[med-svn] [Git][med-team/vsearch][master] 4 commits: Typo

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / vsearch


Commits:
725e9992 by Andreas Tille at 2020-06-12T22:26:11+02:00
Typo

- - - - -
4af98a60 by Andreas Tille at 2020-06-12T22:26:31+02:00
routine-update: debhelper-compat 13

- - - - -
ee1a0406 by Andreas Tille at 2020-06-12T23:29:42+02:00
Do not install docs twice

- - - - -
d9d56fcd by Andreas Tille at 2020-06-12T23:39:14+02:00
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- − debian/man/vsearch.1
- debian/vsearch.docs
- debian/vsearch.install
- debian/vsearch.manpages


Changes:

=====================================
debian/changelog
=====================================
@@ -1,14 +1,19 @@
-vsearch (2.14.2-2) UNRELEASED; urgency=medium
+vsearch (2.14.2-2) unstable; urgency=medium
 
+  [ Nilesh Patra ]
   * Add autopkgtests
   * Add new binary: vsearch-examples
   * Add vsearch binary
   * Install relevant examples
-  * Remove extenal URL
+  * Remove external URL
   * Add manpage
   * Install self-generated manpage
   * Add myself to uploaders
 
+  [ Andreas Tille ]
+  * debhelper-compat 13 (routine-update)
+  * Do not install docs twice
+
  -- Nilesh Patra <npatra974 at gmail.com>  Fri, 12 Jun 2020 16:54:26 +0530
 
 vsearch (2.14.2-1) unstable; urgency=medium


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
            Nilesh Patra <npatra974 at gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                zlib1g-dev,
                libbz2-dev,
                markdown,


=====================================
debian/man/vsearch.1 deleted
=====================================
@@ -1,1114 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
-.TH VSEARCH "1" "June 2020" "vsearch 2.14.2" "User Commands"
-.SH NAME
-vsearch \- tool for processing metagenomic sequences
-.SH SYNOPSIS
-.B vsearch
-[\fI\,OPTIONS\/\fR]
-.SH DESCRIPTION
-vsearch v2.14.2_linux_x86_64, 7.5GB RAM, 8 cores
-https://github.com/torognes/vsearch
-.PP
-Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016)
-VSEARCH: a versatile open source tool for metagenomics
-PeerJ 4:e2584 doi: 10.7717/peerj.2584 https://doi.org/10.7717/peerj.2584
-.PP
-General options
-.TP
-\fB\-\-bzip2_decompress\fR
-decompress input with bzip2 (required if pipe)
-.TP
-\fB\-\-fasta_width\fR INT
-width of FASTA seq lines, 0 for no wrap (80)
-.TP
-\fB\-\-gzip_decompress\fR
-decompress input with gzip (required if pipe)
-.TP
-\fB\-\-help\fR | \fB\-h\fR
-display help information
-.TP
-\fB\-\-log\fR FILENAME
-write messages, timing and memory info to file
-.TP
-\fB\-\-maxseqlength\fR INT
-maximum sequence length (50000)
-.TP
-\fB\-\-minseqlength\fR INT
-min seq length (clust/derep/search: 32, other:1)
-.TP
-\fB\-\-no_progress\fR
-do not show progress indicator
-.TP
-\fB\-\-notrunclabels\fR
-do not truncate labels at first space
-.TP
-\fB\-\-quiet\fR
-output just warnings and fatal errors to stderr
-.TP
-\fB\-\-threads\fR INT
-number of threads to use, zero for all cores (0)
-.TP
-\fB\-\-version\fR | \fB\-v\fR
-display version information
-.PP
-Chimera detection
-.TP
-\fB\-\-uchime_denovo\fR FILENAME
-detect chimeras de novo
-.TP
-\fB\-\-uchime2_denovo\fR FILENAME
-detect chimeras de novo in denoised amplicons
-.TP
-\fB\-\-uchime3_denovo\fR FILENAME
-detect chimeras de novo in denoised amplicons
-.TP
-\fB\-\-uchime_ref\fR FILENAME
-detect chimeras using a reference database
-.IP
-Data
-.TP
-\fB\-\-db\fR FILENAME
-reference database for \fB\-\-uchime_ref\fR
-.IP
-Parameters
-.TP
-\fB\-\-abskew\fR REAL
-minimum abundance ratio (2.0, 16.0 for uchime3)
-.TP
-\fB\-\-dn\fR REAL
-\&'no' vote pseudo\-count (1.4)
-.TP
-\fB\-\-mindiffs\fR INT
-minimum number of differences in segment (3) *
-.TP
-\fB\-\-mindiv\fR REAL
-minimum divergence from closest parent (0.8) *
-.TP
-\fB\-\-minh\fR REAL
-minimum score (0.28) * ignored in uchime2/3
-.TP
-\fB\-\-sizein\fR
-propagate abundance annotation from input
-.TP
-\fB\-\-self\fR
-exclude identical labels for \fB\-\-uchime_ref\fR
-.TP
-\fB\-\-selfid\fR
-exclude identical sequences for \fB\-\-uchime_ref\fR
-.TP
-\fB\-\-xn\fR REAL
-\&'no' vote weight (8.0)
-.IP
-Output
-.TP
-\fB\-\-alignwidth\fR INT
-width of alignment in uchimealn output (80)
-.TP
-\fB\-\-borderline\fR FILENAME
-output borderline chimeric sequences to file
-.TP
-\fB\-\-chimeras\fR FILENAME
-output chimeric sequences to file
-.TP
-\fB\-\-fasta_score\fR
-include chimera score in fasta output
-.TP
-\fB\-\-nonchimeras\fR FILENAME
-output non\-chimeric sequences to file
-.TP
-\fB\-\-relabel\fR STRING
-relabel nonchimeras with this prefix string
-.TP
-\fB\-\-relabel_keep\fR
-keep the old label after the new when relabelling
-.TP
-\fB\-\-relabel_md5\fR
-relabel with md5 digest of normalized sequence
-.TP
-\fB\-\-relabel_self\fR
-relabel with the sequence itself as label
-.TP
-\fB\-\-relabel_sha1\fR
-relabel with sha1 digest of normalized sequence
-.TP
-\fB\-\-sizeout\fR
-include abundance information when relabelling
-.TP
-\fB\-\-uchimealns\fR FILENAME
-output chimera alignments to file
-.TP
-\fB\-\-uchimeout\fR FILENAME
-output to chimera info to tab\-separated file
-.TP
-\fB\-\-uchimeout5\fR
-make output compatible with uchime version 5
-.TP
-\fB\-\-xsize\fR
-strip abundance information in output
-.PP
-Clustering
-.TP
-\fB\-\-cluster_fast\fR FILENAME
-cluster sequences after sorting by length
-.TP
-\fB\-\-cluster_size\fR FILENAME
-cluster sequences after sorting by abundance
-.HP
-\fB\-\-cluster_smallmem\fR FILENAME cluster already sorted sequences (see \fB\-usersort\fR)
-.TP
-\fB\-\-cluster_unoise\fR FILENAME
-denoise Illumina amplicon reads
-.IP
-Parameters (most searching options also apply)
-.TP
-\fB\-\-cons_truncate\fR
-do not ignore terminal gaps in MSA for consensus
-.TP
-\fB\-\-id\fR REAL
-reject if identity lower, accepted values: 0\-1.0
-.TP
-\fB\-\-iddef\fR INT
-id definition, 0\-4=CD\-HIT,all,int,MBL,BLAST (2)
-.TP
-\fB\-\-qmask\fR none|dust|soft
-mask seqs with dust, soft or no method (dust)
-.TP
-\fB\-\-sizein\fR
-propagate abundance annotation from input
-.TP
-\fB\-\-strand\fR plus|both
-cluster using plus or both strands (plus)
-.TP
-\fB\-\-usersort\fR
-indicate sequences not pre\-sorted by length
-.TP
-\fB\-\-minsize\fR INT
-minimum abundance (unoise only) (8)
-.TP
-\fB\-\-unoise_alpha\fR REAL
-alpha parameter (unoise only) (2.0)
-.IP
-Output
-.TP
-\fB\-\-biomout\fR FILENAME
-filename for OTU table output in biom 1.0 format
-.TP
-\fB\-\-centroids\fR FILENAME
-output centroid sequences to FASTA file
-.TP
-\fB\-\-clusterout_id\fR
-add cluster id info to consout and profile files
-.TP
-\fB\-\-clusterout_sort\fR
-order msaout, consout, profile by decr abundance
-.TP
-\fB\-\-clusters\fR STRING
-output each cluster to a separate FASTA file
-.TP
-\fB\-\-consout\fR FILENAME
-output cluster consensus sequences to FASTA file
-.TP
-\fB\-\-mothur_shared_out\fR FN
-filename for OTU table output in mothur format
-.TP
-\fB\-\-msaout\fR FILENAME
-output multiple seq. alignments to FASTA file
-.TP
-\fB\-\-otutabout\fR FILENAME
-filename for OTU table output in classic format
-.TP
-\fB\-\-profile\fR FILENAME
-output sequence profile of each cluster to file
-.TP
-\fB\-\-relabel\fR STRING
-relabel centroids with this prefix string
-.TP
-\fB\-\-relabel_keep\fR
-keep the old label after the new when relabelling
-.TP
-\fB\-\-relabel_md5\fR
-relabel with md5 digest of normalized sequence
-.TP
-\fB\-\-relabel_self\fR
-relabel with the sequence itself as label
-.TP
-\fB\-\-relabel_sha1\fR
-relabel with sha1 digest of normalized sequence
-.TP
-\fB\-\-sizeorder\fR
-sort accepted centroids by abundance, AGC
-.TP
-\fB\-\-sizeout\fR
-write cluster abundances to centroid file
-.TP
-\fB\-\-uc\fR FILENAME
-specify filename for UCLUST\-like output
-.TP
-\fB\-\-xsize\fR
-strip abundance information in output
-.PP
-Convert SFF to FASTQ
-.TP
-\fB\-\-sff_convert\fR FILENAME
-convert given SFF file to FASTQ format
-.IP
-Parameters
-.TP
-\fB\-\-sff_clip\fR
-clip ends of sequences as indicated in file (no)
-.TP
-\fB\-\-fastq_asciiout\fR INT
-FASTQ output quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_qmaxout\fR INT
-maximum base quality value for FASTQ output (41)
-.TP
-\fB\-\-fastq_qminout\fR INT
-minimum base quality value for FASTQ output (0)
-.IP
-Output
-.TP
-\fB\-\-fastqout\fR FILENAME
-output converted sequences to given FASTQ file
-.PP
-Dereplication and rereplication
-.HP
-\fB\-\-derep_fulllength\fR FILENAME dereplicate sequences in the given FASTA file
-.TP
-\fB\-\-derep_prefix\fR FILENAME
-dereplicate sequences in file based on prefixes
-.TP
-\fB\-\-rereplicate\fR FILENAME
-rereplicate sequences in the given FASTA file
-.IP
-Parameters
-.TP
-\fB\-\-maxuniquesize\fR INT
-maximum abundance for output from dereplication
-.TP
-\fB\-\-minuniquesize\fR INT
-minimum abundance for output from dereplication
-.TP
-\fB\-\-sizein\fR
-propagate abundance annotation from input
-.TP
-\fB\-\-strand\fR plus|both
-dereplicate plus or both strands (plus)
-.IP
-Output
-.TP
-\fB\-\-output\fR FILENAME
-output FASTA file
-.TP
-\fB\-\-relabel\fR STRING
-relabel with this prefix string
-.TP
-\fB\-\-relabel_keep\fR
-keep the old label after the new when relabelling
-.TP
-\fB\-\-relabel_md5\fR
-relabel with md5 digest of normalized sequence
-.TP
-\fB\-\-relabel_self\fR
-relabel with the sequence itself as label
-.TP
-\fB\-\-relabel_sha1\fR
-relabel with sha1 digest of normalized sequence
-.TP
-\fB\-\-sizeout\fR
-write abundance annotation to output
-.TP
-\fB\-\-topn\fR INT
-output only n most abundant sequences after derep
-.TP
-\fB\-\-uc\fR FILENAME
-filename for UCLUST\-like dereplication output
-.TP
-\fB\-\-xsize\fR
-strip abundance information in derep output
-.PP
-FASTQ format conversion
-.TP
-\fB\-\-fastq_convert\fR FILENAME
-convert between FASTQ file formats
-.IP
-Parameters
-.TP
-\fB\-\-fastq_ascii\fR INT
-FASTQ input quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_asciiout\fR INT
-FASTQ output quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_qmax\fR INT
-maximum base quality value for FASTQ input (41)
-.TP
-\fB\-\-fastq_qmaxout\fR INT
-maximum base quality value for FASTQ output (41)
-.TP
-\fB\-\-fastq_qmin\fR INT
-minimum base quality value for FASTQ input (0)
-.TP
-\fB\-\-fastq_qminout\fR INT
-minimum base quality value for FASTQ output (0)
-.IP
-Output
-.TP
-\fB\-\-fastqout\fR FILENAME
-FASTQ output filename for converted sequences
-.PP
-FASTQ format detection and quality analysis
-.TP
-\fB\-\-fastq_chars\fR FILENAME
-analyse FASTQ file for version and quality range
-.IP
-Parameters
-.TP
-\fB\-\-fastq_tail\fR INT
-min length of tails to count for fastq_chars (4)
-.PP
-FASTQ quality statistics
-.TP
-\fB\-\-fastq_stats\fR FILENAME
-report statistics on FASTQ file
-.TP
-\fB\-\-fastq_eestats\fR FILENAME
-quality score and expected error statistics
-.TP
-\fB\-\-fastq_eestats2\fR FILENAME
-expected error and length cutoff statistics
-.IP
-Parameters
-.TP
-\fB\-\-ee_cutoffs\fR REAL,...
-fastq_eestats2 expected error cutoffs (0.5,1,2)
-.TP
-\fB\-\-fastq_ascii\fR INT
-FASTQ input quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_qmax\fR INT
-maximum base quality value for FASTQ input (41)
-.TP
-\fB\-\-fastq_qmin\fR INT
-minimum base quality value for FASTQ input (0)
-.HP
-\fB\-\-length_cutoffs\fR INT,INT,INT fastq_eestats2 length (min,max,incr) (50,*,50)
-.IP
-Output
-.TP
-\fB\-\-log\fR FILENAME
-output file for fastq_stats statistics
-.TP
-\fB\-\-output\fR FILENAME
-output file for fastq_eestats(2) statistics
-.PP
-Masking (new)
-.TP
-\fB\-\-fastx_mask\fR FILENAME
-mask sequences in the given FASTA or FASTQ file
-.IP
-Parameters
-.TP
-\fB\-\-fastq_ascii\fR INT
-FASTQ input quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_qmax\fR INT
-maximum base quality value for FASTQ input (41)
-.TP
-\fB\-\-fastq_qmin\fR INT
-minimum base quality value for FASTQ input (0)
-.TP
-\fB\-\-hardmask\fR
-mask by replacing with N instead of lower case
-.TP
-\fB\-\-max_unmasked_pct\fR
-max unmasked % of sequences to keep (100.0)
-.TP
-\fB\-\-min_unmasked_pct\fR
-min unmasked % of sequences to keep (0.0)
-.TP
-\fB\-\-qmask\fR none|dust|soft
-mask seqs with dust, soft or no method (dust)
-.IP
-Output
-.TP
-\fB\-\-fastaout\fR FILENAME
-output to specified FASTA file
-.TP
-\fB\-\-fastqout\fR FILENAME
-output to specified FASTQ file
-.PP
-Masking (old)
-.TP
-\fB\-\-maskfasta\fR FILENAME
-mask sequences in the given FASTA file
-.IP
-Parameters
-.TP
-\fB\-\-hardmask\fR
-mask by replacing with N instead of lower case
-.TP
-\fB\-\-qmask\fR none|dust|soft
-mask seqs with dust, soft or no method (dust)
-.IP
-Output
-.TP
-\fB\-\-output\fR FILENAME
-output to specified FASTA file
-.PP
-Paired\-end reads joining
-.TP
-\fB\-\-fastq_join\fR FILENAME
-join paired\-end reads into one sequence with gap
-.IP
-Data
-.TP
-\fB\-\-reverse\fR FILENAME
-specify FASTQ file with reverse reads
-.TP
-\fB\-\-join_padgap\fR STRING
-sequence string used for padding (NNNNNNNN)
-.TP
-\fB\-\-join_padgapq\fR STRING
-quality string used for padding (IIIIIIII)
-.IP
-Output
-.TP
-\fB\-\-fastaout\fR FILENAME
-FASTA output filename for joined sequences
-.TP
-\fB\-\-fastqout\fR FILENAME
-FASTQ output filename for joined sequences
-.PP
-Paired\-end reads merging
-.HP
-\fB\-\-fastq_mergepairs\fR FILENAME merge paired\-end reads into one sequence
-.IP
-Data
-.TP
-\fB\-\-reverse\fR FILENAME
-specify FASTQ file with reverse reads
-.IP
-Parameters
-.TP
-\fB\-\-fastq_allowmergestagger\fR
-allow merging of staggered reads
-.TP
-\fB\-\-fastq_ascii\fR INT
-FASTQ input quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_maxdiffpct\fR REAL
-maximum percentage diff. bases in overlap (100.0)
-.TP
-\fB\-\-fastq_maxdiffs\fR INT
-maximum number of different bases in overlap (10)
-.TP
-\fB\-\-fastq_maxee\fR REAL
-maximum expected error value for merged sequence
-.TP
-\fB\-\-fastq_maxmergelen\fR
-maximum length of entire merged sequence
-.TP
-\fB\-\-fastq_maxns\fR INT
-maximum number of N's
-.TP
-\fB\-\-fastq_minlen\fR INT
-minimum input read length after truncation (1)
-.TP
-\fB\-\-fastq_minmergelen\fR
-minimum length of entire merged sequence
-.TP
-\fB\-\-fastq_minovlen\fR
-minimum length of overlap between reads (10)
-.TP
-\fB\-\-fastq_nostagger\fR
-disallow merging of staggered reads (default)
-.TP
-\fB\-\-fastq_qmax\fR INT
-maximum base quality value for FASTQ input (41)
-.TP
-\fB\-\-fastq_qmaxout\fR INT
-maximum base quality value for FASTQ output (41)
-.TP
-\fB\-\-fastq_qmin\fR INT
-minimum base quality value for FASTQ input (0)
-.TP
-\fB\-\-fastq_qminout\fR INT
-minimum base quality value for FASTQ output (0)
-.TP
-\fB\-\-fastq_truncqual\fR INT
-base quality value for truncation
-.IP
-Output
-.TP
-\fB\-\-eetabbedout\fR FILENAME
-output error statistics to specified file
-.TP
-\fB\-\-fastaout\fR FILENAME
-FASTA output filename for merged sequences
-.HP
-\fB\-\-fastaout_notmerged_fwd\fR FN FASTA filename for non\-merged forward sequences
-.HP
-\fB\-\-fastaout_notmerged_rev\fR FN FASTA filename for non\-merged reverse sequences
-.TP
-\fB\-\-fastq_eeout\fR
-include expected errors (ee) in FASTQ output
-.TP
-\fB\-\-fastqout\fR FILENAME
-FASTQ output filename for merged sequences
-.HP
-\fB\-\-fastqout_notmerged_fwd\fR FN FASTQ filename for non\-merged forward sequences
-.HP
-\fB\-\-fastqout_notmerged_rev\fR FN FASTQ filename for non\-merged reverse sequences
-.TP
-\fB\-\-label_suffix\fR
-suffix to append to label of merged sequences
-.TP
-\fB\-\-xee\fR
-remove expected errors (ee) info from output
-.PP
-Pairwise alignment
-.TP
-\fB\-\-allpairs_global\fR FILENAME
-perform global alignment of all sequence pairs
-.IP
-Output (most searching options also apply)
-.TP
-\fB\-\-alnout\fR FILENAME
-filename for human\-readable alignment output
-.TP
-\fB\-\-acceptall\fR
-output all pairwise alignments
-.PP
-Restriction site cutting
-.TP
-\fB\-\-cut\fR FILENAME
-filename of FASTA formatted input sequences
-.IP
-Parameters
-.TP
-\fB\-\-cut_pattern\fR STRING
-pattern to match with ^ and _ at cut sites
-.IP
-Output
-.TP
-\fB\-\-fastaout\fR FILENAME
-FASTA filename for fragments on forward strand
-.TP
-\fB\-\-fastaout_rev\fR FILENAME
-FASTA filename for fragments on reverse strand
-.TP
-\fB\-\-fastaout_discarded\fR FN
-FASTA filename for non\-matching sequences
-.HP
-\fB\-\-fastaout_discarded_rev\fR FN FASTA filename for non\-matching, reverse compl.
-.PP
-Reverse complementation
-.TP
-\fB\-\-fastx_revcomp\fR FILENAME
-reverse\-complement seqs in FASTA or FASTQ file
-.IP
-Parameters
-.TP
-\fB\-\-fastq_ascii\fR INT
-FASTQ input quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_qmax\fR INT
-maximum base quality value for FASTQ input (41)
-.TP
-\fB\-\-fastq_qmin\fR INT
-minimum base quality value for FASTQ input (0)
-.IP
-Output
-.TP
-\fB\-\-fastaout\fR FILENAME
-FASTA output filename
-.TP
-\fB\-\-fastqout\fR FILENAME
-FASTQ output filename
-.TP
-\fB\-\-label_suffix\fR STRING
-label to append to identifier in the output
-.PP
-Searching
-.TP
-\fB\-\-search_exact\fR FILENAME
-filename of queries for exact match search
-.TP
-\fB\-\-usearch_global\fR FILENAME
-filename of queries for global alignment search
-.IP
-Data
-.TP
-\fB\-\-db\fR FILENAME
-name of UDB or FASTA database for search
-.IP
-Parameters
-.TP
-\fB\-\-dbmask\fR none|dust|soft
-mask db with dust, soft or no method (dust)
-.TP
-\fB\-\-fulldp\fR
-full dynamic programming alignment (always on)
-.TP
-\fB\-\-gapext\fR STRING
-penalties for gap extension (2I/1E)
-.TP
-\fB\-\-gapopen\fR STRING
-penalties for gap opening (20I/2E)
-.TP
-\fB\-\-hardmask\fR
-mask by replacing with N instead of lower case
-.TP
-\fB\-\-id\fR REAL
-reject if identity lower
-.TP
-\fB\-\-iddef\fR INT
-id definition, 0\-4=CD\-HIT,all,int,MBL,BLAST (2)
-.TP
-\fB\-\-idprefix\fR INT
-reject if first n nucleotides do not match
-.TP
-\fB\-\-idsuffix\fR INT
-reject if last n nucleotides do not match
-.TP
-\fB\-\-leftjust\fR
-reject if terminal gaps at alignment left end
-.TP
-\fB\-\-match\fR INT
-score for match (2)
-.TP
-\fB\-\-maxaccepts\fR INT
-number of hits to accept and show per strand (1)
-.TP
-\fB\-\-maxdiffs\fR INT
-reject if more substitutions or indels
-.TP
-\fB\-\-maxgaps\fR INT
-reject if more indels
-.TP
-\fB\-\-maxhits\fR INT
-maximum number of hits to show (unlimited)
-.TP
-\fB\-\-maxid\fR REAL
-reject if identity higher
-.TP
-\fB\-\-maxqsize\fR INT
-reject if query abundance larger
-.TP
-\fB\-\-maxqt\fR REAL
-reject if query/target length ratio higher
-.TP
-\fB\-\-maxrejects\fR INT
-number of non\-matching hits to consider (32)
-.TP
-\fB\-\-maxsizeratio\fR REAL
-reject if query/target abundance ratio higher
-.TP
-\fB\-\-maxsl\fR REAL
-reject if shorter/longer length ratio higher
-.TP
-\fB\-\-maxsubs\fR INT
-reject if more substitutions
-.TP
-\fB\-\-mid\fR REAL
-reject if percent identity lower, ignoring gaps
-.TP
-\fB\-\-mincols\fR INT
-reject if alignment length shorter
-.TP
-\fB\-\-minqt\fR REAL
-reject if query/target length ratio lower
-.TP
-\fB\-\-minsizeratio\fR REAL
-reject if query/target abundance ratio lower
-.TP
-\fB\-\-minsl\fR REAL
-reject if shorter/longer length ratio lower
-.TP
-\fB\-\-mintsize\fR INT
-reject if target abundance lower
-.TP
-\fB\-\-minwordmatches\fR INT
-minimum number of word matches required (12)
-.TP
-\fB\-\-mismatch\fR INT
-score for mismatch (\fB\-4\fR)
-.TP
-\fB\-\-pattern\fR STRING
-option is ignored
-.TP
-\fB\-\-qmask\fR none|dust|soft
-mask query with dust, soft or no method (dust)
-.TP
-\fB\-\-query_cov\fR REAL
-reject if fraction of query seq. aligned lower
-.TP
-\fB\-\-rightjust\fR
-reject if terminal gaps at alignment right end
-.TP
-\fB\-\-sizein\fR
-propagate abundance annotation from input
-.TP
-\fB\-\-self\fR
-reject if labels identical
-.TP
-\fB\-\-selfid\fR
-reject if sequences identical
-.TP
-\fB\-\-slots\fR INT
-option is ignored
-.TP
-\fB\-\-strand\fR plus|both
-search plus or both strands (plus)
-.TP
-\fB\-\-target_cov\fR REAL
-reject if fraction of target seq. aligned lower
-.TP
-\fB\-\-weak_id\fR REAL
-include aligned hits with >= id; continue search
-.TP
-\fB\-\-wordlength\fR INT
-length of words for database index 3\-15 (8)
-.IP
-Output
-.TP
-\fB\-\-alnout\fR FILENAME
-filename for human\-readable alignment output
-.TP
-\fB\-\-biomout\fR FILENAME
-filename for OTU table output in biom 1.0 format
-.TP
-\fB\-\-blast6out\fR FILENAME
-filename for blast\-like tab\-separated output
-.TP
-\fB\-\-dbmatched\fR FILENAME
-FASTA file for matching database sequences
-.TP
-\fB\-\-dbnotmatched\fR FILENAME
-FASTA file for non\-matching database sequences
-.TP
-\fB\-\-fastapairs\fR FILENAME
-FASTA file with pairs of query and target
-.TP
-\fB\-\-matched\fR FILENAME
-FASTA file for matching query sequences
-.TP
-\fB\-\-mothur_shared_out\fR FN
-filename for OTU table output in mothur format
-.TP
-\fB\-\-notmatched\fR FILENAME
-FASTA file for non\-matching query sequences
-.TP
-\fB\-\-otutabout\fR FILENAME
-filename for OTU table output in classic format
-.TP
-\fB\-\-output_no_hits\fR
-output non\-matching queries to output files
-.TP
-\fB\-\-rowlen\fR INT
-width of alignment lines in alnout output (64)
-.TP
-\fB\-\-samheader\fR
-include a header in the SAM output file
-.TP
-\fB\-\-samout\fR FILENAME
-filename for SAM format output
-.TP
-\fB\-\-sizeout\fR
-write abundance annotation to dbmatched file
-.TP
-\fB\-\-top_hits_only\fR
-output only hits with identity equal to the best
-.TP
-\fB\-\-uc\fR FILENAME
-filename for UCLUST\-like output
-.TP
-\fB\-\-uc_allhits\fR
-show all, not just top hit with uc output
-.TP
-\fB\-\-userfields\fR STRING
-fields to output in userout file
-.TP
-\fB\-\-userout\fR FILENAME
-filename for user\-defined tab\-separated output
-.PP
-Shuffling and sorting
-.TP
-\fB\-\-shuffle\fR FILENAME
-shuffle order of sequences in FASTA file randomly
-.TP
-\fB\-\-sortbylength\fR FILENAME
-sort sequences by length in given FASTA file
-.TP
-\fB\-\-sortbysize\fR FILENAME
-abundance sort sequences in given FASTA file
-.IP
-Parameters
-.TP
-\fB\-\-maxsize\fR INT
-maximum abundance for sortbysize
-.TP
-\fB\-\-minsize\fR INT
-minimum abundance for sortbysize
-.TP
-\fB\-\-randseed\fR INT
-seed for PRNG, zero to use random data source (0)
-.TP
-\fB\-\-sizein\fR
-propagate abundance annotation from input
-.IP
-Output
-.TP
-\fB\-\-output\fR FILENAME
-output to specified FASTA file
-.TP
-\fB\-\-relabel\fR STRING
-relabel sequences with this prefix string
-.TP
-\fB\-\-relabel_keep\fR
-keep the old label after the new when relabelling
-.TP
-\fB\-\-relabel_md5\fR
-relabel with md5 digest of normalized sequence
-.TP
-\fB\-\-relabel_self\fR
-relabel with the sequence itself as label
-.TP
-\fB\-\-relabel_sha1\fR
-relabel with sha1 digest of normalized sequence
-.TP
-\fB\-\-sizeout\fR
-include abundance information when relabelling
-.TP
-\fB\-\-topn\fR INT
-output just first n sequences
-.TP
-\fB\-\-xsize\fR
-strip abundance information in output
-.PP
-Subsampling
-.TP
-\fB\-\-fastx_subsample\fR FILENAME
-subsample sequences from given FASTA/FASTQ file
-.IP
-Parameters
-.TP
-\fB\-\-fastq_ascii\fR INT
-FASTQ input quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_qmax\fR INT
-maximum base quality value for FASTQ input (41)
-.TP
-\fB\-\-fastq_qmin\fR INT
-minimum base quality value for FASTQ input (0)
-.TP
-\fB\-\-randseed\fR INT
-seed for PRNG, zero to use random data source (0)
-.TP
-\fB\-\-sample_pct\fR REAL
-sampling percentage between 0.0 and 100.0
-.TP
-\fB\-\-sample_size\fR INT
-sampling size
-.TP
-\fB\-\-sizein\fR
-consider abundance info from input, do not ignore
-.IP
-Output
-.TP
-\fB\-\-fastaout\fR FILENAME
-output subsampled sequences to FASTA file
-.TP
-\fB\-\-fastaout_discarded\fR FILE
-output non\-subsampled sequences to FASTA file
-.TP
-\fB\-\-fastqout\fR FILENAME
-output subsampled sequences to FASTQ file
-.TP
-\fB\-\-fastqout_discarded\fR
-output non\-subsampled sequences to FASTQ file
-.TP
-\fB\-\-relabel\fR STRING
-relabel sequences with this prefix string
-.TP
-\fB\-\-relabel_keep\fR
-keep the old label after the new when relabelling
-.TP
-\fB\-\-relabel_md5\fR
-relabel with md5 digest of normalized sequence
-.TP
-\fB\-\-relabel_self\fR
-relabel with the sequence itself as label
-.TP
-\fB\-\-relabel_sha1\fR
-relabel with sha1 digest of normalized sequence
-.TP
-\fB\-\-sizeout\fR
-update abundance information in output
-.TP
-\fB\-\-xsize\fR
-strip abundance information in output
-.PP
-Taxonomic classification
-.TP
-\fB\-\-sintax\fR FILENAME
-classify sequences in given FASTA/FASTQ file
-.IP
-Parameters
-.TP
-\fB\-\-db\fR FILENAME
-taxonomic reference db in given FASTA or UDB file
-.TP
-\fB\-\-sintax_cutoff\fR REAL
-confidence value cutoff level (0.0)
-.IP
-Output
-.TP
-\fB\-\-tabbedout\fR FILENAME
-write results to given tab\-delimited file
-.PP
-Trimming and filtering
-.TP
-\fB\-\-fastx_filter\fR FILENAME
-trim and filter sequences in FASTA/FASTQ file
-.TP
-\fB\-\-fastq_filter\fR FILENAME
-trim and filter sequences in FASTQ file
-.TP
-\fB\-\-reverse\fR FILENAME
-FASTQ file with other end of paired\-end reads
-.IP
-Parameters
-.TP
-\fB\-\-fastq_ascii\fR INT
-FASTQ input quality score ASCII base char (33)
-.TP
-\fB\-\-fastq_maxee\fR REAL
-discard if expected error value is higher
-.TP
-\fB\-\-fastq_maxee_rate\fR REAL
-discard if expected error rate is higher
-.TP
-\fB\-\-fastq_maxlen\fR INT
-discard if length of sequence is longer
-.TP
-\fB\-\-fastq_maxns\fR INT
-discard if number of N's is higher
-.TP
-\fB\-\-fastq_minlen\fR INT
-discard if length of sequence is shorter
-.TP
-\fB\-\-fastq_qmax\fR INT
-maximum base quality value for FASTQ input (41)
-.TP
-\fB\-\-fastq_qmin\fR INT
-minimum base quality value for FASTQ input (0)
-.TP
-\fB\-\-fastq_stripleft\fR INT
-delete given number of bases from the 5' end
-.TP
-\fB\-\-fastq_stripright\fR INT
-delete given number of bases from the 3' end
-.TP
-\fB\-\-fastq_truncee\fR REAL
-truncate to given maximum expected error
-.TP
-\fB\-\-fastq_trunclen\fR INT
-truncate to given length (discard if shorter)
-.TP
-\fB\-\-fastq_trunclen_keep\fR INT
-truncate to given length (keep if shorter)
-.TP
-\fB\-\-fastq_truncqual\fR INT
-truncate to given minimum base quality
-.TP
-\fB\-\-maxsize\fR INT
-discard if abundance of sequence is above
-.TP
-\fB\-\-minsize\fR INT
-discard if abundance of sequence is below
-.IP
-Output
-.TP
-\fB\-\-eeout\fR
-include expected errors in output
-.TP
-\fB\-\-fastaout\fR FN
-FASTA filename for passed sequences
-.TP
-\fB\-\-fastaout_discarded\fR FN
-FASTA filename for discarded sequences
-.HP
-\fB\-\-fastaout_discarded_rev\fR FN FASTA filename for discarded reverse sequences
-.TP
-\fB\-\-fastaout_rev\fR FN
-FASTA filename for passed reverse sequences
-.TP
-\fB\-\-fastqout\fR FN
-FASTQ filename for passed sequences
-.TP
-\fB\-\-fastqout_discarded\fR FN
-FASTQ filename for discarded sequences
-.HP
-\fB\-\-fastqout_discarded_rev\fR FN FASTQ filename for discarded reverse sequences
-.TP
-\fB\-\-fastqout_rev\fR FN
-FASTQ filename for passed reverse sequences
-.TP
-\fB\-\-relabel\fR STRING
-relabel filtered sequences with given prefix
-.TP
-\fB\-\-relabel_keep\fR
-keep the old label after the new when relabelling
-.TP
-\fB\-\-relabel_md5\fR
-relabel filtered sequences with md5 digest
-.TP
-\fB\-\-relabel_self\fR
-relabel with the sequence itself as label
-.TP
-\fB\-\-relabel_sha1\fR
-relabel filtered sequences with sha1 digest
-.TP
-\fB\-\-sizeout\fR
-include abundance information when relabelling
-.TP
-\fB\-\-xee\fR
-remove expected errors (ee) info from output
-.TP
-\fB\-\-xsize\fR
-strip abundance information in output
-.PP
-UDB files
-.TP
-\fB\-\-makeudb_usearch\fR FILENAME
-make UDB file from given FASTA file
-.TP
-\fB\-\-udb2fasta\fR FILENAME
-output FASTA file from given UDB file
-.TP
-\fB\-\-udbinfo\fR FILENAME
-show information about UDB file
-.TP
-\fB\-\-udbstats\fR FILENAME
-report statistics about indexed words in UDB file
-.IP
-Parameters
-.TP
-\fB\-\-dbmask\fR none|dust|soft
-mask db with dust, soft or no method (dust)
-.TP
-\fB\-\-hardmask\fR
-mask by replacing with N instead of lower case
-.TP
-\fB\-\-wordlength\fR INT
-length of words for database index 3\-15 (8)
-.IP
-Output
-.TP
-\fB\-\-output\fR FILENAME
-UDB or FASTA output file
-.SH AUTHOR
- This manpage was written by Nilesh Patra for the Debian distribution and
- can be used for any other usage of the program.


=====================================
debian/vsearch.docs
=====================================
@@ -1,2 +1,2 @@
 *.html
-man/*.pdf
+usr/share/doc/vsearch/*


=====================================
debian/vsearch.install
=====================================
@@ -1 +1 @@
-bin/vsearch usr/bin
+usr/bin


=====================================
debian/vsearch.manpages
=====================================
@@ -1 +1 @@
-debian/man/*.1
+usr/share/man/man1/*



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-- 
View it on GitLab: https://salsa.debian.org/med-team/vsearch/-/compare/b7251143cd0f105acb59c694870f057f91824a97...d9d56fcdfe3bad21c80fb65fd5cbd340326bd31c
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