[med-svn] [Git][med-team/wtdbg2][master] 7 commits: routine-update: Rules-Requires-Root: no
Andreas Tille
gitlab at salsa.debian.org
Thu Apr 2 12:52:26 BST 2020
Andreas Tille pushed to branch master at Debian Med / wtdbg2
Commits:
b633573c by Andreas Tille at 2020-04-02T13:03:51+02:00
routine-update: Rules-Requires-Root: no
- - - - -
4f7df062 by Andreas Tille at 2020-04-02T13:03:58+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
- - - - -
39cc1a23 by Andreas Tille at 2020-04-02T13:05:18+02:00
routine-update: Ready to upload to unstable
- - - - -
a50b4487 by Andreas Tille at 2020-04-02T13:17:44+02:00
Cleanup changelog
- - - - -
a6d8e5c7 by Andreas Tille at 2020-04-02T13:39:03+02:00
Add manpages
- - - - -
a065e402 by Andreas Tille at 2020-04-02T13:39:54+02:00
Upload to new
- - - - -
30f72c7d by Andreas Tille at 2020-04-02T13:48:23+02:00
Propagate hardening options
- - - - -
13 changed files:
- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/manpages
- + debian/mans/kbm2.1
- + debian/mans/pgzf.1
- + debian/mans/wtdbg-cns.1
- + debian/mans/wtdbg2.1
- + debian/mans/wtpoa-cns.1
- + debian/patches/hardening.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-wtdbg2 (2.5-1) UNRELEASED; urgency=medium
+wtdbg2 (2.5-1) unstable; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #955548)
- -- Andreas Tille <tille at debian.org> Thu, 02 Apr 2020 11:37:59 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 02 Apr 2020 13:39:43 +0200
=====================================
debian/control
=====================================
@@ -9,6 +9,7 @@ Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/wtdbg2
Vcs-Git: https://salsa.debian.org/med-team/wtdbg2.git
Homepage: https://github.com/ruanjue/wtdbg2
+Rules-Requires-Root: no
Package: wtdbg2
Architecture: any
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,52 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=wtdbg-cns
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Consensuser for wtdbg" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=kbm2
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="simple instance which implemented kmer-binmap" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=pgzf
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Parallel gzip file IO" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=wtpoa-cns
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Consensuser for wtdbg using PO-MSA" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/mans/*.1
=====================================
debian/mans/kbm2.1
=====================================
@@ -0,0 +1,126 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH KBM2 "1" "April 2020" "kbm2 2.5" "User Commands"
+.SH NAME
+kbm2 \- simple instance which implemented kmer-binmap
+.SH SYNOPSIS
+.B kbm
+\fI\,<options> \/\fR[\fI\,start|list|stop\/\fR]
+.SH DESCRIPTION
+Program: kbm is a simple instance which implemented kmer\-binmap
+.IP
+it maps query sequence against reference by kmer matching
+matched kmer\-pairs are bined (256bp) and counted in a matrix
+dynamic programming is used to search the best path
+.PP
+Version: 2.5 (20190621)
+Author: Jue Ruan <ruanjue at gmail.com>
+.SH OPTIONS
+.HP
+\fB\-i\fR <string> File(s) of query sequences, +, [STDIN]
+.HP
+\fB\-d\fR <string> File(s) of reference sequences, +, [<\-i>]
+.TP
+\fB\-L\fR <int>
+Choose the longest subread and drop reads shorter than <int> (5000 recommended for PacBio) [0]
+Negative integer indicate keeping read names, e.g. \fB\-5000\fR.
+.HP
+\fB\-o\fR <string> Output file, [STDOUT]
+.TP
+\fB\-I\fR
+Interactive mode
+e.g. `mkfifo pipe` then `while true; do cat pipe && sleep 1; done | kbm \fB\-t\fR 8 \fB\-I\fR \fB\-d\fR ref.fa \fB\-i\fR \- \fB\-Hk\fR 21 \fB\-S\fR 4`
+then `cat 1.fq >pipe; cat 2.fq >pipe`, fastq format is better in interaction
+.TP
+\fB\-f\fR
+Force overwrite
+.TP
+\fB\-t\fR <int>
+Number of threads, 0: all cores, [1]
+.TP
+\fB\-k\fR <int>
+Kmer\-f size, <= 23, [0]
+.TP
+\fB\-p\fR <int>
+Kmer\-p size, <= 23, [21]
+.TP
+\fB\-K\fR <float>
+Filter high frequency kmers, maybe repetitive, [1000]
+if K >= 1, take the integer value as cutoff, MUST <= 65535
+else, mask the top fraction part high frequency kmers
+.TP
+\fB\-E\fR <int>
+Min kmer frequency, [1]
+.TP
+\fB\-O\fR <int>
+Filter low complexity bins (#indexed_kmer less than <\-O>), [2]
+.TP
+\fB\-S\fR <float>
+Subsampling kmers, 1/(<\-S>) kmers are indexed, [4.00]
+\fB\-S\fR is very useful in saving memeory and speeding up
+please note that subsampling kmers will have less matched length
+.TP
+\fB\-B\fR <int>
+Select no more than n seeds in a query bin, [256]
+If you are using shared kbmidx by other process using \fB\-D\fR too, it will bring wrong behavior
+.TP
+\fB\-D\fR <int>
+Strand of alignment, 1: forward, 2: reverse, 3: both, [3]
+.TP
+\fB\-X\fR <int>
+Max number of bin(256bp) in one gap, [4]
+.TP
+\fB\-Y\fR <int>
+Max number of bin(256bp) in one deviation, [4]
+.TP
+\fB\-Z\fR <float>
+Max fraction of gapped BINs / aligned BINs, [0.6]
+.TP
+\fB\-x\fR <int>
+penalty for BIN gap, [\-7]
+.TP
+\fB\-y\fR <int>
+penalty for BIN deviation, [\-21]
+.TP
+\fB\-z\fR <int>
+Enable refine alignment with \fB\-p\fR <\-z> [0]
+.TP
+\fB\-l\fR <int>
+Min alignment length, [2048]
+.TP
+\fB\-m\fR <int>
+Min matched length, [200]
+.TP
+\fB\-s\fR <float>
+Min similarity, calculated by kmer matched length / aligned length, [0.05]
+.TP
+\fB\-r\fR <float>
+Max length variation of two aligned fragments, [0.25]
+.TP
+\fB\-c\fR
+Insist to query contained reads against all
+.TP
+\fB\-C\fR
+Chainning alignments
+.TP
+\fB\-n\fR <int>
+Max hits per query, [1000]
+.TP
+\fB\-T\fR <int>
+For debug, [0]
+.HP
+\fB\-W\fR <string> Dump kbm index to file, [NULL]
+.HP
+\fB\-R\fR <string> Load kbm index from file, [NULL]
+.TP
+\fB\-q\fR
+Quiet
+.TP
+\fB\-V\fR
+Print version information and then exit
+.PP
+Server start: {kbm \fB\-R\fR <wt.fa.kbmidx> start}, will mmap wt.fa.kbmidx into mmeory
+Server list: {kbm \fB\-R\fR <wt.fa.kbmidx> list [10]}, will list the object tree in file
+Server stop: {kbm \fB\-R\fR <wt.fa.kbmidx> stop}, will remove the mmap object
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/pgzf.1
=====================================
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH PGZF "1" "April 2020" "pgzf 2.5" "User Commands"
+.SH NAME
+pgzf \- Parallel gzip file IO
+.SH SYNOPSIS
+.B pgzf
+[\fI\,options\/\fR] \fI\,file1 \/\fR[\fI\,file2 \/\fR...]
+.SH DESCRIPTION
+PGZF: Parallel gzip file IO
+Author: Jue Ruan <ruanjue at gmail.com>
+Version: 1.1
+.SH OPTIONS
+.TP
+\fB\-d\fR
+Decompress mode
+.TP
+\fB\-t\fR <int>
+Number of threads, [8]
+.TP
+\fB\-f\fR
+Force to overwrite
+.HP
+\fB\-o\fR <string> Output file name, support directory
+.TP
+\fB\-x\fR
+Delete input files after done
+.TP
+\fB\-b\fR <int>
+Block size in MB, 1 ~ 256 [16]
+.TP
+\fB\-l\fR <int>
+Compress level, 1\-9, see gzip, [6]
+.TP
+\fB\-h\fR
+Show this document
+.TP
+\fB\-V\fR
+Print version information and exit
+.SS "File format:"
+.IP
+PGZF fellows standard GZIP format (rfc1952), and is blocked compressed.
+It defines two TAGs in each GZIP header, ZS: block size, ZX: random access index.
+Program pgzf can decompress .pgzf and .gz files. When decompressing .gz files,
+pgzf is in fact a buffered gzip reader. Also, .pgzf files can be decompressed
+by program gzip.
+.PP
+In plan to support random access
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/wtdbg-cns.1
=====================================
@@ -0,0 +1,79 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH WTDBG-CNS "1" "April 2020" "wtdbg-cns 2.5" "User Commands"
+.SH NAME
+wtdbg-cns \- Consensuser for wtdbg
+.SH SYNOPSIS
+.B wtdbg-cns
+[\fI\,options\/\fR]
+.SH DESCRIPTION
+WTDBG\-CNS: Consensuser for wtdbg
+Author: Jue Ruan <ruanjue at gmail.com>
+Version: 1.1
+.SH OPTIONS
+.TP
+\fB\-t\fR <int>
+Number of threads, [1]
+.HP
+\fB\-i\fR <string> Input file(s) *.utg.cns from wtdbg, +, [STDIN]
+.HP
+\fB\-o\fR <string> Output files, [STDOUT]
+.TP
+\fB\-f\fR
+Force overwrite
+.TP
+\fB\-j\fR <int>
+Expected length of node, or say the overlap length of two adject units in layout file, [1000] bp
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-BEG\fR DBG options\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
+.TP
+\fB\-k\fR <int>
+Kmer size for long reads, [15]
+.TP
+\fB\-Z\fR <int>
+Z\-cutoff, drop the lower (score / <\-X>), [4]
+.TP
+\fB\-W\fR <int>
+W\-cutoff, drop the lagger (position), [48]
+In DAG correction, \fB\-W\fR set the bandwidth of alignment
+.TP
+\fB\-H\fR <int>
+High coverage bonus, [1]
+.TP
+\fB\-L\fR <int>
+High coverage cutoff = avg_cov / <\-L> [10]
+.TP
+\fB\-c\fR <int>
+Candidate strategy, 0: best\-kmers, 1: median length, 2: first (include), 3: first (exclude), 4: longest, 5, shortest, [0]
+In DAG correction, force to use strategy 2
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-END\fR DBG options\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
+.TP
+\fB\-M\fR <int>
+Match score, [2]
+.TP
+\fB\-X\fR <int>
+Mismatch score, [\-7]
+.TP
+\fB\-I\fR <int>
+Insertion score, [\-3]
+.TP
+\fB\-D\fR <int>
+Deletion score, [\-4]
+.TP
+\fB\-E\fR <int>
+Gap extension score, [\-2]
+.TP
+\fB\-m\fR <int>
+1: DBG correction; 2: DAG correction, [1]
+.TP
+\fB\-S\fR <int>
+whether to correct structure before error correction, [1]
+.TP
+\fB\-v\fR
+Verbose
+.TP
+\fB\-V\fR
+Print version information and then exit
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/wtdbg2.1
=====================================
@@ -0,0 +1,401 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH WTDBG2 "1" "April 2020" "wtdbg2 2.5" "User Commands"
+.SH NAME
+wtdbg2 \- de novo sequence assembler for long noisy reads
+.SH SYNOPSIS
+.B wtdbg2
+[\fI\,options\/\fR] \fI\,-i <reads.fa> -o <prefix> \/\fR[\fI\,reads.fa \/\fR...]
+.SH DESCRIPTION
+WTDBG: De novo assembler for long noisy sequences
+Author: Jue Ruan <ruanjue at gmail.com>
+Version: 2.5 (20190621)
+.SH OPTIONS
+.HP
+\fB\-i\fR <string> Long reads sequences file (REQUIRED; can be multiple), []
+.HP
+\fB\-o\fR <string> Prefix of output files (REQUIRED), []
+.TP
+\fB\-t\fR <int>
+Number of threads, 0 for all cores, [4]
+.TP
+\fB\-f\fR
+Force to overwrite output files
+.HP
+\fB\-x\fR <string> Presets, comma delimited, []
+.TP
+preset1/rsII/rs: \fB\-p\fR 21 \fB\-S\fR 4 \fB\-s\fR 0.05 \fB\-L\fR 5000
+preset2: \fB\-p\fR 0 \fB\-k\fR 15 \fB\-AS\fR 2 \fB\-s\fR 0.05 \fB\-L\fR 5000
+preset3: \fB\-p\fR 19 \fB\-AS\fR 2 \fB\-s\fR 0.05 \fB\-L\fR 5000
+.IP
+sequel/sq
+.IP
+nanopore/ont:
+.IP
+(genome size < 1G: preset2) \fB\-p\fR 0 \fB\-k\fR 15 \fB\-AS\fR 2 \fB\-s\fR 0.05 \fB\-L\fR 5000
+(genome size >= 1G: preset3) \fB\-p\fR 19 \fB\-AS\fR 2 \fB\-s\fR 0.05 \fB\-L\fR 5000
+.IP
+preset4/corrected/ccs: \fB\-p\fR 21 \fB\-k\fR 0 \fB\-AS\fR 4 \fB\-K\fR 0.05 \fB\-s\fR 0.5
+.HP
+\fB\-g\fR <number> Approximate genome size (k/m/g suffix allowed) [0]
+.TP
+\fB\-X\fR <float>
+Choose the best <float> depth from input reads(effective with \fB\-g\fR) [50.0]
+.TP
+\fB\-L\fR <int>
+Choose the longest subread and drop reads shorter than <int> (5000 recommended for PacBio) [0]
+Negative integer indicate tidying read names too, e.g. \fB\-5000\fR.
+.TP
+\fB\-k\fR <int>
+Kmer fsize, 0 <= k <= 23, [0]
+.TP
+\fB\-p\fR <int>
+Kmer psize, 0 <= p <= 23, [21]
+k + p <= 25, seed is <k\-mer>+<p\-homopolymer\-compressed>
+.TP
+\fB\-K\fR <float>
+Filter high frequency kmers, maybe repetitive, [1000.05]
+>= 1000 and indexing >= (1 \- 0.05) * total_kmers_count
+.TP
+\fB\-S\fR <float>
+Subsampling kmers, 1/(<\-S>) kmers are indexed, [4.00]
+\fB\-S\fR is very useful in saving memeory and speeding up
+please note that subsampling kmers will have less matched length
+.TP
+\fB\-l\fR <float>
+Min length of alignment, [2048]
+.TP
+\fB\-m\fR <float>
+Min matched length by kmer matching, [200]
+.TP
+\fB\-R\fR
+Enable realignment mode
+.TP
+\fB\-A\fR
+Keep contained reads during alignment
+.TP
+\fB\-s\fR <float>
+Min similarity, calculated by kmer matched length / aligned length, [0.05]
+.TP
+\fB\-e\fR <int>
+Min read depth of a valid edge, [3]
+.TP
+\fB\-q\fR
+Quiet
+.TP
+\fB\-v\fR
+Verbose (can be multiple)
+.TP
+\fB\-V\fR
+Print version information and then exit
+.TP
+\fB\-\-help\fR
+Show more options
+.IP
+** more options **
+\fB\-\-cpu\fR <int>
+.IP
+See \fB\-t\fR 0, default: all cores
+.HP
+\fB\-\-input\fR <string> +
+.IP
+See \fB\-i\fR
+.HP
+\fB\-\-force\fR
+.IP
+See \fB\-f\fR
+.HP
+\fB\-\-prefix\fR <string>
+.IP
+See \fB\-o\fR
+.HP
+\fB\-\-preset\fR <string>
+.IP
+See \fB\-x\fR
+.HP
+\fB\-\-kmer\-fsize\fR <int>
+.IP
+See \fB\-k\fR 0
+.HP
+\fB\-\-kmer\-psize\fR <int>
+.IP
+See \fB\-p\fR 21
+.HP
+\fB\-\-kmer\-depth\-max\fR <float>
+.IP
+See \fB\-K\fR 1000.05
+.HP
+\fB\-E\fR, \fB\-\-kmer\-depth\-min\fR <int>
+.IP
+Min kmer frequency, [2]
+.HP
+\fB\-\-kmer\-subsampling\fR <float>
+.IP
+See \fB\-S\fR 4.0
+.HP
+\fB\-\-kbm\-parts\fR <int>
+.IP
+Split total reads into multiple parts, index one part by one to save memory, [1]
+.HP
+\fB\-\-aln\-kmer\-sampling\fR <int>
+.IP
+Select no more than n seeds in a query bin, default: 256
+.HP
+\fB\-\-dp\-max\-gap\fR <int>
+.IP
+Max number of bin(256bp) in one gap, [4]
+.HP
+\fB\-\-dp\-max\-var\fR <int>
+.IP
+Max number of bin(256bp) in one deviation, [4]
+.HP
+\fB\-\-dp\-penalty\-gap\fR <int>
+.IP
+Penalty for BIN gap, [\-7]
+.HP
+\fB\-\-dp\-penalty\-var\fR <int>
+.IP
+Penalty for BIN deviation, [\-21]
+.HP
+\fB\-\-aln\-min\-length\fR <int>
+.IP
+See \fB\-l\fR 2048
+.HP
+\fB\-\-aln\-min\-match\fR <int>
+.IP
+See \fB\-m\fR 200. Here the num of matches counting basepair of the matched kmer's regions
+.HP
+\fB\-\-aln\-min\-similarity\fR <float>
+.IP
+See \fB\-s\fR 0.05
+.HP
+\fB\-\-aln\-max\-var\fR <float>
+.IP
+Max length variation of two aligned fragments, default: 0.25
+.HP
+\fB\-\-aln\-dovetail\fR <int>
+.IP
+Retain dovetail overlaps only, the max overhang size is <\-\-aln\-dovetail>, the value should be times of 256, \fB\-1\fR to disable filtering, default: 256
+.HP
+\fB\-\-aln\-strand\fR <int>
+.IP
+1: forward, 2: reverse, 3: both. Please don't change the deault vaule 3, unless you exactly know what you are doing
+.HP
+\fB\-\-aln\-maxhit\fR <int>
+.IP
+Max n hits for each read in build graph, default: 1000
+.HP
+\fB\-\-aln\-bestn\fR <int>
+.IP
+Use best n hits for each read in build graph, 0: keep all, default: 500
+<prefix>.alignments always store all alignments
+.HP
+\fB\-R\fR, \fB\-\-realign\fR
+.IP
+Enable re\-alignment, see \fB\-\-realn\-kmer\-psize\fR=\fI\,15\/\fR, \fB\-\-realn\-kmer\-subsampling\fR=\fI\,1\/\fR, \fB\-\-realn\-min\-length\fR=\fI\,2048\/\fR, \fB\-\-realn\-min\-match\fR=\fI\,200\/\fR, \fB\-\-realn\-min\-similarity\fR=\fI\,0\/\fR.1, \fB\-\-realn\-max\-var\fR=\fI\,0\/\fR.25
+.HP
+\fB\-\-realn\-kmer\-psize\fR <int>
+.IP
+Set kmer\-psize in realignment, (kmer\-ksize always eq 0), default:15
+.HP
+\fB\-\-realn\-kmer\-subsampling\fR <int>
+.IP
+Set kmer\-subsampling in realignment, default:1
+.HP
+\fB\-\-realn\-min\-length\fR <int>
+.IP
+Set aln\-min\-length in realignment, default: 2048
+.HP
+\fB\-\-realn\-min\-match\fR <int>
+.IP
+Set aln\-min\-match in realignment, default: 200
+.HP
+\fB\-\-realn\-min\-similarity\fR <float>
+.IP
+Set aln\-min\-similarity in realignment, default: 0.1
+.HP
+\fB\-\-realn\-max\-var\fR <float>
+.IP
+Set aln\-max\-var in realignment, default: 0.25
+.HP
+\fB\-A\fR, \fB\-\-aln\-noskip\fR
+.IP
+Even a read was contained in previous alignment, still align it against other reads
+.HP
+\fB\-\-keep\-multiple\-alignment\-parts\fR
+.IP
+By default, wtdbg will keep only the best alignment between two reads after chainning. This option will disable it, and keep multiple
+.HP
+\fB\-\-verbose\fR +
+.IP
+See \fB\-v\fR. \fB\-vvvv\fR will display the most detailed information
+.HP
+\fB\-\-quiet\fR
+.IP
+See \fB\-q\fR
+.HP
+\fB\-\-limit\-input\fR <int>
+.IP
+Limit the input sequences to at most <int> M bp. Usually for test
+.HP
+\fB\-L\fR <int>, \fB\-\-tidy\-reads\fR <int>
+.IP
+Default: 0. Pick longest subreads if possible. Filter reads less than <\-\-tidy\-reads>. Please add \fB\-\-tidy\-name\fR or set \fB\-\-tidy\-reads\fR to nagetive value
+if want to rename reads. Set to 0 bp to disable tidy. Suggested value is 5000 for pacbio RSII reads
+.HP
+\fB\-\-tidy\-name\fR
+.IP
+Rename reads into 'S%010d' format. The first read is named as S0000000001
+.HP
+\fB\-\-rdname\-filter\fR <string>
+.IP
+A file contains lines of reads name to be discarded in loading. If you want to filter reads by yourself, please also set \fB\-X\fR 0
+.HP
+\fB\-\-rdname\-includeonly\fR <string>
+.IP
+Reverse manner with \fB\-\-rdname\-filter\fR
+.HP
+\fB\-g\fR <number>, \fB\-\-genome\-size\fR <number>
+.IP
+Provide genome size, e.g. 100.4m, 2.3g. In this version, it is used with \fB\-X\fR/\-\-rdcov\-cutoff in selecting reads just after readed all.
+.HP
+\fB\-X\fR <float>, \fB\-\-rdcov\-cutoff\fR <float>
+.IP
+Default: 50.0. Retaining 50.0 folds of genome coverage, combined with \fB\-g\fR and \fB\-\-rdcov\-filter\fR.
+.HP
+\fB\-\-rdcov\-filter\fR [0|1]
+.IP
+Default 0. Strategy 0: retaining longest reads. Strategy 1: retaining medain length reads.
+.HP
+\fB\-\-err\-free\-nodes\fR
+.IP
+Select nodes from error\-free\-sequences only. E.g. you have contigs assembled from NGS\-WGS reads, and long noisy reads.
+You can type '\-\-err\-free\-seq your_ctg.fa \fB\-\-input\fR your_long_reads.fa \fB\-\-err\-free\-nodes\fR' to perform assembly somehow act as long\-reads scaffolding
+.HP
+\fB\-\-node\-len\fR <int>
+.IP
+The default value is 1024, which is times of KBM_BIN_SIZE(always equals 256 bp). It specifies the length of intervals (or call nodes after selecting).
+kbm indexs sequences into BINs of 256 bp in size, so that many parameter should be times of 256 bp. There are: \fB\-\-node\-len\fR, \fB\-\-node\-ovl\fR, \fB\-\-aln\-min\-length\fR, \fB\-\-aln\-dovetail\fR . Other parameters are counted in BINs, \fB\-\-dp\-max\-gap\fR, \fB\-\-dp\-max\-var\fR .
+.HP
+\fB\-\-node\-matched\-bins\fR <int>
+.IP
+Min matched bins in a node, default:1
+.HP
+\fB\-\-node\-ovl\fR <int>
+.IP
+Default: 256. Max overlap size between two adjacent intervals in any read. It is used in selecting best nodes representing reads in graph
+.HP
+\fB\-\-node\-drop\fR <float>
+.IP
+Default: 0.25. Will discard an node when has more this ratio intervals are conflicted with previous generated node
+.HP
+\fB\-e\fR <int>, \fB\-\-edge\-min=\fR<int>
+.IP
+Default: 3. The minimal depth of a valid edge is set to 3. In another word, Valid edges must be supported by at least 3 reads
+When the sequence depth is low, have a try with \fB\-\-edge\-min\fR 2. Or very high, try \fB\-\-edge\-min\fR 4
+.HP
+\fB\-\-edge\-max\-span\fR <int>
+.IP
+Default: 1024 BINs. Program will build edges of length no large than 1024
+.HP
+\fB\-\-drop\-low\-cov\-edges\fR
+.IP
+Don't attempt to rescue low coverage edges
+.HP
+\fB\-\-node\-min\fR <int>
+.IP
+Min depth of an interval to be selected as valid node. Defaultly, this value is automaticly the same with \fB\-\-edge\-min\fR.
+.HP
+\fB\-\-node\-max\fR <int>
+.IP
+Nodes with too high depth will be regarded as repetitive, and be masked. Default: 200, more than 200 reads contain this node
+.HP
+\fB\-\-ttr\-cutoff\-depth\fR <int>, 0
+.HP
+\fB\-\-ttr\-cutoff\-ratio\fR <float>, 0.5
+.IP
+Tiny Tandom Repeat. A node located inside ttr will bring noisy in graph, should be masked. The pattern of such nodes is:
+depth >= <\-\-ttr\-cutoff\-depth>, and none of their edges have depth greater than depth * <\-\-ttr\-cutoff\-ratio 0.5>
+set \fB\-\-ttr\-cutoff\-depth\fR 0 to disable ttr masking
+.HP
+\fB\-\-dump\-kbm\fR <string>
+.IP
+Dump kbm index into file for loaded by `kbm` or `wtdbg`
+.HP
+\fB\-\-dump\-seqs\fR <string>
+.IP
+Dump kbm index (only sequences, no k\-mer index) into file for loaded by `kbm` or `wtdbg`
+Please note: normally load it with \fB\-\-load\-kbm\fR, not with \fB\-\-load\-seqs\fR
+.HP
+\fB\-\-load\-kbm\fR <string>
+.IP
+Instead of reading sequences and building kbm index, which is time\-consumed, loading kbm\-index from already dumped file.
+Please note that, once kbm\-index is mmaped by kbm \fB\-R\fR <kbm\-index> start, will just get the shared memory in minute time.
+See `kbm` \fB\-R\fR <your_seqs.kbmidx> [start | stop]
+.HP
+\fB\-\-load\-seqs\fR <string>
+.IP
+Similar with \fB\-\-load\-kbm\fR, but only use the sequences in kbmidx, and rebuild index in process's RAM.
+.HP
+\fB\-\-load\-alignments\fR <string> +
+.IP
+`wtdbg` output reads' alignments into <\-\-prefix>.alignments, program can load them to fastly build assembly graph. Or you can offer
+other source of alignments to `wtdbg`. When \fB\-\-load\-alignment\fR, will only reading long sequences but skip building kbm index
+You can type \fB\-\-load\-alignments\fR <file> more than once to load alignments from many files
+.HP
+\fB\-\-load\-clips\fR <string>
+.IP
+Combined with \fB\-\-load\-nodes\fR. Load reads clips. You can find it in `wtdbg`'s <\-\-prefix>.clps
+.HP
+\fB\-\-load\-nodes\fR <sting>
+.IP
+Load dumped nodes from previous execution for fast construct the assembly graph, should be combined with \fB\-\-load\-clips\fR. You can find it in `wtdbg`'s <\-\-prefix>.1.nodes
+.HP
+\fB\-\-bubble\-step\fR <int>
+.IP
+Max step to search a bubble, meaning the max step from the starting node to the ending node. Default: 40
+.HP
+\fB\-\-tip\-step\fR <int>
+.IP
+Max step to search a tip, 10
+.HP
+\fB\-\-ctg\-min\-length\fR <int>
+.IP
+Min length of contigs to be output, 5000
+.HP
+\fB\-\-ctg\-min\-nodes\fR <int>
+.IP
+Min num of nodes in a contig to be ouput, 3
+.HP
+\fB\-\-minimal\-output\fR
+.IP
+Will generate as less output files (<\-\-prefix>.*) as it can
+.HP
+\fB\-\-bin\-complexity\-cutoff\fR <int>
+.IP
+Used in filtering BINs. If a BIN has less indexed valid kmers than <\-\-bin\-complexity\-cutoff 2>, masks it.
+.HP
+\fB\-\-no\-local\-graph\-analysis\fR
+.IP
+Before building edges, for each node, local\-graph\-analysis reads all related reads and according nodes, and builds a local graph to judge whether to mask it
+The analysis aims to find repetitive nodes
+.HP
+\fB\-\-no\-read\-length\-sort\fR
+.IP
+Defaultly, `wtdbg` sorts input sequences by length DSC. The order of reads affects the generating of nodes in selecting important intervals
+.HP
+\fB\-\-keep\-isolated\-nodes\fR
+.IP
+In graph clean, `wtdbg` normally masks isolated (orphaned) nodes
+.HP
+\fB\-\-no\-read\-clip\fR
+.IP
+Defaultly, `wtdbg` clips a input sequence by analyzing its overlaps to remove high error endings, rolling\-circle repeats (see PacBio CCS), and chimera.
+When building edges, clipped region won't contribute. However, `wtdbg` will use them in the final linking of unitigs
+.HP
+\fB\-\-no\-chainning\-clip\fR
+.IP
+Defaultly, performs alignments chainning in read clipping
+** If '\-\-aln\-bestn 0 \fB\-\-no\-read\-clip\fR', alignments will be parsed directly, and less RAM spent on recording alignments
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/mans/wtpoa-cns.1
=====================================
@@ -0,0 +1,108 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH WTPOA-CNS "1" "April 2020" "wtpoa-cns 2.5" "User Commands"
+.SH NAME
+wtpoa-cns \- Consensuser for wtdbg using PO-MSA
+.SH SYNOPSIS
+.B wtpoa-cns
+[\fI\,options\/\fR]
+.SH DESCRIPTION
+WTPOA\-CNS: Consensuser for wtdbg using PO\-MSA
+Author: Jue Ruan <ruanjue at gmail.com>
+Version: 2.5 (20190621)
+.SH OPTIONS
+.TP
+\fB\-t\fR <int>
+Number of threads, [4]
+.HP
+\fB\-d\fR <string> Reference sequences for SAM input, will invoke sorted\-SAM input mode
+.TP
+\fB\-u\fR <int>
+XORed flags to handle SAM input. [0]
+0x1: Only process reference regions present in/between SAM alignments
+0x2: Don't fileter secondary/supplementary SAM records with flag (0x100 | 0x800)
+.TP
+\fB\-r\fR
+Force to use reference mode
+.HP
+\fB\-p\fR <string> Similar with \fB\-d\fR, but translate SAM into wtdbg layout file
+.HP
+\fB\-i\fR <string> Input file(s) *.ctg.lay from wtdbg, +, [STDIN]
+.IP
+Or sorted SAM files when having \fB\-d\fR/\-p
+.HP
+\fB\-o\fR <string> Output files, [STDOUT]
+.TP
+\fB\-f\fR
+Force overwrite
+.TP
+\fB\-j\fR <int>
+Expected max length of node, or say the overlap length of two adjacent units in layout file, [1500] bp
+overlap will be default to 1500(or 150 for sam\-sr) when having \fB\-d\fR/\-p, block size will be 2.5 * overlap
+.TP
+\fB\-b\fR <int>
+Bonus for tri\-bases match, [0]
+.TP
+\fB\-M\fR <int>
+Match score, [2]
+.TP
+\fB\-X\fR <int>
+Mismatch score, [\-5]
+.TP
+\fB\-I\fR <int>
+Insertion score, [\-2]
+.TP
+\fB\-D\fR <int>
+Deletion score, [\-4]
+.TP
+\fB\-H\fR <float>
+Homopolymer merge score used in dp\-call\-cns mode, [\-3]
+.TP
+\fB\-B\fR <expr>
+Bandwidth in POA, [Wmin[,Wmax[,mat_rate]]], mat_rate = matched_bases/total_bases [64,1024,0.92]
+Program will double bandwidth from Wmin to Wmax when mat_rate is lower than setting
+.TP
+\fB\-W\fR <int>
+Window size in the middle of the first read for fast align remaining reads, [200]
+If $W is negative, will disable fast align, but use the abs($W) as Band align score cutoff
+.TP
+\fB\-w\fR <int>
+Min size of aligned size in window, [$W * 0.5]
+.TP
+\fB\-A\fR
+Abort TriPOA when any read cannot be fast aligned, then try POA
+.TP
+\fB\-S\fR <int>
+Shuffle mode, 0: don't shuffle reads, 1: by shared kmers, 2: subsampling. [1]
+.TP
+\fB\-R\fR <int>
+Realignment bandwidth, 0: disable, [16]
+.TP
+\fB\-c\fR <int>
+Consensus mode: 0, run\-length; 1, dp\-call\-cns, [0]
+.TP
+\fB\-C\fR <int>
+Min count of bases to call a consensus base, [3]
+.TP
+\fB\-F\fR <float>
+Min frequency of non\-gap bases to call a consensus base, [0.5]
+.TP
+\fB\-N\fR <int>
+Max number of reads in PO\-MSA [20]
+Keep in mind that I am not going to generate high accurate consensus sequences here
+.HP
+\fB\-x\fR <string> Presets, []
+.TP
+sam\-sr: polishs contigs from short reads mapping, accepts sorted SAM files
+shorted for '\-j 50 \fB\-W\fR 0 \fB\-R\fR 0 \fB\-b\fR 1 \fB\-c\fR 1 \fB\-N\fR 50 \fB\-rS\fR 2'
+.TP
+\fB\-q\fR
+Quiet
+.TP
+\fB\-v\fR
+Verbose
+.TP
+\fB\-V\fR
+Print version information and then exit
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/patches/hardening.patch
=====================================
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 02 Apr 2020 11:37:59 +0200
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -11,12 +11,12 @@ TIMESTAMP=$(shell date)
+ endif
+
+ ifeq (1, ${DEBUG})
+-CFLAGS=-g3 -W -Wall -Wno-unused-but-set-variable -O0 -DDEBUG=1 -DVERSION="$(VERSION)" -DRELEASE="$(RELEASE)" -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -msse4.2
++CFLAGS+=-g3 -W -Wall -Wno-unused-but-set-variable -O0 -DDEBUG=1 -DVERSION="$(VERSION)" -DRELEASE="$(RELEASE)" -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -msse4.2
+ else
+-CFLAGS=-g3 -W -Wall -Wno-unused-but-set-variable -O4 -DVERSION="$(VERSION)" -DRELEASE="$(RELEASE)" -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -msse4.2
++CFLAGS+=-g3 -W -Wall -Wno-unused-but-set-variable -O4 -DVERSION="$(VERSION)" -DRELEASE="$(RELEASE)" -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -msse4.2
+ endif
+
+-GLIBS=-lm -lrt -lpthread -lz
++GLIBS=-lm -lrt -lpthread -lz $(LDFLAGS)
+ GENERIC_SRC=mem_share.h chararray.h sort.h list.h pgzf.h sort.h list.h dna.h thread.h filereader.h filewriter.h bitvec.h bit2vec.h bitsvec.h hashset.h
+
+ PROGS=kbm2 wtdbg2 wtdbg-cns wtpoa-cns pgzf
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
fix_install.patch
+hardening.patch
=====================================
debian/rules
=====================================
@@ -6,7 +6,7 @@ export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/ruanjue/wtdbg2/issues
+Bug-Submit: https://github.com/ruanjue/wtdbg2/issues/new
Reference:
Author: Jue Ruan and Heng Li
Title: Fast and accurate long-read assembly with wtdbg2
@@ -10,3 +12,5 @@ Reference:
PMID: 31819265
URL: https://www.nature.com/articles/s41592-019-0669-3
eprint: https://www.nature.com/articles/s41592-019-0669-3.pdf
+Repository: https://github.com/ruanjue/wtdbg2.git
+Repository-Browse: https://github.com/ruanjue/wtdbg2
View it on GitLab: https://salsa.debian.org/med-team/wtdbg2/-/compare/1f3ec74b3b677ae35deba1ca598c279c4e750f0c...30f72c7dfbaf9effc09d4360eac9c0e8f93cd4b3
--
View it on GitLab: https://salsa.debian.org/med-team/wtdbg2/-/compare/1f3ec74b3b677ae35deba1ca598c279c4e750f0c...30f72c7dfbaf9effc09d4360eac9c0e8f93cd4b3
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