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commit 30ca906bd494b488dc836d53d2ffc068410ff4d4 Author: Andreas Tille <[email protected]> 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 <[email protected]> -.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 <[email protected]> -.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 index dcf4553..0000000 --- a/debian/python-cutadapt.manpages +++ /dev/null @@ -1 +0,0 @@ -debian/cutadapt.man1 diff --git a/debian/python3-cutadapt.manpages b/debian/python3-cutadapt.manpages deleted file mode 100644 index 2e88559..0000000 --- a/debian/python3-cutadapt.manpages +++ /dev/null @@ -1 +0,0 @@ -debian/cutadapt3.man1 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cutadapt.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
