[med-svn] [python-cutadapt] 08/12: Only one single manpage

Mon Jun 20 13:39:52 UTC 2016

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tille pushed a commit to branch master
in repository python-cutadapt.

commit 30ca906bd494b488dc836d53d2ffc068410ff4d4
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 20 15:27:45 2016 +0200

    Only one single manpage
---
 debian/cutadapt.1                | 301 ++++++++++++++++++++++++++++++++++++++
 debian/cutadapt.man1             | 307 ---------------------------------------
 debian/cutadapt.manpages         |   1 +
 debian/cutadapt3.man1            | 307 ---------------------------------------
 debian/python-cutadapt.manpages  |   1 -
 debian/python3-cutadapt.manpages |   1 -
 6 files changed, 302 insertions(+), 616 deletions(-)

diff --git a/debian/cutadapt.1 b/debian/cutadapt.1
new file mode 100644
index 0000000..6bce735
--- /dev/null
+++ b/debian/cutadapt.1
@@ -0,0 +1,301 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH CUTADAPT "1" "June 2016" "cutadapt 1.10" "User Commands"
+.SH NAME
+cutadapt \- remove adapter sequences from high-throughput sequencing reads
+.SH SYNOPSIS
+.IP
+.B cutadapt
+\fB\-a\fR ADAPTER [options] [\-o output.fastq] input.fastq
+.P
+For paired-end reads:
+.IP
+.B cutadapt
+\fB\-a\fR ADAPT1 \fB\-A\fR ADAPT2 [options] \fB\-o\fR out1.fastq \fB\-p\fR out2.fastq in1.fastq in2.fastq
+.SH DESCRIPTION
+Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
+characters are supported. The reverse complement is *not* automatically
+searched. All reads from input.fastq will be written to output.fastq with the
+adapter sequence removed. Adapter matching is error\-tolerant. Multiple adapter
+sequences can be given (use further \fB\-a\fR options), but only the best\-matching
+adapter will be removed.
+.PP
+Input may also be in FASTA format. Compressed input and output is supported and
+auto\-detected from the file name (.gz, .xz, .bz2). Use the file name '\-' for
+standard input/output. Without the \fB\-o\fR option, output is sent to standard output.
+.SH OPTIONS
+.TP
+\fB\-\-help\fR
+show all command\-line options
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-debug\fR
+Print debugging information.
+.TP
+\fB\-f\fR FORMAT, \fB\-\-format\fR=\fI\,FORMAT\/\fR
+Input file format; can be either 'fasta', 'fastq' or
+\&'sra\-fastq'. Ignored when reading csfasta/qual files.
+Default: auto\-detect from file name extension.
+.IP
+Finding adapters::
+.IP
+Parameters \fB\-a\fR, \fB\-g\fR, \fB\-b\fR specify adapters to be removed from each read
+(or from the first read in a pair if data is paired). If specified
+multiple times, only the best matching adapter is trimmed (but see the
+\fB\-\-times\fR option). When the special notation 'file:FILE' is used,
+adapter sequences are read from the given FASTA file.
+.TP
+\fB\-a\fR ADAPTER, \fB\-\-adapter\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter ligated to the 3' end (paired
+data: of the first read). The adapter and subsequent
+bases are trimmed. If a '$' character is appended
+('anchoring'), the adapter is only found if it is a
+suffix of the read.
+.TP
+\fB\-g\fR ADAPTER, \fB\-\-front\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter ligated to the 5' end (paired
+data: of the first read). The adapter and any
+preceding bases are trimmed. Partial matches at the 5'
+end are allowed. If a '^' character is prepended
+('anchoring'), the adapter is only found if it is a
+prefix of the read.
+.TP
+\fB\-b\fR ADAPTER, \fB\-\-anywhere\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter that may be ligated to the 5'
+or 3' end (paired data: of the first read). Both types
+of matches as described under \fB\-a\fR und \fB\-g\fR are allowed.
+If the first base of the read is part of the match,
+the behavior is as with \fB\-g\fR, otherwise as with \fB\-a\fR. This
+option is mostly for rescuing failed library
+preparations \- do not use if you know which end your
+adapter was ligated to!
+.TP
+\fB\-e\fR ERROR_RATE, \fB\-\-error\-rate\fR=\fI\,ERROR_RATE\/\fR
+Maximum allowed error rate (no. of errors divided by
+the length of the matching region). Default: 0.1
+.TP
+\fB\-\-no\-indels\fR
+Allow only mismatches in alignments. Default: allow
+both mismatches and indels
+.TP
+\fB\-n\fR COUNT, \fB\-\-times\fR=\fI\,COUNT\/\fR
+Remove up to COUNT adapters from each read. Default: 1
+.TP
+\fB\-O\fR MINLENGTH, \fB\-\-overlap\fR=\fI\,MINLENGTH\/\fR
+If the overlap between the read and the adapter is
+shorter than MINLENGTH, the read is not modified.
+Reduces the no. of bases trimmed due to random adapter
+matches. Default: 3
+.TP
+\fB\-\-match\-read\-wildcards\fR
+Interpret IUPAC wildcards in reads. Default: False
+.TP
+\fB\-N\fR, \fB\-\-no\-match\-adapter\-wildcards\fR
+Do not interpret IUPAC wildcards in adapters.
+.TP
+\fB\-\-no\-trim\fR
+Match and redirect reads to output/untrimmed\-output as
+usual, but do not remove adapters.
+.TP
+\fB\-\-mask\-adapter\fR
+Mask adapters with 'N' characters instead of trimming
+them.
+.IP
+Additional read modifications:
+.TP
+\fB\-u\fR LENGTH, \fB\-\-cut\fR=\fI\,LENGTH\/\fR
+Remove bases from each read (first read only if
+paired). If LENGTH is positive, remove bases from the
+beginning. If LENGTH is negative, remove bases from
+the end. Can be used twice if LENGTHs have different
+signs.
+.TP
+\fB\-q\fR [5'CUTOFF,]3'CUTOFF, \fB\-\-quality\-cutoff\fR=\fI\,[5\/\fR'CUTOFF,]3'CUTOFF
+Trim low\-quality bases from 5' and/or 3' ends of each
+read before adapter removal. Applied to both reads if
+data is paired. If one value is given, only the 3' end
+is trimmed. If two comma\-separated cutoffs are given,
+the 5' end is trimmed with the first cutoff, the 3'
+end with the second.
+.TP
+\fB\-\-nextseq\-trim\fR=\fI\,3\/\fR'CUTOFF
+NextSeq\-specific quality trimming (each read). Trims
+also dark cycles appearing as high\-quality G bases
+(EXPERIMENTAL).
+.TP
+\fB\-\-quality\-base\fR=\fI\,QUALITY_BASE\/\fR
+Assume that quality values in FASTQ are encoded as
+ascii(quality + QUALITY_BASE). This needs to be set to
+64 for some old Illumina FASTQ files. Default: 33
+.TP
+\fB\-\-trim\-n\fR
+Trim N's on ends of reads.
+.TP
+\fB\-x\fR PREFIX, \fB\-\-prefix\fR=\fI\,PREFIX\/\fR
+Add this prefix to read names. Use {name} to insert
+the name of the matching adapter.
+.TP
+\fB\-y\fR SUFFIX, \fB\-\-suffix\fR=\fI\,SUFFIX\/\fR
+Add this suffix to read names; can also include {name}
+.TP
+\fB\-\-strip\-suffix\fR=\fI\,STRIP_SUFFIX\/\fR
+Remove this suffix from read names if present. Can be
+given multiple times.
+.TP
+\fB\-\-length\-tag\fR=\fI\,TAG\/\fR
+Search for TAG followed by a decimal number in the
+description field of the read. Replace the decimal
+number with the correct length of the trimmed read.
+For example, use \fB\-\-length\-tag\fR 'length=' to correct
+fields like 'length=123'.
+.IP
+Filtering of processed reads:
+.TP
+\fB\-\-discard\-trimmed\fR, \fB\-\-discard\fR
+Discard reads that contain an adapter. Also use \fB\-O\fR to
+avoid discarding too many randomly matching reads!
+.TP
+\fB\-\-discard\-untrimmed\fR, \fB\-\-trimmed\-only\fR
+Discard reads that do not contain the adapter.
+.TP
+\fB\-m\fR LENGTH, \fB\-\-minimum\-length\fR=\fI\,LENGTH\/\fR
+Discard trimmed reads that are shorter than LENGTH.
+Reads that are too short even before adapter removal
+are also discarded. In colorspace, an initial primer
+is not counted. Default: 0
+.TP
+\fB\-M\fR LENGTH, \fB\-\-maximum\-length\fR=\fI\,LENGTH\/\fR
+Discard trimmed reads that are longer than LENGTH.
+Reads that are too long even before adapter removal
+are also discarded. In colorspace, an initial primer
+is not counted. Default: no limit
+.TP
+\fB\-\-max\-n\fR=\fI\,COUNT\/\fR
+Discard reads with too many N bases. If COUNT is an
+integer, it is treated as the absolute number of N
+bases. If it is between 0 and 1, it is treated as the
+proportion of N's allowed in a read.
+.IP
+Output:
+.TP
+\fB\-\-quiet\fR
+Print only error messages.
+.TP
+\fB\-o\fR FILE, \fB\-\-output\fR=\fI\,FILE\/\fR
+Write trimmed reads to FILE. FASTQ or FASTA format is
+chosen depending on input. The summary report is sent
+to standard output. Use '{name}' in FILE to
+demultiplex reads into multiple files. Default: write
+to standard output
+.TP
+\fB\-\-info\-file\fR=\fI\,FILE\/\fR
+Write information about each read and its adapter
+matches into FILE. See the documentation for the file
+format.
+.TP
+\fB\-r\fR FILE, \fB\-\-rest\-file\fR=\fI\,FILE\/\fR
+When the adapter matches in the middle of a read,
+write the rest (after the adapter) into FILE.
+.TP
+\fB\-\-wildcard\-file\fR=\fI\,FILE\/\fR
+When the adapter has N bases (wildcards), write
+adapter bases matching wildcard positions to FILE.
+When there are indels in the alignment, this will
+often not be accurate.
+.TP
+\fB\-\-too\-short\-output\fR=\fI\,FILE\/\fR
+Write reads that are too short (according to length
+specified by \fB\-m\fR) to FILE. Default: discard reads
+.TP
+\fB\-\-too\-long\-output\fR=\fI\,FILE\/\fR
+Write reads that are too long (according to length
+specified by \fB\-M\fR) to FILE. Default: discard reads
+.TP
+\fB\-\-untrimmed\-output\fR=\fI\,FILE\/\fR
+Write reads that do not contain the adapter to FILE.
+Default: output to same file as trimmed reads
+.IP
+Colorspace options:
+.TP
+\fB\-c\fR, \fB\-\-colorspace\fR
+Enable colorspace mode: Also trim the color that is
+adjacent to the found adapter.
+.TP
+\fB\-d\fR, \fB\-\-double\-encode\fR
+Double\-encode colors (map 0,1,2,3,4 to A,C,G,T,N).
+.TP
+\fB\-t\fR, \fB\-\-trim\-primer\fR
+Trim primer base and the first color (which is the
+transition to the first nucleotide)
+.TP
+\fB\-\-strip\-f3\fR
+Strip the _F3 suffix of read names
+.TP
+\fB\-\-maq\fR, \fB\-\-bwa\fR
+MAQ\- and BWA\-compatible colorspace output. This
+enables \fB\-c\fR, \fB\-d\fR, \fB\-t\fR, \fB\-\-strip\-f3\fR and \fB\-y\fR '/1'.
+.TP
+\fB\-\-no\-zero\-cap\fR
+Do not change negative quality values to zero in
+colorspace data. By default, they are since many tools
+have problems with negative qualities.
+.TP
+\fB\-z\fR, \fB\-\-zero\-cap\fR
+Change negative quality values to zero. This is
+enabled by default when \fB\-c\fR/\-\-colorspace is also
+enabled. Use the above option to disable it.
+.IP
+Paired\-end options:
+.IP
+The \fB\-A\fR/\-G/\-B/\-U options work like their \fB\-a\fR/\-b/\-g/\-u counterparts, but
+are applied to the second read in each pair.
+.TP
+\fB\-A\fR ADAPTER
+3' adapter to be removed from second read in a pair.
+.TP
+\fB\-G\fR ADAPTER
+5' adapter to be removed from second read in a pair.
+.TP
+\fB\-B\fR ADAPTER
+5'/3 adapter to be removed from second read in a pair.
+.TP
+\fB\-U\fR LENGTH
+Remove LENGTH bases from second read in a pair (see
+\fB\-\-cut\fR).
+.TP
+\fB\-p\fR FILE, \fB\-\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to FILE.
+.TP
+\fB\-\-pair\-filter=\fR(any|both)
+Which of the reads in a paired\-end read have to match
+the filtering criterion in order for it to be
+filtered. Default: any
+.TP
+\fB\-\-interleaved\fR
+Read and write interleaved paired\-end reads.
+.TP
+\fB\-\-untrimmed\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to this FILE when no
+adapter was found in the first read. Use this option
+together with \fB\-\-untrimmed\-output\fR when trimming pairedend reads. Default: output to same file as trimmed
+reads
+.TP
+\fB\-\-too\-short\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to this file if pair is
+too short. Use together with \fB\-\-too\-short\-output\fR.
+.TP
+\fB\-\-too\-long\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to this file if pair is
+too long. Use together with \fB\-\-too\-long\-output\fR.
+.SH SEE ALSO
+See http://cutadapt.readthedocs.org/ for full documentation.
+.SS Citation
+Marcel Martin. Cutadapt removes adapter sequences from high\-throughput
+sequencing reads. EMBnet.Journal, 17(1):10\-12, May 2011.
+http://dx.doi.org/10.14806/ej.17.1.200
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/cutadapt.man1 b/debian/cutadapt.man1
deleted file mode 100644
index 4a2023b..0000000
--- a/debian/cutadapt.man1
+++ /dev/null
@@ -1,307 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
-.TH CUTADAPT "1" "August 2015" "cutadapt 1.8.3" "User Commands"
-.SH NAME
-cutadapt \- manual page for cutadapt 1.8.3
-.SH DESCRIPTION
-cutadapt version 1.8.3
-Copyright \(co 2010\-2015 Marcel Martin <marcel.martin at scilifelab.se>
-.PP
-cutadapt removes adapter sequences from high\-throughput sequencing reads.
-.SS "Usage:"
-.IP
-cutadapt \fB\-a\fR ADAPTER [options] [\-o output.fastq] input.fastq
-.SS "For paired-end reads:"
-.IP
-cutadapt \fB\-a\fR ADAPT1 \fB\-A\fR ADAPT2 [options] \fB\-o\fR out1.fastq \fB\-p\fR out2.fastq in1.fastq in2.fastq
-.PP
-Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
-characters are supported. The reverse complement is *not* automatically
-searched. All reads from input.fastq will be written to output.fastq with the
-adapter sequence removed. Adapter matching is error\-tolerant. Multiple adapter
-sequences can be given (use further \fB\-a\fR options), but only the best\-matching
-adapter will be removed.
-.PP
-Input may also be in FASTA format. Compressed input and output is supported and
-auto\-detected from the file name (.gz, .xz, .bz2). Use the file name '\-' for
-standard input/output. Without the \fB\-o\fR option, output is sent to standard output.
-.SS "Some other available features are:"
-.IP
-* Various other adapter types (5' adapters, "mixed" 5'/3' adapters etc.)
-* Trimming a fixed number of bases
-* Quality trimming
-* Trimming colorspace reads
-* Filtering reads by various criteria
-.PP
-Use "cutadapt \fB\-\-help\fR" to see all command\-line options.
-See http://cutadapt.readthedocs.org/ for full documentation.
-.SH OPTIONS
-.TP
-\fB\-\-version\fR
-show program's version number and exit
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show this help message and exit
-.TP
-\fB\-f\fR FORMAT, \fB\-\-format\fR=\fI\,FORMAT\/\fR
-Input file format; can be either 'fasta', 'fastq' or
-\&'sra\-fastq'. Ignored when reading csfasta/qual files
-(default: auto\-detect from file name extension).
-.IP
-Options that influence how the adapters are found:
-.IP
-Each of the following three parameters (\fB\-a\fR, \fB\-b\fR, \fB\-g\fR) can be used
-multiple times and in any combination to search for an entire set of
-adapters of possibly different types. Only the best matching adapter
-is trimmed from each read (but see the \fB\-\-times\fR option). Instead of
-giving an adapter directly, you can also write file:FILE and the
-adapter sequences will be read from the given FILE (which must be in
-FASTA format).
-.TP
-\fB\-a\fR ADAPTER, \fB\-\-adapter\fR=\fI\,ADAPTER\/\fR
-Sequence of an adapter that was ligated to the 3' end.
-The adapter itself and anything that follows is
-trimmed. If the adapter sequence ends with the '$'
-character, the adapter is anchored to the end of the
-read and only found if it is a suffix of the read.
-.TP
-\fB\-g\fR ADAPTER, \fB\-\-front\fR=\fI\,ADAPTER\/\fR
-Sequence of an adapter that was ligated to the 5' end.
-If the adapter sequence starts with the character '^',
-the adapter is 'anchored'. An anchored adapter must
-appear in its entirety at the 5' end of the read (it
-is a prefix of the read). A non\-anchored adapter may
-appear partially at the 5' end, or it may occur within
-the read. If it is found within a read, the sequence
-preceding the adapter is also trimmed. In all cases,
-the adapter itself is trimmed.
-.TP
-\fB\-b\fR ADAPTER, \fB\-\-anywhere\fR=\fI\,ADAPTER\/\fR
-Sequence of an adapter that was ligated to the 5' or
-3' end. If the adapter is found within the read or
-overlapping the 3' end of the read, the behavior is
-the same as for the \fB\-a\fR option. If the adapter overlaps
-the 5' end (beginning of the read), the initial
-portion of the read matching the adapter is trimmed,
-but anything that follows is kept.
-.TP
-\fB\-e\fR ERROR_RATE, \fB\-\-error\-rate\fR=\fI\,ERROR_RATE\/\fR
-Maximum allowed error rate (no. of errors divided by
-the length of the matching region) (default: 0.1)
-.TP
-\fB\-\-no\-indels\fR
-Do not allow indels in the alignments (allow only
-mismatches). Currently only supported for anchored
-adapters. (default: allow both mismatches and indels)
-.TP
-\fB\-n\fR COUNT, \fB\-\-times\fR=\fI\,COUNT\/\fR
-Try to remove adapters at most COUNT times. Useful
-when an adapter gets appended multiple times (default:
-1).
-.TP
-\fB\-O\fR LENGTH, \fB\-\-overlap\fR=\fI\,LENGTH\/\fR
-Minimum overlap length. If the overlap between the
-read and the adapter is shorter than LENGTH, the read
-is not modified. This reduces the no. of bases trimmed
-purely due to short random adapter matches (default:
-3).
-.TP
-\fB\-\-match\-read\-wildcards\fR
-Allow IUPAC wildcards in reads (default: False).
-.TP
-\fB\-N\fR, \fB\-\-no\-match\-adapter\-wildcards\fR
-Do not interpret IUPAC wildcards in adapters.
-.IP
-Options for filtering of processed reads:
-.TP
-\fB\-\-discard\-trimmed\fR, \fB\-\-discard\fR
-Discard reads that contain the adapter instead of
-trimming them. Also use \fB\-O\fR in order to avoid throwing
-away too many randomly matching reads!
-.TP
-\fB\-\-discard\-untrimmed\fR, \fB\-\-trimmed\-only\fR
-Discard reads that do not contain the adapter.
-.TP
-\fB\-m\fR LENGTH, \fB\-\-minimum\-length\fR=\fI\,LENGTH\/\fR
-Discard trimmed reads that are shorter than LENGTH.
-Reads that are too short even before adapter removal
-are also discarded. In colorspace, an initial primer
-is not counted (default: 0).
-.TP
-\fB\-M\fR LENGTH, \fB\-\-maximum\-length\fR=\fI\,LENGTH\/\fR
-Discard trimmed reads that are longer than LENGTH.
-Reads that are too long even before adapter removal
-are also discarded. In colorspace, an initial primer
-is not counted (default: no limit).
-.TP
-\fB\-\-no\-trim\fR
-Match and redirect reads to output/untrimmed\-output as
-usual, but do not remove adapters.
-.TP
-\fB\-\-max\-n\fR=\fI\,LENGTH\/\fR
-The max proportion of N's allowed in a read. A number
-< 1 will be treated as a proportion while a number > 1
-will be treated as the maximum number of N's
-contained.
-.TP
-\fB\-\-mask\-adapter\fR
-Mask adapters with 'N' characters instead of trimming
-them.
-.IP
-Options that influence what gets output to where:
-.TP
-\fB\-\-quiet\fR
-Do not print a report at the end.
-.TP
-\fB\-o\fR FILE, \fB\-\-output\fR=\fI\,FILE\/\fR
-Write modified reads to FILE. FASTQ or FASTA format is
-chosen depending on input. The summary report is sent
-to standard output. Use '{name}' in FILE to
-demultiplex reads into multiple files. (default:
-trimmed reads are written to standard output)
-.TP
-\fB\-\-info\-file\fR=\fI\,FILE\/\fR
-Write information about each read and its adapter
-matches into FILE. See the documentation for the file
-format.
-.TP
-\fB\-r\fR FILE, \fB\-\-rest\-file\fR=\fI\,FILE\/\fR
-When the adapter matches in the middle of a read,
-write the rest (after the adapter) into FILE.
-.TP
-\fB\-\-wildcard\-file\fR=\fI\,FILE\/\fR
-When the adapter has wildcard bases ('N's), write
-adapter bases matching wildcard positions to FILE.
-When there are indels in the alignment, this will
-often not be accurate.
-.TP
-\fB\-\-too\-short\-output\fR=\fI\,FILE\/\fR
-Write reads that are too short (according to length
-specified by \fB\-m\fR) to FILE. (default: discard reads)
-.TP
-\fB\-\-too\-long\-output\fR=\fI\,FILE\/\fR
-Write reads that are too long (according to length
-specified by \fB\-M\fR) to FILE. (default: discard reads)
-.TP
-\fB\-\-untrimmed\-output\fR=\fI\,FILE\/\fR
-Write reads that do not contain the adapter to FILE.
-(default: output to same file as trimmed reads)
-.IP
-Additional modifications to the reads:
-.TP
-\fB\-u\fR LENGTH, \fB\-\-cut\fR=\fI\,LENGTH\/\fR
-Remove LENGTH bases from the beginning or end of each
-read. If LENGTH is positive, the bases are removed
-from the beginning of each read. If LENGTH is
-negative, the bases are removed from the end of each
-read. This option can be specified twice if the
-LENGTHs have different signs.
-.TP
-\fB\-q\fR [5'CUTOFF,]3'CUTOFF, \fB\-\-quality\-cutoff\fR=\fI\,[5\/\fR'CUTOFF,]3'CUTOFF
-Trim low\-quality bases from 5' and/or 3' ends of reads
-before adapter removal. If one value is given, only
-the 3' end is trimmed. If two comma\-separated cutoffs
-are given, the 5' end is trimmed with the first
-cutoff, the 3' end with the second. The algorithm is
-the same as the one used by BWA (see documentation).
-(default: no trimming)
-.TP
-\fB\-\-quality\-base\fR=\fI\,QUALITY_BASE\/\fR
-Assume that quality values are encoded as
-ascii(quality + QUALITY_BASE). The default (33) is
-usually correct, except for reads produced by some
-versions of the Illumina pipeline, where this should
-be set to 64. (Default: 33)
-.TP
-\fB\-\-trim\-n\fR
-Trim N's on ends of reads.
-.TP
-\fB\-x\fR PREFIX, \fB\-\-prefix\fR=\fI\,PREFIX\/\fR
-Add this prefix to read names
-.TP
-\fB\-y\fR SUFFIX, \fB\-\-suffix\fR=\fI\,SUFFIX\/\fR
-Add this suffix to read names
-.TP
-\fB\-\-strip\-suffix\fR=\fI\,STRIP_SUFFIX\/\fR
-Remove this suffix from read names if present. Can be
-given multiple times.
-.TP
-\fB\-c\fR, \fB\-\-colorspace\fR
-Colorspace mode: Also trim the color that is adjacent
-to the found adapter.
-.TP
-\fB\-d\fR, \fB\-\-double\-encode\fR
-When in colorspace, double\-encode colors (map
-0,1,2,3,4 to A,C,G,T,N).
-.TP
-\fB\-t\fR, \fB\-\-trim\-primer\fR
-When in colorspace, trim primer base and the first
-color (which is the transition to the first
-nucleotide)
-.TP
-\fB\-\-strip\-f3\fR
-For colorspace: Strip the _F3 suffix of read names
-.TP
-\fB\-\-maq\fR, \fB\-\-bwa\fR
-MAQ\- and BWA\-compatible colorspace output. This
-enables \fB\-c\fR, \fB\-d\fR, \fB\-t\fR, \fB\-\-strip\-f3\fR and \fB\-y\fR '/1'.
-.TP
-\fB\-\-length\-tag\fR=\fI\,TAG\/\fR
-Search for TAG followed by a decimal number in the
-description field of the read. Replace the decimal
-number with the correct length of the trimmed read.
-For example, use \fB\-\-length\-tag\fR 'length=' to correct
-fields like 'length=123'.
-.TP
-\fB\-\-no\-zero\-cap\fR
-Do not change negative quality values to zero.
-Colorspace quality values of \fB\-1\fR would appear as spaces
-in the output FASTQ file. Since many tools have
-problems with that, negative qualities are converted
-to zero when trimming colorspace data. Use this option
-to keep negative qualities.
-.TP
-\fB\-z\fR, \fB\-\-zero\-cap\fR
-Change negative quality values to zero. This is
-enabled by default when \fB\-c\fR/\-\-colorspace is also
-enabled. Use the above option to disable it.
-.IP
-Paired\-end options.:
-.IP
-The \fB\-A\fR/\-G/\-B/\-U options work like their \fB\-a\fR/\-b/\-g/\-u counterparts.
-.TP
-\fB\-A\fR ADAPTER
-3' adapter to be removed from the second read in a
-pair.
-.TP
-\fB\-G\fR ADAPTER
-5' adapter to be removed from the second read in a
-pair.
-.TP
-\fB\-B\fR ADAPTER
-5'/3 adapter to be removed from the second read in a
-pair.
-.TP
-\fB\-U\fR LENGTH
-Remove LENGTH bases from the beginning or end of each
-read (see \fB\-\-cut\fR).
-.TP
-\fB\-p\fR FILE, \fB\-\-paired\-output\fR=\fI\,FILE\/\fR
-Write second read in a pair to FILE.
-.TP
-\fB\-\-untrimmed\-paired\-output\fR=\fI\,FILE\/\fR
-Write the second read in a pair to this FILE when no
-adapter was found in the first read. Use this option
-together with \fB\-\-untrimmed\-output\fR when trimming pairedend reads. (Default: output to same file as trimmed
-reads.)
-.SH "SEE ALSO"
-The full documentation for
-.B cutadapt
-is maintained as a Texinfo manual.  If the
-.B info
-and
-.B cutadapt
-programs are properly installed at your site, the command
-.IP
-.B info cutadapt
-.PP
-should give you access to the complete manual.
diff --git a/debian/cutadapt.manpages b/debian/cutadapt.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/cutadapt.manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/cutadapt3.man1 b/debian/cutadapt3.man1
deleted file mode 100644
index 4a2023b..0000000
--- a/debian/cutadapt3.man1
+++ /dev/null
@@ -1,307 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
-.TH CUTADAPT "1" "August 2015" "cutadapt 1.8.3" "User Commands"
-.SH NAME
-cutadapt \- manual page for cutadapt 1.8.3
-.SH DESCRIPTION
-cutadapt version 1.8.3
-Copyright \(co 2010\-2015 Marcel Martin <marcel.martin at scilifelab.se>
-.PP
-cutadapt removes adapter sequences from high\-throughput sequencing reads.
-.SS "Usage:"
-.IP
-cutadapt \fB\-a\fR ADAPTER [options] [\-o output.fastq] input.fastq
-.SS "For paired-end reads:"
-.IP
-cutadapt \fB\-a\fR ADAPT1 \fB\-A\fR ADAPT2 [options] \fB\-o\fR out1.fastq \fB\-p\fR out2.fastq in1.fastq in2.fastq
-.PP
-Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
-characters are supported. The reverse complement is *not* automatically
-searched. All reads from input.fastq will be written to output.fastq with the
-adapter sequence removed. Adapter matching is error\-tolerant. Multiple adapter
-sequences can be given (use further \fB\-a\fR options), but only the best\-matching
-adapter will be removed.
-.PP
-Input may also be in FASTA format. Compressed input and output is supported and
-auto\-detected from the file name (.gz, .xz, .bz2). Use the file name '\-' for
-standard input/output. Without the \fB\-o\fR option, output is sent to standard output.
-.SS "Some other available features are:"
-.IP
-* Various other adapter types (5' adapters, "mixed" 5'/3' adapters etc.)
-* Trimming a fixed number of bases
-* Quality trimming
-* Trimming colorspace reads
-* Filtering reads by various criteria
-.PP
-Use "cutadapt \fB\-\-help\fR" to see all command\-line options.
-See http://cutadapt.readthedocs.org/ for full documentation.
-.SH OPTIONS
-.TP
-\fB\-\-version\fR
-show program's version number and exit
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show this help message and exit
-.TP
-\fB\-f\fR FORMAT, \fB\-\-format\fR=\fI\,FORMAT\/\fR
-Input file format; can be either 'fasta', 'fastq' or
-\&'sra\-fastq'. Ignored when reading csfasta/qual files
-(default: auto\-detect from file name extension).
-.IP
-Options that influence how the adapters are found:
-.IP
-Each of the following three parameters (\fB\-a\fR, \fB\-b\fR, \fB\-g\fR) can be used
-multiple times and in any combination to search for an entire set of
-adapters of possibly different types. Only the best matching adapter
-is trimmed from each read (but see the \fB\-\-times\fR option). Instead of
-giving an adapter directly, you can also write file:FILE and the
-adapter sequences will be read from the given FILE (which must be in
-FASTA format).
-.TP
-\fB\-a\fR ADAPTER, \fB\-\-adapter\fR=\fI\,ADAPTER\/\fR
-Sequence of an adapter that was ligated to the 3' end.
-The adapter itself and anything that follows is
-trimmed. If the adapter sequence ends with the '$'
-character, the adapter is anchored to the end of the
-read and only found if it is a suffix of the read.
-.TP
-\fB\-g\fR ADAPTER, \fB\-\-front\fR=\fI\,ADAPTER\/\fR
-Sequence of an adapter that was ligated to the 5' end.
-If the adapter sequence starts with the character '^',
-the adapter is 'anchored'. An anchored adapter must
-appear in its entirety at the 5' end of the read (it
-is a prefix of the read). A non\-anchored adapter may
-appear partially at the 5' end, or it may occur within
-the read. If it is found within a read, the sequence
-preceding the adapter is also trimmed. In all cases,
-the adapter itself is trimmed.
-.TP
-\fB\-b\fR ADAPTER, \fB\-\-anywhere\fR=\fI\,ADAPTER\/\fR
-Sequence of an adapter that was ligated to the 5' or
-3' end. If the adapter is found within the read or
-overlapping the 3' end of the read, the behavior is
-the same as for the \fB\-a\fR option. If the adapter overlaps
-the 5' end (beginning of the read), the initial
-portion of the read matching the adapter is trimmed,
-but anything that follows is kept.
-.TP
-\fB\-e\fR ERROR_RATE, \fB\-\-error\-rate\fR=\fI\,ERROR_RATE\/\fR
-Maximum allowed error rate (no. of errors divided by
-the length of the matching region) (default: 0.1)
-.TP
-\fB\-\-no\-indels\fR
-Do not allow indels in the alignments (allow only
-mismatches). Currently only supported for anchored
-adapters. (default: allow both mismatches and indels)
-.TP
-\fB\-n\fR COUNT, \fB\-\-times\fR=\fI\,COUNT\/\fR
-Try to remove adapters at most COUNT times. Useful
-when an adapter gets appended multiple times (default:
-1).
-.TP
-\fB\-O\fR LENGTH, \fB\-\-overlap\fR=\fI\,LENGTH\/\fR
-Minimum overlap length. If the overlap between the
-read and the adapter is shorter than LENGTH, the read
-is not modified. This reduces the no. of bases trimmed
-purely due to short random adapter matches (default:
-3).
-.TP
-\fB\-\-match\-read\-wildcards\fR
-Allow IUPAC wildcards in reads (default: False).
-.TP
-\fB\-N\fR, \fB\-\-no\-match\-adapter\-wildcards\fR
-Do not interpret IUPAC wildcards in adapters.
-.IP
-Options for filtering of processed reads:
-.TP
-\fB\-\-discard\-trimmed\fR, \fB\-\-discard\fR
-Discard reads that contain the adapter instead of
-trimming them. Also use \fB\-O\fR in order to avoid throwing
-away too many randomly matching reads!
-.TP
-\fB\-\-discard\-untrimmed\fR, \fB\-\-trimmed\-only\fR
-Discard reads that do not contain the adapter.
-.TP
-\fB\-m\fR LENGTH, \fB\-\-minimum\-length\fR=\fI\,LENGTH\/\fR
-Discard trimmed reads that are shorter than LENGTH.
-Reads that are too short even before adapter removal
-are also discarded. In colorspace, an initial primer
-is not counted (default: 0).
-.TP
-\fB\-M\fR LENGTH, \fB\-\-maximum\-length\fR=\fI\,LENGTH\/\fR
-Discard trimmed reads that are longer than LENGTH.
-Reads that are too long even before adapter removal
-are also discarded. In colorspace, an initial primer
-is not counted (default: no limit).
-.TP
-\fB\-\-no\-trim\fR
-Match and redirect reads to output/untrimmed\-output as
-usual, but do not remove adapters.
-.TP
-\fB\-\-max\-n\fR=\fI\,LENGTH\/\fR
-The max proportion of N's allowed in a read. A number
-< 1 will be treated as a proportion while a number > 1
-will be treated as the maximum number of N's
-contained.
-.TP
-\fB\-\-mask\-adapter\fR
-Mask adapters with 'N' characters instead of trimming
-them.
-.IP
-Options that influence what gets output to where:
-.TP
-\fB\-\-quiet\fR
-Do not print a report at the end.
-.TP
-\fB\-o\fR FILE, \fB\-\-output\fR=\fI\,FILE\/\fR
-Write modified reads to FILE. FASTQ or FASTA format is
-chosen depending on input. The summary report is sent
-to standard output. Use '{name}' in FILE to
-demultiplex reads into multiple files. (default:
-trimmed reads are written to standard output)
-.TP
-\fB\-\-info\-file\fR=\fI\,FILE\/\fR
-Write information about each read and its adapter
-matches into FILE. See the documentation for the file
-format.
-.TP
-\fB\-r\fR FILE, \fB\-\-rest\-file\fR=\fI\,FILE\/\fR
-When the adapter matches in the middle of a read,
-write the rest (after the adapter) into FILE.
-.TP
-\fB\-\-wildcard\-file\fR=\fI\,FILE\/\fR
-When the adapter has wildcard bases ('N's), write
-adapter bases matching wildcard positions to FILE.
-When there are indels in the alignment, this will
-often not be accurate.
-.TP
-\fB\-\-too\-short\-output\fR=\fI\,FILE\/\fR
-Write reads that are too short (according to length
-specified by \fB\-m\fR) to FILE. (default: discard reads)
-.TP
-\fB\-\-too\-long\-output\fR=\fI\,FILE\/\fR
-Write reads that are too long (according to length
-specified by \fB\-M\fR) to FILE. (default: discard reads)
-.TP
-\fB\-\-untrimmed\-output\fR=\fI\,FILE\/\fR
-Write reads that do not contain the adapter to FILE.
-(default: output to same file as trimmed reads)
-.IP
-Additional modifications to the reads:
-.TP
-\fB\-u\fR LENGTH, \fB\-\-cut\fR=\fI\,LENGTH\/\fR
-Remove LENGTH bases from the beginning or end of each
-read. If LENGTH is positive, the bases are removed
-from the beginning of each read. If LENGTH is
-negative, the bases are removed from the end of each
-read. This option can be specified twice if the
-LENGTHs have different signs.
-.TP
-\fB\-q\fR [5'CUTOFF,]3'CUTOFF, \fB\-\-quality\-cutoff\fR=\fI\,[5\/\fR'CUTOFF,]3'CUTOFF
-Trim low\-quality bases from 5' and/or 3' ends of reads
-before adapter removal. If one value is given, only
-the 3' end is trimmed. If two comma\-separated cutoffs
-are given, the 5' end is trimmed with the first
-cutoff, the 3' end with the second. The algorithm is
-the same as the one used by BWA (see documentation).
-(default: no trimming)
-.TP
-\fB\-\-quality\-base\fR=\fI\,QUALITY_BASE\/\fR
-Assume that quality values are encoded as
-ascii(quality + QUALITY_BASE). The default (33) is
-usually correct, except for reads produced by some
-versions of the Illumina pipeline, where this should
-be set to 64. (Default: 33)
-.TP
-\fB\-\-trim\-n\fR
-Trim N's on ends of reads.
-.TP
-\fB\-x\fR PREFIX, \fB\-\-prefix\fR=\fI\,PREFIX\/\fR
-Add this prefix to read names
-.TP
-\fB\-y\fR SUFFIX, \fB\-\-suffix\fR=\fI\,SUFFIX\/\fR
-Add this suffix to read names
-.TP
-\fB\-\-strip\-suffix\fR=\fI\,STRIP_SUFFIX\/\fR
-Remove this suffix from read names if present. Can be
-given multiple times.
-.TP
-\fB\-c\fR, \fB\-\-colorspace\fR
-Colorspace mode: Also trim the color that is adjacent
-to the found adapter.
-.TP
-\fB\-d\fR, \fB\-\-double\-encode\fR
-When in colorspace, double\-encode colors (map
-0,1,2,3,4 to A,C,G,T,N).
-.TP
-\fB\-t\fR, \fB\-\-trim\-primer\fR
-When in colorspace, trim primer base and the first
-color (which is the transition to the first
-nucleotide)
-.TP
-\fB\-\-strip\-f3\fR
-For colorspace: Strip the _F3 suffix of read names
-.TP
-\fB\-\-maq\fR, \fB\-\-bwa\fR
-MAQ\- and BWA\-compatible colorspace output. This
-enables \fB\-c\fR, \fB\-d\fR, \fB\-t\fR, \fB\-\-strip\-f3\fR and \fB\-y\fR '/1'.
-.TP
-\fB\-\-length\-tag\fR=\fI\,TAG\/\fR
-Search for TAG followed by a decimal number in the
-description field of the read. Replace the decimal
-number with the correct length of the trimmed read.
-For example, use \fB\-\-length\-tag\fR 'length=' to correct
-fields like 'length=123'.
-.TP
-\fB\-\-no\-zero\-cap\fR
-Do not change negative quality values to zero.
-Colorspace quality values of \fB\-1\fR would appear as spaces
-in the output FASTQ file. Since many tools have
-problems with that, negative qualities are converted
-to zero when trimming colorspace data. Use this option
-to keep negative qualities.
-.TP
-\fB\-z\fR, \fB\-\-zero\-cap\fR
-Change negative quality values to zero. This is
-enabled by default when \fB\-c\fR/\-\-colorspace is also
-enabled. Use the above option to disable it.
-.IP
-Paired\-end options.:
-.IP
-The \fB\-A\fR/\-G/\-B/\-U options work like their \fB\-a\fR/\-b/\-g/\-u counterparts.
-.TP
-\fB\-A\fR ADAPTER
-3' adapter to be removed from the second read in a
-pair.
-.TP
-\fB\-G\fR ADAPTER
-5' adapter to be removed from the second read in a
-pair.
-.TP
-\fB\-B\fR ADAPTER
-5'/3 adapter to be removed from the second read in a
-pair.
-.TP
-\fB\-U\fR LENGTH
-Remove LENGTH bases from the beginning or end of each
-read (see \fB\-\-cut\fR).
-.TP
-\fB\-p\fR FILE, \fB\-\-paired\-output\fR=\fI\,FILE\/\fR
-Write second read in a pair to FILE.
-.TP
-\fB\-\-untrimmed\-paired\-output\fR=\fI\,FILE\/\fR
-Write the second read in a pair to this FILE when no
-adapter was found in the first read. Use this option
-together with \fB\-\-untrimmed\-output\fR when trimming pairedend reads. (Default: output to same file as trimmed
-reads.)
-.SH "SEE ALSO"
-The full documentation for
-.B cutadapt
-is maintained as a Texinfo manual.  If the
-.B info
-and
-.B cutadapt
-programs are properly installed at your site, the command
-.IP
-.B info cutadapt
-.PP
-should give you access to the complete manual.
diff --git a/debian/python-cutadapt.manpages b/debian/python-cutadapt.manpages
deleted file mode 100644
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--- a/debian/python-cutadapt.manpages
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-debian/cutadapt.man1
diff --git a/debian/python3-cutadapt.manpages b/debian/python3-cutadapt.manpages
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--- a/debian/python3-cutadapt.manpages
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-debian/cutadapt3.man1

-- 
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