTTCTGCTT
+>26
+TCTGAACTCCAGTAACGAGTGGATATC
+>17
+GAAGACGGCATACAAGATTGTTGACTG
+>22
+TGAACTCCAGTCAAGTGAAACGATCTC
+>50
+ACGCTACGCTATCACGTATGCCGTCTT
+>103
+TCGGGTGCCAAGGAACTCCAGTCACAT
+>141
+ATACATCTCGTATACCGTCTTCTGCTT
+>113
+TCGGGTGCCAAGGAACTCCAGTCACGG
+>84
+GAGATTACTACGCATCTCGTGGGCTCG
+>122
+CGTGGCCATCTCGAATGCCGTCTTCTG
+>139
+TCCAGTCACCGGAATATCTCGTATGCC
+>42
+CAGAAGACGGCATACGAGATTCGCCTT
+>107
+TGTGTGACTGGAGATCCTTGGCACCCG
+>140
+CATACGAGATAGCAAGGTGACTGGAGT
+>6
+GGTGACTGGAGTTAAGACGTGTGCTCT
+>30
+TCTCTTATACACAACTCCGAGCCCACG
+>122
+CAGTCACGTGGCCATCTCGTATGCCGT
+>19
+GTCACATGTCAGAATCTCGTATGCCGT
+>41
+GCGTGTAGATCTCAGTGGTCGCCGTAT
+>1
+GTGACTGGAGTTCAGACGTGTGCTCTT
+>15
+GTCTGAACTCCAGACACGGCTACATCT
+>4
+TCCGATCTCAAGCAGAAGACGGCATAC
+>119
+GAAGACGGCATACAAGATCTCTACGTG
+>129
+GTCACATTCCTATATCGTATGCCGTCT
+>107
+GATCACTGTGTGAATGGAGTTCCTTGG
+>9
+ATACGAGATCACTATGTGACTGGAGTT
+>24
+CTGAACTCCAGTCACGTTTCGGAATCT
+>116
+TGGAACTGTGACTAGAGTTCCTTGGCA
+>13
+GAAGACGGCATACAAGATCTGATCGTG
+>30
+TCTTATACACATCACCGAGCCCACGAG
+>49
+CAGAGAGGATCTCATATGCCGTCTTCT
+>133
+TCGTGGTGACTGGAGTTCCTTGGCACC
+>8
+CAGTCACTGACCAATCTCGTATGCCGT
+>33
+TCTAGTGTAGATCACGGTGGTCGCCGT
+>21
+TGCGGACGTGACTAGAGTTCAGACGTG
+>37
+GACGACTCCTTACATGTAGATCTCGGT
+>124
+GTACGGTGACTGGAGTTCCTTGGCACC
+>69
+TACACTTATGCGAACGTCGGCAGCGTC
+>149
+GCATACGAGATCTACGAGTGACTGGAG
+>124
+GAGATCGTACGGTAACTGGAGTTCCTT
+>105
+GCCAAGGAACTCCAGTCACTTAGGCAT
+>150
+CAGTCACTCGGCAATCTCGTATGCCGT
diff -r 9982e346abc4 -r d34c645ab63f test-data/bduk_output_quhist1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_output_quhist1.tabular	Thu Nov 11 16:35:39 2021 +0000
@@ -0,0 +1,101 @@
+#BaseNum	Read1_linear	Read1_log	Read2_linear	Read2_log
+1	16.400	4.332	32.940	32.694
+2	24.580	19.293	32.680	30.545
+3	29.880	28.913	32.720	32.218
+4	35.400	35.023	35.740	28.139
+5	35.610	35.076	35.980	34.688
+6	36.070	35.819	36.130	35.232
+7	36.030	35.134	35.750	28.304
+8	36.210	35.891	35.760	30.427
+9	37.770	36.724	37.550	36.174
+10	37.770	36.627	37.890	36.829
+11	38.130	34.528	37.720	35.825
+12	38.120	37.610	37.930	36.724
+13	37.600	29.816	37.860	33.975
+14	39.600	38.822	39.490	29.436
+15	39.240	37.118	39.430	34.527
+16	39.370	37.815	39.670	29.527
+17	39.230	35.062	39.310	34.199
+18	39.410	38.456	39.700	38.264
+19	39.470	38.621	38.680	28.791
+20	39.170	36.390	39.340	38.126
+21	39.340	38.280	39.320	37.141
+22	38.870	32.580	38.480	25.015
+23	39.370	37.125	38.850	32.436
+24	38.940	36.347	39.200	37.110
+25	38.560	36.248	39.000	28.586
+26	38.810	33.655	38.460	29.005
+27	38.930	35.395	38.560	25.539
+28	39.090	37.259	38.190	23.947
+29	38.610	25.879	38.730	30.749
+30	38.540	33.271	38.520	32.796
+31	38.840	33.517	38.040	30.447
+32	38.730	36.053	38.530	27.397
+33	38.340	34.385	38.880	35.605
+34	38.470	28.217	38.430	32.167
+35	37.350	30.035	38.560	26.684
+36	37.380	20.434	38.900	32.524
+37	37.810	32.591	38.450	34.632
+38	38.150	33.133	38.750	35.749
+39	37.660	31.924	38.420	26.003
+40	38.040	34.153	38.730	36.080
+41	37.970	35.596	39.020	37.708
+42	37.240	31.069	39.380	33.973
+43	37.740	29.175	38.840	35.607
+44	38.070	34.040	38.400	23.939
+45	37.690	30.131	38.160	26.507
+46	37.160	26.236	37.990	32.407
+47	37.820	35.168	37.330	29.388
+48	37.920	35.623	37.850	31.413
+49	38.150	34.322	37.830	27.255
+50	38.250	34.017	38.260	36.442
+51	38.060	36.455	36.270	30.125
+52	37.240	34.726	37.000	33.291
+53	37.700	32.804	37.210	34.667
+54	37.740	33.699	37.520	34.736
+55	37.780	33.713	37.880	35.604
+56	37.470	31.063	37.880	35.326
+57	36.680	26.593	36.810	22.646
+58	36.390	26.714	37.140	31.327
+59	35.960	29.732	36.900	20.404
+60	35.500	27.738	36.440	21.355
+61	35.800	28.761	36.200	20.579
+62	34.880	22.760	36.570	21.483
+63	35.560	30.716	36.180	21.372
+64	35.460	30.521	35.970	20.108
+65	35.090	25.249	35.450	20.127
+66	35.240	31.736	35.330	20.499
+67	35.230	25.003	35.410	21.618
+68	34.870	25.901	35.400	21.693
+69	34.560	24.095	35.200	21.684
+70	34.670	29.988	34.730	21.372
+71	35.010	32.741	34.710	21.582
+72	33.750	21.148	34.060	18.014
+73	34.130	29.634	34.040	18.342
+74	34.080	21.493	33.840	17.025
+75	33.590	20.367	33.380	16.366
+76	31.930	18.529	33.300	17.088
+77	32.400	18.486	32.360	15.307
+78	32.840	18.708	32.170	15.246
+79	33.190	18.732	32.130	15.504
+80	32.680	17.826	32.770	15.850
+81	32.690	17.578	32.640	15.552
+82	32.510	16.664	32.800	15.822
+83	31.640	15.134	32.350	15.209
+84	31.220	15.026	32.320	15.547
+85	31.270	14.413	32.170	15.387
+86	31.310	14.436	32.520	15.576
+87	32.130	14.923	32.070	15.354
+88	31.610	14.417	31.780	15.361
+89	31.240	14.665	32.290	15.854
+90	31.130	14.606	31.730	15.508
+91	31.350	14.867	32.120	14.926
+92	31.270	14.282	32.040	14.910
+93	31.790	14.879	31.770	14.676
+94	31.010	13.468	31.380	14.768
+95	30.280	12.737	31.220	14.847
+96	30.310	12.852	31.050	14.129
+97	30.390	12.411	31.160	13.935
+98	30.150	12.394	30.960	13.893
+99	30.300	11.964	30.610	13.166
+100	29.860	11.945	30.460	12.397
diff -r 9982e346abc4 -r d34c645ab63f test-data/bduk_outputu1.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_outputu1.fastqsanger	Thu Nov 11 16:35:39 2021 +0000
@@ -0,0 +1,102 @@
+@XXXXXXXXXX:7:1101:1582:1835#/1
+NGCTTCAGTTGGTACAGGTGTGTCACCCGTAGTTTGTAGGCTTGGAAGCCTGTAAGCTGTAGGGAACGTGGCAAGAACCAGATCTGGCCTTCCATATCTC
++
+!1=DDDDDAFFDDEFFG@AGHBCFHIFIEGIC?DBFGIFF?FGDFIBFFII8BCFIEEF.@FFIIEFFCE=??B@>A@@@BBBAD>A:?BBBBB@>>>B:
+@XXXXXXXXXX:7:1101:1610:1859#/1
+NTTATGTGTTACGTGAATCTCCTGAAGACAGCAGAAACTAGGTTGGTGAATTCTTATCCATTCTGCCATTCTGTATCTTTTAAGTGGAGCATTTAGGCTA
++
+!1=DDFDFHHHHHHJJIJJJJJJJJJJJIJIIJJJIJIJJJJIJJJIIJJJIJJJIIJJJJIIJJJJGIJJJIHJHHHHHHHFFFFFFDDDEEDEDDCDD
+@XXXXXXXXXX:7:1101:1743:1871#/1
+NCGGGATGGAGGCAGGGCAAGCGGATGCAGGCCCAGCCCTGCCCTTACAGGTAGCTGGAAGTGACGAAGGAGTGGGGCCCCCGGACTCTGCTCAGGTGGA
++
+!1=DDDFFHHHHHIJJJEGGGIHIGIIGGGIIIJEHHHGGCCHIIIFHHFHADDCDDC@CECECCDDB7?BB9?BA>9<@DDB>>9>CD>:>CA9A:A@A
+@XXXXXXXXXX:7:1101:1536:1878#/1
+NGGCCTTTTTGGACAGGTGGTGTGTGGTGGCCTTGGTATGTGCTTTCTCGTGTTACATCGCGCCATCATTGGTATATGGTTAGTGTGTTGGTTAGTAGGC
++
+!1=DDDFEHHHHCGGIJFHIECHEFHIGGGGIJI<BBFGEIFGIIJIIJJJEGGEGGIHCCBHBFFCCEDEEC@CDDDC3>:95>@ABCAA<?C?>CDCC
+@XXXXXXXXXX:7:1101:2990:100153#/1
+GCCAGGAGTGACTGTGTTGTTCTTTGCTTTATATACATAAGCGCATCTCTTGCCCAAATAGAATTCTGTTTCATCTCGGGCGTAAACACCTTCAATTTTA
++
+@@@DDDFDBFHDFH<EHGIHGCHEGHGIIGIIEGFEIGGIIIIII<GICCE@4?BBFHGHAEGIHHIICDHEEEAAHFBEDD@B@B@><@D>CDDDDCCB
+@XXXXXXXXXX:7:1101:1624:1906#/1
+NCCAGGTTTAAGGCATTACATCGAGGGGCTGAACTTGAGACAGTCCCTGAAAATGTAAGAACAGGAGCTAGAACTTGCTTATGGGAAGGGCCTAGGGAGA
++
+!1=DDFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJIJJIJIIJJJJJJJGIJJIIJIECGIHHHHFFFFEECEECEDDDDDDCDCDDDDDDDDDDDDD@
+@XXXXXXXXXX:7:1101:1666:1926#/1
+NGCAAACTGGTCAGGACCTGGAGCTGCTTGCCTGGCCTTGGCACAAGAGGCCGACATATGCCCAGCCCCTAGGAGTGACAGATCCGTCCTCTGTGGGAAC
++
+!1BDFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJIJJJJJJIJJJJJJJJJJJJJJJHHHHHHFFFFDDDDDDCCDBDDDDDDDDDDDDDDDDDDDDBCD
+@XXXXXXXXXX:7:1101:2921:100163#/1
+CTCCGGATGCCAAAGGATCTGACAGTGTATCTAGCTTTGGAAAACACAGGGGTCTGCCCTGTGAGCTGCTCCAACACCTTGGCTGCTCGCGTCAGTCTGT
++
+CCBFFFFFHHHHHJJJIJIIIJJJJHIFFHGIIHEIJIIIIIJIIGIIIICHHHHIJIIEHHJIHHFHHFFFFFFBDDDDDCDDDDDDDDD@B@@CCDDD
+@XXXXXXXXXX:7:1101:1513:1929#/1
+NCACTATCAAGGTTAGTGTCTATATCTACTTGAGANAAAATACTGAAAATTCAGTGTATGAAGCCAAATCCTGATTTAACAAGTTATTGGTAGTATAAGT
++
+!1:ABDDDDFFF:ACGFGFHHFIFAHEEHDFI@F8!1:CFEFFIGEFGIII>GIFICGGII@FFFIEFEADGIIEIFFFFFFFEEDDDDBDAC>>;;BA5
+@XXXXXXXXXX:7:1101:2759:100170#/1
+CTGCTCATCACATTCCAGATGCCATCACAGGCAATGACCATGAATTCATGGTCGTCAGTGAGAGTCAGCACCTTGATGTCAGGAAGGGCTGAAATCATCT
++
+CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJIJJJJJJHIIJJJIJJJJJJJHHHHHHHFFFFFEEDDDDDBCDDDDDDD
+@XXXXXXXXXX:7:1101:1708:1937#/1
+NGGTCGGTGTCCTTTTTTGGCGTCAAACTTATAGAGGGAAGCAGGGAATCTACCCAACCAAAGCCAATGAACAGTCAGTCAGTCCATCTAGTTAAGGTTC
++
+!1=BDDDDFDHHHIJJIJIJGIJIGGIJIGAGFHGHIGA=FCDFGHJJHEHFHHEFFFDABCDCDCCCDCDDDDDACDDCDDCAAACCDDDDDDACCACD
+@XXXXXXXXXX:7:1101:2981:100211#/1
+GGGGTCAGTGGGAAAGGTGTCAATGGGACTTCGGTCTCCATGCCGAAACACCAAAGTCACAAACTTCAACTCCTTGGCTAGTACACTTCGGTCTAGCCAG
++
+@@CFDDDFFFFHHEIGGHIIIIJJIIDHIGGIJFGBHIIIGGGGGGGIIJJHJGIG=DECEEEFFFFCDCCE@CC@?CDCBDDCDCCCCBB?B@>CACAB
+@XXXXXXXXXX:7:1101:1688:1946#/1
+NCCGCCTTCTTTCTCTACTTCGTGACCTTTTGTGGTCCCGAGACCTGCTGCATCTTCTGTCTGATGTTCGGCTTGAGTGTCTACTTCCTGAACGACTTCT
++
+!1:BDAAD<DDDDIEE>DBEEFEEFIIIIIEADEC?C>DD<?D@?@BDDDEEDIEIEDE=CEE>CE?CCC6=?###########################
+@XXXXXXXXXX:7:1101:2767:100225#/1
+CGCCTGGTGTCAATGCGCACATCTGGAGTTCCCATCTCCTTCATGGCAAATTTCCGAATCTCTTTGAGTGCCCGAGGTGCACGCTTCTTGAAGCCCACTC
++
+@@@FDFFFGHHHFJJIJIIIIJIJIJIGHBD@DFGGGJIFIJJJJIIIIIGHIIGIJFIJJIJIG@EECCHEEDCAD>ACCCDDDDDACCAC@CDDDDDD
+@XXXXXXXXXX:7:1101:1536:1959#/1
+NGATACTGTTGGGTCAGGACCAGGGCCTGCACCACCGAAATTCTGTCTTTTACAAACTGGACCAAGCGGTTGAGAATACAGGGGCCGAAGAGTAGGATTA
++
+!4:BB?DDHHDHAE?ECB@=GGI=<;CG@B;<D@DG:@FFABFBG<=FFGFHIIGGH@>==AEC?DECA<;8;3<AC>CCCC8&-5>@@59?4::>>>CC
+@XXXXXXXXXX:7:1101:2797:100234#/1
+GTGCTGGTCTCTCTCCACGATCTCTTACGTGCTAGCAGGGTGAACAAGGACGCCTCGCTGTCATTGCACTCACGCCACAGGAGCCTGGCACATTTCCGCT
++
++:?BDD8DFFFB8ED;@GF8A3?FH?B<)11?@FG<E<;@F629?BF@?2=A;4C6BE7-,7@;@;@A>;@CBB?=88?5(95983?(8<><AA######
+@XXXXXXXXXX:7:1101:1552:1976#/1
+NTGATGAGTTTGCTAATACAATGCCAGTCAGGCCACCTACGGTGAAAAGAAAGATGAATCCTAGGGCTCAGAGCACTGCAGCAGATCATTTCATATTGCT
++
+!1=DDFFFFHFHGJJJJIJJJJJJJJJJJIIJFGHGIIIJIJGHIEIIJJJHIGIIJGJIIJJJBHIIJHHHHHDEFCECEEEEDDDDDEFEEEEEEEDD
+@XXXXXXXXXX:7:1101:1748:1978#/1
+NCGCTGAGCAGGGCAGGCAGTGGTGGAGGCAGCCCCCCAAGACCCCATCTCTATCACAGTGAGAGCATCTGAACTCCAAAGCCACGACAGAACAGCTCCC
++
+!1=DFFFFHHHHHIJJJJIJIJJFHJIIJIJJGJJIIJAHGGGHHHHFFFFFFEEDECE@CDDCDDDCDDDACCCCDDDDCDDDDDDDDBDDCCC@ACDD
+@XXXXXXXXXX:7:1101:2779:100239#/1
+TGGGTGCTCTCCTTGGTCAGCTGCTGCTCGAACAGAGCACTTCTAGATACAGAGTTGGACCCAGACACAGCAGGGGTGGCCATGGCGGCTGGGAAAGACC
++
+@@@?DD?DFHHFFHIEEHIBGI9CFHFGCB::CGIGHG@BF<FHFHD@DDDBBDBFGH<C;C;==;C;;?H;;?<>88=@?C##################
+@XXXXXXXXXX:7:1101:1593:1980#/1
+NGGCACCAGAAGCATGAGCATAGGCAGAGCCATTTCCACCATGCTGACGGCAGGCAAGAAGAAGACAAAAATGAACCCCTTTCATGCTTGTTTAGAAATG
++
+!1=DFFFFHHHHGJJJJJJJJIJJIJJJIGJIIJJJJGIIIJJJJJIIJJJJJJIIJHHHHHFFFFFEEDDDDDDDDDDDDDDDEDDDEDDDDDDDDDDD
+@XXXXXXXXXX:7:1101:2946:100242#/1
+TGGGGATGTTGTTAAAAAAAATACAGGCTCCCCCACAACTGGGGTGCCTGGGGGGAACTTGGTCTGCTTCAGCCCAAGAGGAATCAAAAGATCAAAAGCA
++
+@@@FFDDDHHHHHJIIGIJIGEGIIJJIIJJGJJEECDEA=FHI-=?B?CEDDDD5583:AC3::94:CAACCDBABD8?BA?CCDDDDD@CCACCDCBD
+@XXXXXXXXXX:7:1101:1987:1781#/1
+NTTAGCAGGTCCTCGTAGCGTTTCCGCAACTCTCGGAATCTGGAGTCTTCGGAGTGCAACTCTGAGGGTCCCGGGAAACTTGCGCGGCTCGCCTCGGCCA
++
+!1=DDFFFHHHHHJJJJJIJJJJIJJJJJJJJJJJJJJJGJJJJIIHIJJJIJHHGHFFFFFFCEEDDDDDDDDDBDDDDDDDDDDDDDDBBDDD9B?B<
+@XXXXXXXXXX:7:1101:3046:100006#/1
+CTGTACAGCATGGATGTGGACAGGGAAAACAGCAAGTGCACACAGTGGGACAGGCCACAGGACAGGCTGGGAGTGAATAAAGAGTTCACACTGCTTCCCT
++
+CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJIJJJFHIJJIIJIGGHIJJJJJJIJJIIJJJHHHHFFFD=C;?CDCDDD@>?>@CACDACCDDCDDDD
+@XXXXXXXXXX:7:1101:1900:1788#/1
+NCCCGCTGCCCACGCCACTGTCCCGGCGCTGCCCTGGGCGCGGAATGCGCGTTAGGCAATCCCCGGTCTGCGCGTCCCACACGCAGATGTGGCCTGCCAG
++
+!1=DFFFFGHHGHJJJIJJIJJJJGIIJJJIIJJIJJJIHFFDDDDDDDDDBDDDDDDDDDDDDBD@BDDDB>BB<BBDDDDDDDDDDDECDDBDDDDC@
+@XXXXXXXXXX:7:1101:3214:100027#/1
+GGCTGAGGTACTGAATGAGGAACAGCAGGAGGTAACGTCTGAGGGTGCGGCTGGGGAACGGTTTGCACAGGGGTGGCTGTAGGAGCAGGAGGTGAAACAC
++
+@@@FFDFF?DFHHIIIIIIGIIGHGIIGIIII?FHHGDFGIGGIC6?FHIIFIHHH59;=B559=33:55<(830588<((>:(98<CB02&28>CA>98
+@XXXXXXXXXX:7:1101:1848:1879#/1
+NCTTCTTCTTCCTCATGTTTTTTGATCAACTGCTCCACTTCTTTTTGTTTGAGAACTCTGATTACTGTCTTTCCATTCTCTCTTGTTAGTGTTGCAATTT
diff -r 9982e346abc4 -r d34c645ab63f test-data/bduk_outputu2.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_outputu2.fastqsanger	Thu Nov 11 16:35:39 2021 +0000
@@ -0,0 +1,102 @@
+@XXXXXXXXXX:7:1101:1582:1835#/2
+GCAATGATGGGGCCGCTCCCGGGGCCACACCTGCTTCTGGATCCGCTGCTTCCAAGTTCCTTTGCCTCCCTCCTGGCATCACTGTCTGCGACTCAGGCCG
++
+@@@DDDADHFHGFEGIGIIIGEGFD@FHA@GIGIJJIJJEAHHEBEDACEAC@CDDDC@@CCCCDCD@AD9?BCCDDCCDDDDDDDDCC99BBDDCACBB
+@XXXXXXXXXX:7:1101:1610:1859#/2
+CAATAACACAGTCCAAAATATATGTATGTATGTATATATATATGCAGGCAACAAATAGCACAATGAATAAAATAGTACTTCATCTCAGTACTAACATTGA
++
+C@BFFFFFHHGHDIIJJJJJJIIJHIJJHIJIJJIGIJIJJJJJFIIJJIIIIIJJJIJJJJJJJJIJJJIJJJJEGIIJJIJHHHHHCDFFFFFFEEEE
+@XXXXXXXXXX:7:1101:1743:1871#/2
+GCTTCCAAGGGACAAAGTCCTGCCCTTGGGTGTGGAAGACACCGTGGACAAGCTCAAGATGCTGGAAGGCCGCAAGACCAGCATCCGCAAGTCAGTGCAG
++
+CCCFFFFFHHHHHJJJJJIIJHEHJIJJJIEDGIIIJIGGGIJIGEIIIIJIIIIIHGHHHHFFFFFFFDB>B@BDDCDDDDDDDCB?@BDCCDDDDDDD
+@XXXXXXXXXX:7:1101:1536:1878#/2
+TGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCC
++
+@@@DFFFFHGFHGIJJJJJJJAFDHICDFHGIJIIJEEIJGIJGHJIJJIFAAAFGBGGFFFHGHFDFDFBCBDDDD<ACDDDCADEDDDDCD:>CDDCC
+@XXXXXXXXXX:7:1101:2990:100153#/2
+TGGAGGCCTGCTGGGAACGGGACTTCTAAAAGGAACTATGTCTGGAAGGCTGTGGTCCAAGGCCATTTTTGCTGGCTATAAGCGGGGTCTCCGGAACCAA
++
+@@@DDDDFHHFDHJJIGGHIJHIJJJJJGGGHJEGIIJJJIJJJIJJII?=FFHIHGGIJIHHHHFFC@BBCCEDDDDDECCDBDBD09CDDDDBBB??1
+@XXXXXXXXXX:7:1101:1624:1906#/2
+GGCTGGTCTGTCCCCTCTGCATCTGGGGCTCCTCCTGGCCCTTCTCCCGCTGCCTGTCCTGCCTCCTGGCCCTGCAGCAGCACCTTGCCCAGTGATCTTT
++
+CCCFFFFFHGHHHJJJJJJJIJJJIJJJIJIJJIJJIJIJJJJJJGGIJJFGIJGHHIFHHHHHFFDFDEEDDDD?CDDDDDDDDDCCDCDDCCCDCCCD
+@XXXXXXXXXX:7:1101:1666:1926#/2
+GGCTGTGGGAACTCTAGCTGCTGTCAGCCCCTCCTGTAGGAGCTGGCCCTGCCCAGGCTCCTGACTTCCCTCAGGAAGTCTTTCTGTCTTTCTCCATCAG
++
+CCCFFFFFHHFHHJJIJJJJJJIJJJJJJJJJJJJJJJJIIJJJJIJJJJIJJIJJIIJJJIHCHHGHFFFFBEE>@B>CDDDCDDDDDDDDDACDDCCD
+@XXXXXXXXXX:7:1101:2921:100163#/2
+GAAAAGGAGAACCCCATGCGGGAACTTCGCATCCGCAAACTCTGTCTCAACATCTGTGTTGGGGAGAGTGGAGACAGACTGACGCGAGCAGCCAAGGTGT
++
+CCCFFFFFHHGHHJJIJJJJJJIIJJJIIIGDHIGIJJJIJJ>HHGEHHGEHFFFFCDEEDCBDDDBB>C@DDCDDDDDDDDDDB@BD@BDDDBDDD:@@
+@XXXXXXXXXX:7:1101:1513:1929#/2
+AAAATGAGGGCCCGTAACAGAACCAGTGTGTGTATAACGAAAACCATGTATAAAATGGGCCTATCACCCTTGTCAGAGATATAAATTACCACATTTGCCT
++
+?@@;;D>DFH:;?EFD:F<FE?;CBF:DCG?FD4?FIGHIGIJJGFGIFG@FGGDHIHIGHHGFFFFFECEDADCDACA>CAADACDDCDCC<ACDDDDD
+@XXXXXXXXXX:7:1101:2759:100170#/2
+GGTCACCATGGATGGGCGAGTCAACGGGGGCCTCAACCTCTCCAGAGCCATTGGGGACCACTTCTATAAGAGAAACAAGAACCTGCCACCTGAGGAACAG
++
+CC@FFFFFHHHHHJJJJJIJGIIJJJJJJIJJGGHHCEFFFFEEEEDDDDDDDDDDDDDDDDDDDDEEDDDDCDDDDDDDDDDDDDDDDDDDDCDC?ABD
+@XXXXXXXXXX:7:1101:1708:1937#/2
+GAATACTTTGTGTTTACCCACTGCCCCCTGACCACTGCTGAAGGCAGAAAGGGACGATCACCTACAGTACCTGGTTTGGGTCTTTATTCTCTCATTCTAG
++
+B@BFFFFFHHCFHIJIHGIGIIJJGGIJJGIIIGIGGIJJEIGIHHJJJJIHIIJJIJHHHGFBEFFCCEEDCD;@A?BB?ACCCCCCCCACD@DADA@C
+@XXXXXXXXXX:7:1101:2981:100211#/2
+TTCCTCCTAACTCCTGCCAGAAACAGCTCTCCTCAACATGAGAGCTGCACCCCTCCTCCTGGCCAGGGCAGCAAGCCTTAGCCTTGGCTTCTTGTTTCTG
++
+@@BFFFFFHBDHHIHIIIIGGGADGGIGIEHIIIIJJIIIE<BHAHHHIGFGIJJJJIIHIBDGGEAEFFF;>CCABCDCDDCACDCCAA?@CD4:<@AC
+@XXXXXXXXXX:7:1101:1688:1946#/2
+GAGAAAGGGAAGAAAGAGAAAGGAAAAGACGAAGGGAAGAGGAAGAAAGAGAAAAAGAAAGGGCTCGTGACAGAGAAAGAAGAAAGAGAAGTCGTTCACG
++
+BB@ADFFFHDDHAGGHGHGGHEHGIJJIIJIIJJJJ<FH;FGDEGEGHGIFHEGIJFFHHFDFFEDDBDDDDCCCACCDABDDDDDCCCCDCCD@B?CDD
+@XXXXXXXXXX:7:1101:2767:100225#/2
+TGCAGAATGGCTCCCGCAAAGAAGGGTGGCGAGAAGAAAAAGGGCCGTTCTGCCATCAACGAAGTGGTAACCCGAGAATACACCATCAACATTCACAAGC
++
+@@@FFFFF<FFHHGGIJIIGGGIII>):?FF:FGGGIJIJIHCHHHFBCE;ACDDDDDCA@<@DBDDCDDCDDDDDDDDD@CCCDAA@>ACC>>A@@C1<
+@XXXXXXXXXX:7:1101:1536:1959#/2
+GAGACAAAAATTGTTTGAATCAGGACAAGGGAGGTTTGAGGGACTGTTTAACAGGTCCCCATGGTTCACGACCCTGATATCCACCATTATGGGCCCTCTG
++
+@8@1:?:=DD>D<CE+A:+C?+AF++++281)?D):?HD=FG6((?88=CFFCHG7=@HH@9?3.)7772?3,9;A(((5>;5>BBAA:>CCD?8@BD9A
+@XXXXXXXXXX:7:1101:2797:100234#/2
+GGAAACGCTGGAGAAGACAGTGTTGCTAGTCTGTTCCTGTTCGTGAGAATGCTTTGAATGGAGGCTCACTGTGCTGCGGCGGCTGCGGCCGTAGCGGGCG
++
+B1=+:A+0A::A2+2A2A3A<+2<?9<*119:9:1CC:DDFF<)800//9/>8E=<)/8@@@6C(6==737==>>@########################
+@XXXXXXXXXX:7:1101:1552:1976#/2
+TGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGT
++
+CCCFFFFFHHHHHIIGIGGIHJIGHHJIECGGGHJIJJJJJJJJJGHIJJGGHGIIEHIIJDIJFHFFFFF@CCCEECDDDDDCDDDB@BDDBBBDDCD>
+@XXXXXXXXXX:7:1101:1748:1978#/2
+CAAGGAGCTGTTCTGTCGTGGCTTTGGAATTCAGATGCTCTCACTGTGATAGAGATGGGGTCTTGGGGGGCTGGGAGCTGTTCTGTCGTGGCTTTGGAGT
++
+B@@FFFFFHHHHHJJIIJHIJIJJJJJIIJJIJJJJJIJJJJIJJJGHFGGHHIIIJIJJ@GIIJJIHFDDDDDDABBDCCDDEDDDB?BDDDDCCDCDA
+@XXXXXXXXXX:7:1101:2779:100239#/2
+GCTGTGGTTACCTGTCCCCTGCCCCTGGCCTCCAGCCAGCTGCCAGTGGCCCCTCAGCTGCCTGTGGTGAGGCAATACTTAGCTAGGTTCTTAGACGGCC
++
+?<?BBDDEFADA?ECCFFGEHDIDB;;FBG>GDHFGGGAFEHE?F@8?>F;CFCEADEEG@EEHAEFBDEEED7A>CACDECD>C@A(5>>C@>A#####
+@XXXXXXXXXX:7:1101:1593:1980#/2
+GGCTGTTCTCGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCTAGCCGTCACATTTC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJFHIIJJJJJIIJJJJJJJJJJJJJJJIHIJJJJJHIJJJJJJJHEEEFEEEEDECDDDDDDDDDBDDDCDDEE
+@XXXXXXXXXX:7:1101:2946:100242#/2
+AATCCCTTCACCCCAGTTGCCAAACAGACCCCCCACCCCCTGGATTTTCCTTCTCCCTCCATCCCTTGACGGTTCTGGCCTTCCCAAACTGCTTTTGATC
++
+C@CFFFFFHHHFFHBHHHEIJJIIIJIIJCGGIIGIHHIJIG@D;DCE>>?AEEFF@@DB(.;>?;CC@>=',5<CC>ADCDCCDA>B?CDD>ACCC0>C
+@XXXXXXXXXX:7:1101:1987:1781#/2
+GCCGCAACCTGCACAGCCATGCCCGGGCAAGAACTCAGGACGCTGAATGGCTCTCAGATGCTCCTGGTGTTGCTGGTGCTCTCGTGGCTGCCGCATGGGG
++
+CCCFFFFFHHHHHJJJJJJIJJJJJJJJJJJJJJJJJJIIJIJJJJJHHHHHFFFFFFEEEEEEDDDCCBDDDDDDDDDDDDDDDDDDDDDD<@BBDBBD
+@XXXXXXXXXX:7:1101:3046:100006#/2
+GACGAGATGGAGTTCACCGAGGCCGAGAGCAACATGAATGACCTGGTGTCCGAGTACCAGCAGTACCAGGATGCCACAGCCGAGGAGGAGGGCGAGTTCG
++
+CCCFFFFFHHHHFIJJJJJIIJIJJIHIIIJJJIIJJJGIJJJIJJIJHGEHFFFEEEEEDDDDDDDDDDDCDDDDDDDDDDDDDDDDBDDBDD<B9@CB
+@XXXXXXXXXX:7:1101:1900:1788#/2
+CGGCTATGCGCCACCCGAGACGGAGATCGTGCCGCTTGTGCTGCGCGGCCACCTCATGGACATCGAGTGCCTGGCCAGCGACGGCATGCTGCTGGTGAGC
++
+CCCFFFFFGHHHHJJJJJJHHJJIFHIJJHHIIIJJJIIIJJJJJHFDDD@@DDDDCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCDD<?C@C
+@XXXXXXXXXX:7:1101:3214:100027#/2
+CACAACAACTGCTACTTCAGTTGCGCAGACAGTATCAACACCCACAACACAAGATCAGACCCCAAGTTCTGCTGTTTCAGTTGCCACGCCTACAGTTAGT
++
+@CCFFFFFGFHHHIIJJJIIHIIIIIJ<GIIG?DHIJJGIIJBHJJJJJIGCGGHHJJHHHHFDEF;ACEEEDDDDDCEDDDDCDCDDDDDDDCCDDDD>
+@XXXXXXXXXX:7:1101:1848:1879#/2
+GGAGAAATGACCTTGAAGTCAGCACTTGCTTTAGCTATCAAAGTACTAAATAAGACCATGGATGTTAGTAAACTCTCTGCTGAAAAAGTGGAAATTGCAA