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stop with an error message if Q values are below or above thresholds
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frederic-mahe committed Dec 18, 2024
1 parent 894a07f commit 479bd48
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9 changes: 5 additions & 4 deletions man/commands/fragments/option_fastq_qmax.md
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`--fastq_qmax` *positive integer*
: Specify the maximal quality score accepted when reading fastq
sequences. Reads with higher quality scores are discarded. Accepted
values range from 0 to 93 if the offset is 33 (see `--fastq_ascii`),
or range from 0 to 62 if the offset is 64. The default is 41, which
is usual for recent Sanger/Illumina 1.8+ files.
sequences. Stop with an error message if a quality scores higher
than the specified value is read. Accepted values range from 0 to 93
if the offset is 33 (see `--fastq_ascii`), or range from 0 to 62 if
the offset is 64. The default is 41, which is usual for recent
Sanger/Illumina 1.8+ files.
11 changes: 6 additions & 5 deletions man/commands/fragments/option_fastq_qmin.md
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@@ -1,7 +1,8 @@
`--fastq_qmin` *positive integer*
: Specify the minimal quality score accepted when reading fastq
sequences. Reads with lower quality scores are discarded. Accepted
values range from 0 to 93 if the offset is 33 (see `--fastq_ascii`),
or range from 0 to 62 if the offset is 64. The default is 0, which
is usual for recent Sanger/Illumina 1.8+ files. Older formats may
use scores between -5 and 2.
sequences. Stop with an error message if a quality scores lower than
the specified value is read. Accepted values range from 0 to 93 if
the offset is 33 (see `--fastq_ascii`), or range from 0 to 62 if the
offset is 64. The default is 0, which is usual for recent
Sanger/Illumina 1.8+ files. Older formats may use scores between -5
and 2.

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