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seqtk sample ignores interleaved reads #217

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ElDeveloper opened this issue Oct 4, 2024 · 0 comments
Open

seqtk sample ignores interleaved reads #217

ElDeveloper opened this issue Oct 4, 2024 · 0 comments

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@ElDeveloper
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Here's a minimal example to reproduce:

data

cat << EOF >> fwd.fastq
@LH00285:102:22KNYJLT3:2:1101:7768:1032 1:N:0:AACCATAGAA+CCATCTCGCC
TCCCAACGGCAGCGTCTCCCTGACGACGCGTCCGCCCCTGTCACGCAGGTAACGACGGACGGCCCCGTCGAAGCCTTTCTCGGCGGTGACGTTTCCCACAGCGTCGAGGGTGAACTCGTAGCTCACTGTNTCTTATACACATCTCCGAGC
+
9I9I-IIII9-III-IIIII99IIII9IIIII9II9II9I9IIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII#IIIIIIIIIIIIIIIIIIII
@LH00285:102:22KNYJLT3:2:1101:10542:1032 1:N:0:ANCCATAGAA+CCATCTCGCC
TNCTTCATACAAAACTGATATTCCTTATCCATGTTTCTTTACACATGTTCGGGAACTTTGGCTAAGTGTGGTATCTATATTCAATACGTCTGTAGATGTTGAATCTTTTCATTTTCATCCAGCTTTACANTCTATTCGATTTGATCTTTT
+
9#IIIIIII-9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII#III-II9IIIIIIIIIIIII
@LH00285:102:22KNYJLT3:2:1101:11762:1032 1:N:0:ANCCATAGAA+CCATCTCGCC
TNTCTGTTCGGAATGGAAAGAGGTGGAACCCTTGTGCTATAACCACCTAAATTAAGGACTTAGCTGTACTAAATAATTTTTTCAATCAACCACTACAAAAGATCAACACAGTTTAGCACAAAGTCCCAANCTACCGTCTATTCAATTTTA
+
I#II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII#IIIIIIIIIIIIIIIIIIII
@LH00285:102:22KNYJLT3:2:1101:13186:1032 1:N:0:ANCCATAGAA+CCATCTCGCC
TNAGCGGTAAAGAGAGAGATATTTTTTAAGAAATCCCGTCTGTTACTCATAACATCATTCTATTTAAATAGGCTTATTTACAGAAATAAGGCAATGAATACGGGTTGCGATATTGATACCAGTACAAACNGTGGGAAGCCGCCTCCTTAT
+
9#I9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII#IIIIIIIIIIIIIIIIIIII
EOF

cat << EOF >> rev.fastq
@LH00285:102:22KNYJLT3:2:1101:7768:1032 2:N:0:AACCATAGAA+CCATCTCGCC
TGAGCTACGAGTTCACCCTCGACGCTGTGGGAAACGTCACCGCCGAGAAAGGCTTCGACGGGGCCGTCCGTCGTTACCTGCGTGACAGGGGCGGACGCGTCGTCAGGGAGACGCTGCCGTCGGGACTGTCTCTTATACATATCTGACGCT
+
9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII
@LH00285:102:22KNYJLT3:2:1101:10542:1032 2:N:0:ANCCATAGAA+CCATCTCGCC
TGGTAGATGCAGGTTCCTGTAAAAGAGACCTTTACCACGAAAGATAAGATCCAGTAAAAGTGAATGAAAAGATCAAATCGAAGAGATTGTAAAGCTGGATGAAAATGAAAAGATTCAACATCTACAGACGTATTGAATATAGATACCACA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@LH00285:102:22KNYJLT3:2:1101:11762:1032 2:N:0:ANCCATAGAA+CCATCTCGCC
TCTATAGCTTTACTACCGTACGGCTATGGCAATGCTTAAAATTGAATAGACGGTAGGTTGGGACTTTGTGCTAAACTGTGTTGATCTTTTGTAGTGGTTGATTGAAAAAATTATTTAGTACAGCTAAGTCCTTAATTTAGGTGGTTATAG
+
9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@LH00285:102:22KNYJLT3:2:1101:13186:1032 2:N:0:ANCCATAGAA+CCATCTCGCC
TCAGAATATTGCCCGTGAGCTAGGCCGTCCGGTTAAATGGAACCCGGCTACATTAAGCTTCGGTAATGATAAGGAGGCGGCTTCCCACCGTTTGTACTGGTATCAATATCGCAACCCGTATTCATTGCCTTATTTCTGTAAATAAGCCTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
EOF

command:

seqtk mergepe fwd.fastq rev.fastq | seqtk sample -s 4 - 2

output

@LH00285:102:22KNYJLT3:2:1101:13186:1032 2:N:0:ANCCATAGAA+CCATCTCGCC
TCAGAATATTGCCCGTGAGCTAGGCCGTCCGGTTAAATGGAACCCGGCTACATTAAGCTTCGGTAATGATAAGGAGGCGGCTTCCCACCGTTTGTACTGGTATCAATATCGCAACCCGTATTCATTGCCTTATTTCTGTAAATAAGCCTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@LH00285:102:22KNYJLT3:2:1101:10542:1032 1:N:0:ANCCATAGAA+CCATCTCGCC
TNCTTCATACAAAACTGATATTCCTTATCCATGTTTCTTTACACATGTTCGGGAACTTTGGCTAAGTGTGGTATCTATATTCAATACGTCTGTAGATGTTGAATCTTTTCATTTTCATCCAGCTTTACANTCTATTCGATTTGATCTTTT
+
9#IIIIIII-9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII#III-II9IIIIIIIIIIIII
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