[med-svn] [Git][med-team/dextractor][master] 3 commits: Remove unneeded doc-base
Shayan Doust
gitlab at salsa.debian.org
Mon Jun 29 17:21:23 BST 2020
Shayan Doust pushed to branch master at Debian Med / dextractor
Commits:
6dba7950 by Shayan Doust at 2020-06-29T16:20:55+01:00
Remove unneeded doc-base
- - - - -
3ad2e0fa by Shayan Doust at 2020-06-29T16:56:48+01:00
Fix spacing issue in control
- - - - -
07a3603c by Shayan Doust at 2020-06-29T17:21:08+01:00
Write manpages by hand
- - - - -
6 changed files:
- debian/control
- + debian/dextractor.manpages
- − debian/doc-base
- + debian/mans/dexqv.1
- + debian/mans/dexta.1
- + debian/mans/dextract.1
Changes:
=====================================
debian/control
=====================================
@@ -20,7 +20,7 @@ Description: the Dextractor and compression command library
files produced by the PacBio RS II sequencer, or from the source BAM
files produced by the PacBio Sequel sequencer.
.
- For each of the three extracted file types -- .fasta, .quiva, and
+ For each of the three extracted file types -- .fasta, .quiva, and
.arrow -- the library contains commands to compress the given file
type, and to decompress it, which is a reversible process delivering
the original uncompressed file. The compressed .fasta files, with the
=====================================
debian/dextractor.manpages
=====================================
@@ -0,0 +1 @@
+debian/mans/*.1
=====================================
debian/doc-base deleted
=====================================
@@ -1,20 +0,0 @@
-Document: dextractor
-Title: <title for this doc>
-Author: <author of this doc>
-Abstract: <if you have no better clue the short and
- long description from debian/control might fit here as well>
-Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
-
-# pick one of the below options
-Format: Text
-Files: /usr/share/doc/dextractor/<pkg>.txt.gz
-
-Format: html
-Index: /usr/share/doc/dextractor/html/index.html
-Files: /usr/share/doc/dextractor/html/*
-
-Format: pdf
-Files: /usr/share/doc/dextractor/<pkg>.pdf.gz
-
-Format: postscript
-Files: /usr/share/doc/dextractor/<pkg>.ps.gz
=====================================
debian/mans/dexqv.1
=====================================
@@ -0,0 +1,24 @@
+.TH DEXQV "1" "June 2020" "dexqv" "User Commands"
+.SH NAME
+dexqv \- compress a set of .quiva files
+.SH SYNOPSIS
+.B dexqv
+[\fI\,-vkl\/\fR] \fI\,<path:quiva> \/\fR...
+.SH DESCRIPTION
+Dexqv compresses a set of .quiva files into new files with a .dexqv extension. That is, submitting G.quiva will result in a compressed image G.dexqv, and G.quiva will not longer exist.
+
+The -k flag prevents the removal of G.quiva. With -v set progress is reported, otherwise the command runs silently. If slightly more compression is desired at the expense of being a bit "lossy" then set the -l option. This option is experimental in that it remains to be seen if Quiver gives the same results with the scaled values responsible for the loss. Undexqv reverses the compression of dexqv, replacing the uncompressed image of G.dexqv with G.quiva. The flags are analgous to the v & k flags for dexqv. The compression factor is typically 3.4 or so (4.0 or so with -l set).
+
+By .fastq convention each QV vector is output by undexqv as a line without intervening new-lines, and by default the Deletion Tag vector is in lower case letters. The -U option specifies upper case letters should instead be used for said vector.
+.SH "SEE ALSO"
+The full documentation for
+.B dexqv:
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B dexqv
+programs are properly installed at your site, the command
+.IP
+.B info dexqv
+.PP
+should give you access to the complete manual.
=====================================
debian/mans/dexta.1
=====================================
@@ -0,0 +1,24 @@
+.TH DEXTA "1" "June 2020" "dexta" "User Commands"
+.SH NAME
+dexta \- compress a set of .fasta files
+.SH SYNOPSIS
+.B dexta
+[\fI\,-vk\/\fR] \fI\,<path:fasta> \/\fR...
+.SH DESCRIPTION
+Dexta compresses a set of .fasta files (produced by either Pacbio's software or dextract) and replaces them with new files with a .dexta extension. That is, submitting G.fasta will result in a compressed image G.dexta, and G.fasta will no longer exist.
+
+With the -k option the .fasta source is not removed. If -v is set, then the program reports its progress on each file. Otherwise it runs completely silently (good for batch jobs to an HPC cluster). The compression factor is always slightly better than 4.0. Undexta reverses the compression of dexta, replacing the uncompressed image of G.dexta with G.fasta. By default the sequences output by undexta are in lower case and 80 chars per line. The -U option specifies upper case should be used, and the characters per line, or line width, can be set to any positive value with the -w option
+
+With the -i option set, the program runs as a UNIX pipe that takes .fasta (.dexta) input from the standard input and writes .dexta (.fasta) to the standard output. In this case the -k option has no effect.
+.SH "SEE ALSO"
+The full documentation for
+.B dexta:
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B dexta
+programs are properly installed at your site, the command
+.IP
+.B info dexta
+.PP
+should give you access to the complete manual.
=====================================
debian/mans/dextract.1
=====================================
@@ -0,0 +1,36 @@
+.TH DEXTRACT "1" "June 2020" "dextract" "User Commands"
+.SH NAME
+dextract \- pull information needed for assembly from source HDF5 files made by PacBio RS II sequencer
+.SH SYNOPSIS
+.B dextract
+[\fI\,-vq\/\fR] [\fI\,-o\/\fR[\fI\,<path>\/\fR]] [\fI\,-l<int(500)>\/\fR] [\fI\,-s<int(750)>\/\fR] \fI\,<input:bax_h5> \/\fR...
+.SH DESCRIPTION
+.nr step 1 1
+Dextract takes a series of .bax.h5 or .subreads.[bs]am files as input, and depending on the option flags settings produces:
+.IP \n[step] 3
+(-f) a.fasta file containing subread sequences, each with a "standard" Pacbio header consisting of the movie name, well number, pulse range, and read quality value.
+.IP \n+[step]
+(-a) a FASTA format .arrow file containing the pulse width stream for each subread, with a header that contains the movie name and the 4 channel SNR values.
+.IP \n+[step]
+(-q) a FASTAQ-like .quiva file containing for each subread the same header as the .fasta file above, save that it starts with an @-sign, followed by the 5 quality value streams used by Quiver, one per line, where the order of the streams is: deletion QVs, deletion Tags, insertion QVs, merge QVs, and last substitution QVs.
+
+.nr step 1 1
+If the -v option is set then the program reports the processing of each PacBio input file, otherwise it runs silently. If none of the -f, -a, or -q flags is set, then by default -f is assumed. The destination of the extracted information is controlled by the -o parameter as follows:
+.IP \n[step] 3
+If -o is absent, then for each input file X.bax.h5 or X.subreads.[bs]am, dextract will produce X.fasta, X.arrow, and/or X.quiva as per the option flags.
+.IP \n+[step]
+If -o is present and followed by a path Y, then the concatenation of the output for the input files is placed in Y.fasta, Y.arrow, and/or Y.quiva as per the option flags.
+.IP \n+[step]
+If -o is present but with no following path, then the output is sent to the standard output (to enable a UNIX pipe if desired). In this case only one of the flags -f, -a, or -q can be set.
+.SH "SEE ALSO"
+The full documentation for
+.B dextract:
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B dextract:
+programs are properly installed at your site, the command
+.IP
+.B info dextract
+.PP
+should give you access to the complete manual.
View it on GitLab: https://salsa.debian.org/med-team/dextractor/-/compare/c69de00ff502b924a3509b608234f0090f6cb5b7...07a3603c909917dd862c5a1aaffd82e432effa8b
--
View it on GitLab: https://salsa.debian.org/med-team/dextractor/-/compare/c69de00ff502b924a3509b608234f0090f6cb5b7...07a3603c909917dd862c5a1aaffd82e432effa8b
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