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Merge pull request #5577 from bernt-matthias/topic/cutadapt-length-pa…
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cutadapt improvements
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@mvdbeek
mvdbeek committed Dec 17, 2023
2 parents 0d01923 + 68d7365 commit c37e2ae
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Showing 20 changed files with 648 additions and 375 deletions.
467 changes: 306 additions & 161 deletions tools/cutadapt/cutadapt.xml
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294 changes: 81 additions & 213 deletions tools/cutadapt/macros.xml
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80 changes: 80 additions & 0 deletions tools/cutadapt/test-data/cutadapt/cut/illumina64.fastq
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Original file line number Diff line number Diff line change
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@14569
AAGTTTATTCCTGGACGAAGGAAGAAAAGGCCAGATGGGAAACAAGAACAAGCCCCTGTTGAAGACGCAGGGCC
+
cceeeeceeeee`dedbdbdb_^b`abU_cacadabd`dLMZ[XTcT^a^adaaaddcd`aL^`^_`Y\]^`Y_
@19211
AGA
+
^\`
@9180
GAGGG
+
b`bLb
@19132
TGTGATTATCCACTGGTATAT
+
Z[QZZLZ[]J[SHZNaZ[_Ia
@15868
CTGCCAAGGCTGCCCCCAAA
+
`c`cc\`\Lb]bL`[`a]L`
@1424
GGCCCCAGACTTGCTCCCCCAACAAGGACAATGTCCAAGGAGTGTCCCC
+
eeeeeeeea`bbdaaadad`Oaaaaccada_aa_d`_X`_^`[`_[_W^
@7855
GTGGGGGCT
+
]^\]FW]Z`
@17943
ACATGGGACCAGAAAACACCACCAGGGGTTTGGGGCTGTCCTGAG
+
ccc`\^`aba\b^`\FR`OOPYG[[W```[Ra_RR_\]\\P\_H_
@11100
CGGATAACTGAAAATGCATTTTTAACGCCATGACCGTGTCTCAAGGACCCGCTGTGGAAG
+
b`b_b_a\bc^Tabadaddcddd``bdaa_^aJ\^_\]\\__O[___L^\_aaa^^^UJ^
@15663
AGGT
+
aaKa
@4698
CCAATTGGCACCCCTCTGCCTTCAGCCATT
+
cccc\`ccc\caccZccccc]^`LY\bL_b
@20649
TCTGGACTGGATCTTTAGGATGGTGGAGATGATCTGGATGTAGGACAAAAGAACCAGGCAGAAGGGTG
+
eeeeeaddadacdddebeccdddadd\^abbT_]bccTac]]b]L^][]Ve[^ZaY_^_^`\\Y]^Y`
@17259

+

@6003
CTTCAACTCATCTTGTTATTAATACCATCAATATCCCATGAGGCTCATAAAACGAGTCTTTCTTCTTGGAAACATGACCAAGATTGGGCAAACGT
+
fffffffffffffffffdffecfcefeffdcfdeeebbbdbccccc\db\`^aa`^Y^^^cbcbaa`bbWY^^^__S_YYR]GWY]\]]XX\_`S
@4118
TCAAATTGTACTGCAAAGAAGGTCCCAGCTGGTCTCTTCTGGGAGTGATCTAACTAACTTAAG
+
dc^ddeeeeeedeee`ceceddadadddcbde_dedc_ec_a^^b\b\\]VIPZY^T^^^\L_
@18416
GTGGGGAAGCCGAAGAAGCAGCGGAGATCGATTGTAAGAACGACG
+
dddacaabdbea\d^cce\da`dd_^__`a`a`b[_^__^\^^^_
@20115
TGAAAAAGGAAAACATGGTAGTTTTCTTGTATGAGAGAGCCAGAGCCACCTTGGAGATTTTGTTCTCTCTGTGCG
+
ed^eeafffaddfecdddabc^_badd`bd_ddadaa^bbcad\d\__^_\aaa_aY____aaN_\cdc\^aaYb
@16139
TCATCCGAAGAGTTGGCAGGCCCTGTGAATTGTGAAAACAGTATACCCACCCCTTTCCC
+
cabacacY^c\daaddaadad^\ad_a\Y`[ZQ]Y^^OYQ^X^YT\\]U\^RRX^\YJ^
@14123
GATTTGGGGAAAGGAAACAATAGTTGAGTTTGGGCCACGGGAAATTCAAGATGCCTGGTATGTC
+
cccccccac^bYbbT_aa_Yb^^Ta\\^]]aaTaaaaab\b\XL`VZZV]QYYY[aa^^^^_^^
@8766
ACCTGTAAGGTCCGCTCCTGGTGGACACCCACGAAGTCCAGGGCCTCAGGCAGGAAGTTGTAGCGCAGAGTTTTGAGCAGCTGCTCCATC
+
fcfffffcffeffeeefdefddeecdccacddfdYd`d^\_^`\_abbc\b[ba^Y^Z_^^H^Z_^Y_Y_OKWPZR]]Z]`Z``Z^UHZ^
8 changes: 8 additions & 0 deletions tools/cutadapt/test-data/cutadapt/cut/maxee.fastq
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@empty

+

@ee_0.8
ACGTTGCA
+
++++++++
8 changes: 8 additions & 0 deletions tools/cutadapt/test-data/cutadapt/cut/polya.1.fasta
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Original file line number Diff line number Diff line change
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>polyA
AAACTTCAGAACAG
>polyAlong
CTTAGTTCAATWTTAACCAAACTTCAGAACAG
>polyA2
AAACTTAACAAGAACAAG
>nopoly
GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG
8 changes: 8 additions & 0 deletions tools/cutadapt/test-data/cutadapt/cut/polya.2.fasta
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>polyA
CTGTTCTGAAGTTT
>polyAlong
CTGTTCTGAAGTTTGGTTAAWATTGAACTAAG
>polyA2
CTTGTTCTTGTTAAGTTT
>nopoly
TCTGAAGTTTGGTTAAWATTGAACTAA
8 changes: 8 additions & 0 deletions tools/cutadapt/test-data/cutadapt/cut/polya.legacy.1.fasta
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
>polyA
AAACTTCAG
>polyAlong
CTTAGTTCAATWTTAACCAAACTTCAGAACAG
>polyA2
AAACTTAAC
>nopoly
GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG
4 changes: 4 additions & 0 deletions tools/cutadapt/test-data/cutadapt/cut/simple.fasta
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Original file line number Diff line number Diff line change
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>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
Binary file added tools/cutadapt/test-data/cutadapt/cut/simple.fasta.gz
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4 changes: 4 additions & 0 deletions tools/cutadapt/test-data/cutadapt/cut/wildcard.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
>1
TGCATGCA
>2
TGCATGCA
6 changes: 6 additions & 0 deletions tools/cutadapt/test-data/cutadapt/cut/wildcardN.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
>perfect
TTT
>withN
TTT
>1mism
TTTGGGGCGG
80 changes: 80 additions & 0 deletions tools/cutadapt/test-data/cutadapt/data/illumina64.fastq
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Original file line number Diff line number Diff line change
@@ -0,0 +1,80 @@
@14569
AAGTTTATTCCTGGACGAAGGAAGAAAAGGCCAGATGGGAAACAAGAACAAGCCCCTGTTGAAGACGCAGGGCCAACAGGGGCCAACGAAGCTGC
+
cceeeeceeeee`dedbdbdb_^b`abU_cacadabd`dLMZ[XTcT^a^adaaaddcd`aL^`^_`Y\]^`Y_BBBBBBBBBBBBBBBBBBBBB
@19211
AGAGGGCGTGTGATTGCTGGATGTGGGCGGGGGGCCGGGGGAGCCCCATGGGCAGGAGACCTGAGAGCCAGGCGGTGAGGCACTATGAACGCGAG
+
^\`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@9180
GAGGGGCAGCGACTAGTCACCGGACCTGTCAGGCAAGCATAAGCCGTGCGTCAGCACCACGCTGACGGTGCTCCCGCACTCGCGGGACGCGCCAC
+
b`bLbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@19132
TGTGATTATCCACTGGTATATCGGCGTGCCGTCCGCACGAGGAAAAAAGGCATTATTGTTGTGGATCTGTACCATCGTTTGTCCCGTTACCCTTC
+
Z[QZZLZ[]J[SHZNaZ[_IaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@15868
CTGCCAAGGCTGCCCCCAAACCTGGCCCTCCGCGCACCCCACCACGGATCCTGACGTCCTGTCCCCCGCGGCTATGACAGCCAAGTCCCGTCAGC
+
`c`cc\`\Lb]bL`[`a]L`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@1424
GGCCCCAGACTTGCTCCCCCAACAAGGACAATGTCCAAGGAGTGTCCCCTGGGAAGGGTGGGCCTCCCCAGGTGCGGGCGGTGGGCACTGCCCCC
+
eeeeeeeea`bbdaaadad`Oaaaaccada_aa_d`_X`_^`[`_[_W^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@7855
GTGGGGGCTACAATGTGGCTCCAAGTTTTTTCCCGGGAGGTAAGGCCGGGAGCCCCCGCCCTGAGGGGGCGGGAAAGAGGAAGCCCGACGCGGAC
+
]^\]FW]Z`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@17943
ACATGGGACCAGAAAACACCACCAGGGGTTTGGGGCTGTCCTGAGGCTCGGGTAGCAAGCAGCGGGGCTCCGTGTCCAAGCACGCCGGTGTCACC
+
ccc`\^`aba\b^`\FR`OOPYG[[W```[Ra_RR_\]\\P\_H_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@11100
CGGATAACTGAAAATGCATTTTTAACGCCATGACCGTGTCTCAAGGACCCGCTGTGGAAGGGGCGCCGCAGCCAGAAGCTGGCCATGTCAGCGCG
+
b`b_b_a\bc^Tabadaddcddd``bdaa_^aJ\^_\]\\__O[___L^\_aaa^^^UJ^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@15663
AGGTGAAGTGGCAGGAGGACCGCCGGAAGAAGCTCTTCAGAACTCAGGGGGAGGGGGAAAGCAGAAACCAGAAGTCCAGTGAGCAGGGGGCTGAG
+
aaKaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@4698
CCAATTGGCACCCCTCTGCCTTCAGCCATTCCCTCTGGCTACTGCTCTCTGGTCGGGGCGCCTGGGCGACAGACTCTCTCCCCCCACCCCCCCGC
+
cccc\`ccc\caccZccccc]^`LY\bL_bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@20649
TCTGGACTGGATCTTTAGGATGGTGGAGATGATCTGGATGTAGGACAAAAGAACCAGGCAGAAGGGTGTCATCAGAAGAACACTGCTAGACACCA
+
eeeeeaddadacdddebeccdddadd\^abbT_]bccTac]]b]L^][]Ve[^ZaY_^_^`\\Y]^Y`BBBBBBBBBBBBBBBBBBBBBBBBBBB
@17259
GCCTTGTGTTGTTCCTGGCATCACCGCAGGGAGCCCTGGGGGGCCAGGCGGGCGCTGACCCTGGGCACTGCCGCGCCTGGAGGGGCTGAGCACCG
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@6003
CTTCAACTCATCTTGTTATTAATACCATCAATATCCCATGAGGCTCATAAAACGAGTCTTTCTTCTTGGAAACATGACCAAGATTGGGCAAACGT
+
fffffffffffffffffdffecfcefeffdcfdeeebbbdbccccc\db\`^aa`^Y^^^cbcbaa`bbWY^^^__S_YYR]GWY]\]]XX\_`S
@4118
TCAAATTGTACTGCAAAGAAGGTCCCAGCTGGTCTCTTCTGGGAGTGATCTAACTAACTTAAGCTGACCCTGTGACTGGCTGAGGATAATCCCTT
+
dc^ddeeeeeedeee`ceceddadadddcbde_dedc_ec_a^^b\b\\]VIPZY^T^^^\L_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@18416
GTGGGGAAGCCGAAGAAGCAGCGGAGATCGATTGTAAGAACGACGTCCATGACCAGGGTTGGTGGAGACTGCTTCTCTGCATGCGGGGGAAGGCG
+
dddacaabdbea\d^cce\da`dd_^__`a`a`b[_^__^\^^^_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@20115
TGAAAAAGGAAAACATGGTAGTTTTCTTGTATGAGAGAGCCAGAGCCACCTTGGAGATTTTGTTCTCTCTGTGCGCACCAGTGATGACACAGGGG
+
ed^eeafffaddfecdddabc^_badd`bd_ddadaa^bbcad\d\__^_\aaa_aY____aaN_\cdc\^aaYbBBBBBBBBBBBBBBBBBBBB
@16139
TCATCCGAAGAGTTGGCAGGCCCTGTGAATTGTGAAAACAGTATACCCACCCCTTTCCCGGAGCAGGACGCTGAATGTCCAGAGGATGCCAGACC
+
cabacacY^c\daaddaadad^\ad_a\Y`[ZQ]Y^^OYQ^X^YT\\]U\^RRX^\YJ^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@14123
GATTTGGGGAAAGGAAACAATAGTTGAGTTTGGGCCACGGGAAATTCAAGATGCCTGGTATGTCAAGTCTGGCAGTTGAAGCAGCAGGGCTGGCG
+
cccccccac^bYbbT_aa_Yb^^Ta\\^]]aaTaaaaab\b\XL`VZZV]QYYY[aa^^^^_^^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@8766
ACCTGTAAGGTCCGCTCCTGGTGGACACCCACGAAGTCCAGGGCCTCAGGCAGGAAGTTGTAGCGCAGAGTTTTGAGCAGCTGCTCCATCAGGGA
+
fcfffffcffeffeeefdefddeecdccacddfdYd`d^\_^`\_abbc\b[ba^Y^Z_^^H^Z_^Y_Y_OKWPZR]]Z]`Z``Z^UHZ^BBBBB
16 changes: 16 additions & 0 deletions tools/cutadapt/test-data/cutadapt/data/maxee.fastq
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
@empty

+

@ee_1
A
+
!
@ee_0.8
ACGTTGCA
+
++++++++
@ee_1.01
TGGACGTTGCA
+
+5+++++++++
8 changes: 8 additions & 0 deletions tools/cutadapt/test-data/cutadapt/data/polya.1.fasta
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
>polyA
AAACTTCAGAACAGAAAAAAAAAAAAAAAAAAAAA
>polyAlong
CTTAGTTCAATWTTAACCAAACTTCAGAACAGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA
>polyA2
AAACTTAACAAGAACAAGAAAAAAAAAAAAAAAAAAAAA
>nopoly
GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG
8 changes: 8 additions & 0 deletions tools/cutadapt/test-data/cutadapt/data/polya.2.fasta
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
>polyA
TTTTTTTTTTTTTTTTTTTTTCTGTTCTGAAGTTT
>polyAlong
TTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTCTGTTCTGAAGTTTGGTTAAWATTGAACTAAG
>polyA2
TTTTTTTTTTTTTTTTTTTTTCTTGTTCTTGTTAAGTTT
>nopoly
TCTGAAGTTTGGTTAAWATTGAACTAA
7 changes: 7 additions & 0 deletions tools/cutadapt/test-data/cutadapt/data/simple.fasta
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
# a comment
# another one
>first_sequence
SEQUENCE1
>second_sequence
SEQUEN
CE2
Binary file added tools/cutadapt/test-data/cutadapt/data/simple.fasta.gz
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Binary file not shown.
4 changes: 4 additions & 0 deletions tools/cutadapt/test-data/cutadapt/data/wildcard.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
>1
ANGTACGTTGCATGCA
>2
ACGTANGTTGCATGCA
6 changes: 6 additions & 0 deletions tools/cutadapt/test-data/cutadapt/data/wildcardN.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
>perfect
TTTGGGGGGG
>withN
TTTGGNGGGG
>1mism
TTTGGGGCGG
7 changes: 6 additions & 1 deletion tools/cutadapt/test-data/cutadapt_rest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,9 @@
"quality_trimmed": null,
"quality_trimmed_read1": null,
"quality_trimmed_read2": null,
"poly_a_trimmed": null,
"poly_a_trimmed_read1": null,
"poly_a_trimmed_read2": null,
"output": 35,
"output_read1": 35,
"output_read2": null
Expand Down Expand Up @@ -81,5 +84,7 @@
}
}
],
"adapters_read2": null
"adapters_read2": null,
"poly_a_trimmed_read1": null,
"poly_a_trimmed_read2": null
}

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