[med-svn] r13862 - trunk/packages/mira/trunk/debian

Fri Jun 7 07:15:59 UTC 2013

Author: tille
Date: 2013-06-07 07:15:58 +0000 (Fri, 07 Jun 2013)
New Revision: 13862

Modified:
   trunk/packages/mira/trunk/debian/changelog
   trunk/packages/mira/trunk/debian/convert_project.1
   trunk/packages/mira/trunk/debian/scftool.1
Log:
Fixed existing manpages


Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================

--- trunk/packages/mira/trunk/debian/changelog	2013-06-07 06:56:11 UTC (rev 13861)
+++ trunk/packages/mira/trunk/debian/changelog	2013-06-07 07:15:58 UTC (rev 13862)
@@ -21,7 +21,8 @@
   
   [ Andreas Tille ]
   * delete debian/README.source which is outdated / wrong
-  * debian/{mira.1,miradiff.1,miramer.1}: Wrote manpage for some programs
+  * debian/{mira.1,miradiff.1,miramer.1, scftool.1, convert_project.1}:
+    Wrote manpage for some programs
   * Removed debian/obsolete.mira-assembler.install
 
  -- Andreas Tille <tille at debian.org>  Fri, 07 Jun 2013 08:34:21 +0200

Modified: trunk/packages/mira/trunk/debian/convert_project.1
===================================================================
--- trunk/packages/mira/trunk/debian/convert_project.1	2013-06-07 06:56:11 UTC (rev 13861)
+++ trunk/packages/mira/trunk/debian/convert_project.1	2013-06-07 07:15:58 UTC (rev 13862)
@@ -1,16 +1,13 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.42.1.
-.TH CONVERT_PROJECT "1" "June 2013" "convert_project (MIRALIB version 3.9.17 ())" "User Commands"
+.TH CONVERT_PROJECT "1" "June 2013" "3.9.17" "User Commands"
 .SH NAME
 convert_project \- convert assembly and sequencing file types
 .SH DESCRIPTION
-.PP
-convert_project (MIRALIB version 3.9.17 ())
-.PP
-Author:  Bastien Chevreux       (bach at chevreux.org)
-.PP
-Usage:
-convert_project [\-f <fromtype>] [\-t <totype> [\-t <totype> ...]]
-.IP
+This program is part of the MIRA assembler package. converting project file
+types into other types.   Please check out the
+documentation below for more detailed information about convert_project.
+.SH SYNOPSIS
+.IP convert_project
+[\-f <fromtype>] [\-t <totype> [\-t <totype> ...]]
 [\-aChimMsuZ]
 [\-AcflnNoqrtvxXyz {...}]
 {infile} {outfile} [<totype> <totype> ...]
@@ -190,13 +187,8 @@
 \fB\-S\fR <name>
 (name)Scheme for renaming reads, important for paired\-ends
 Only 'solexa' is currently supported.
-.HP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-The following switches work only when input (CAF or MAF)
-contains contigs. Beware: CAF and MAf can also contain
-just reads.
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.SS The following switches work only when input (CAF or MAF) contains contigs.
+Beware: CAF and MAf can also contain just reads.
 .TP
 \fB\-M\fR
 Do not extract contigs (or their consensus), but the
@@ -279,270 +271,6 @@
 caf2html, exp2fasta, ... etc. Any combination of "<validfromtype>2<validtotype>"
 can be used as program name (also using links) so as that convert_project
 automatically sets \fB\-f\fR and \fB\-t\fR accordingly.
-.TP
-\fB\-f\fR <fromtype>
-load this type of project files, where fromtype is:
-.TP
-caf
-a complete assembly or single sequences from CAF
-.TP
-maf
-a complete assembly or single sequences from CAF
-.TP
-fasta
-sequences from a FASTA file
-.TP
-fastq
-sequences from a FASTQ file
-.TP
-gbf
-sequences from a GBF file
-.TP
-phd
-sequences from a PHD file
-.TP
-fofnexp
-sequences in EXP files from file of filenames
-.TP
-\fB\-t\fR <totype>
-write the sequences/assembly to this type (multiple
-mentions of \fB\-t\fR are allowed):
-.TP
-ace
-sequences or complete assembly to ACE
-.TP
-caf
-sequences or complete assembly to CAF
-.TP
-maf
-sequences or complete assembly to MAF
-.TP
-sam
-complete assembly to SAM
-.TP
-samnbb
-like above, but leaving out reference (backbones) in mapping assemblies
-.TP
-gbf
-sequences or consensus to GBF
-.TP
-gff3
-consensus to GFF3
-.TP
-wig
-assembly coverage info to wiggle file
-.TP
-gcwig
-assembly gc content info to wiggle file
-.TP
-fasta
-sequences or consensus to FASTA file (qualities to
-.IP
-\&.qual)
-.TP
-fastq
-sequences or consensus to FASTQ file
-.TP
-exp
-sequences or complete assembly to EXP files in
-.IP
-directories. Complete assemblies are suited for gap4
-import as directed assembly.
-Note: using caf2gap to import into gap4 is recommended though
-.TP
-text
-complete assembly to text alignment (only when \fB\-f\fR is
-.IP
-caf, maf or gbf)
-.TP
-html
-complete assembly to HTML (only when \fB\-f\fR is caf, maf or
-.IP
-gbf)
-.TP
-tcs
-complete assembly to tcs
-.TP
-hsnp
-surrounding of SNP tags (SROc, SAOc, SIOc) to HTML
-(only when \fB\-f\fR is caf, maf or gbf)
-.TP
-asnp
-analysis of SNP tags
-(only when \fB\-f\fR is caf, maf or gbf)
-.TP
-cstats
-contig statistics file like from MIRA
-(only when source contains contigs)
-.TP
-crlist
-contig read list file like from MIRA
-(only when source contains contigs)
-.TP
-maskedfasta
-reads where sequencing vector is masked out
-(with X) to FASTA file (qualities to .qual)
-.TP
-scaf
-sequences or complete assembly to single sequences CAF
-.TP
-\fB\-a\fR
-Append to target files instead of rewriting
-.TP
-\fB\-A\fR <string>
-String with MIRA parameters to be parsed
-Useful when setting parameters affecting consensus
-calling like \fB\-CO\fR:mrpg etc.
-E.g.: \fB\-a\fR "454_SETTINGS \fB\-CO\fR:mrpg=3"
-.TP
-\fB\-b\fR
-Blind data
-Replaces all bases in reads/contigs with a 'c'
-.TP
-\fB\-C\fR
-Perform hard clip to reads
-When reading formats which define clipping points, will
-.IP
-save only the unclipped part into the result file.
-.IP
-Applies only to files/formats which do not contain
-.IP
-contigs.
-.TP
-\fB\-d\fR
-Delete gap only columns
-When output is contigs: delete columns that are
-.IP
-entirely gaps (like after having deleted reads during
-editing in gap4 or similar)
-.IP
-When output is reads: delete gaps in reads
-.TP
-\fB\-F\fR
-Filter to read groups
-Special use case, do not use yet.
-.TP
-\fB\-m\fR
-Make contigs (only for \fB\-t\fR = caf or maf)
-Encase single reads as contig singlets into the CAF/MAF
-file.
-.TP
-\fB\-n\fR <filename>
-when given, selects only reads or contigs given by
-name in that file.
-.TP
-\fB\-i\fR
-when \fB\-n\fR is used, inverts the selection
-.TP
-\fB\-o\fR
-fastq quality Offset (only for \fB\-f\fR = 'fastq')
-Offset of quality values in FASTQ file. Default of 0
-tries to automatically recognise.
-.TP
-\fB\-Q\fR <quality>
-Set default quality for bases in file types without quality values
-Furthermore, do not stop if expected quality files are missing (e.g. '.fasta')
-.TP
-\fB\-R\fR <name>
-Rename contigs/singlets/reads with given name string
-to which a counter is appended.
-Known bug: will create duplicate names if input
-.IP
-contains contigs/singlets as well as free reads, i.e.
-reads not in contigs nor singlets.
-.TP
-\fB\-S\fR <name>
-(name)Scheme for renaming reads, important for paired\-ends
-Only 'solexa' is currently supported.
-.HP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-The following switches work only when input (CAF or MAF)
-contains contigs. Beware: CAF and MAf can also contain
-just reads.
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.TP
-\fB\-M\fR
-Do not extract contigs (or their consensus), but the
-sequence of the reads they are composed of.
-.TP
-\fB\-N\fR <filename>
-like \fB\-n\fR, but sorts output according to order given
-in file.
-.TP
-\fB\-r\fR [cCqf]
-Recalculate consensus and / or consensus quality values
-and / or SNP feature tags.
-\&'c' recalc cons & cons qualities (with IUPAC)
-\&'C' recalc cons & cons qualities (forcing non\-IUPAC)
-\&'q' recalc consensus qualities only
-\&'f' recalc SNP features
-Note: only the last of cCq is relevant, f works as a
-.IP
-switch and can be combined with cQq (e.g. "\-r C \fB\-r\fR f")
-.IP
-Note: if the CAF/MAF contains multiple strains,
-recalculation of cons & cons qualities is forced, you
-.IP
-can just influence whether IUPACs are used or not.
-.TP
-\fB\-s\fR
-split output into multiple files instead of creating a
-single file
-.TP
-\fB\-u\fR
-\&'fillUp strain genomes'
-Fill holes in the genome of one strain (N or @)
-with sequence from a consensus of other strains
-Takes effect only with \fB\-r\fR and \fB\-t\fR gbf or fasta/q
-in FASTA/Q: bases filled up are in lower case
-in GBF: bases filled up are in upper case
-.TP
-\fB\-q\fR <integer>
-Defines minimum quality a consensus base of a strain
-must have, consensus bases below this will be 'N'
-Default: 0
-Only used with \fB\-r\fR, and \fB\-f\fR is caf/maf and \fB\-t\fR is (fasta
-.IP
-or gbf)
-.TP
-\fB\-v\fR
-Print version number and exit
-.TP
-\fB\-x\fR <integer>
-Minimum contig or read length
-When loading, discard all contigs / reads with a
-length less than this value. Default: 0 (=switched off)
-Note: not applied to reads in contigs!
-.TP
-\fB\-X\fR <integer>
-Similar to \fB\-x\fR but applies only to reads and
-then to the clipped length.
-.TP
-\fB\-y\fR <integer>
-Minimum average contig coverage
-When loading, discard all contigs with an
-average coverage less than this value.
-Default: 1
-.TP
-\fB\-z\fR <integer>
-Minimum number of reads in contig
-When loading, discard all contigs with a
-number of reads less than this value.
-Default: 0 (=switched off)
-.TP
-\fB\-l\fR <integer>
-when output as text or HTML: number of bases shown in
-one alignment line. Default: 60.
-.TP
-\fB\-c\fR <character>
-when output as text or HTML: character used to pad
-endgaps. Default: ' ' (blank)
-.PP
-Aliases:
-caf2html, exp2fasta, ... etc. Any combination of "<validfromtype>2<validtotype>"
-can be used as program name (also using links) so as that convert_project
-automatically sets \fB\-f\fR and \fB\-t\fR accordingly.
 .SH EXAMPLES
 .IP
 convert_project source.maf dest.sam
@@ -552,3 +280,23 @@
 convert_project \-x 2000 \-y 10 source.caf dest.caf
 .IP
 caf2html \-l 100 \-c . source.caf dest
+.SH "SEE ALSO"
+A more extensive documentation is provided in the mira-doc package and can be found at
+/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
+.PP
+You can also subscribe one of the MIRA mailing lists at
+.IP
+http://www.chevreux.org/mira_mailinglists.html
+.PP
+After subscribing, mail general questions to the MIRA talk mailing list:
+.IP
+mira_talk at freelists.org
+.SH BUGS
+To report bugs or ask for features, please use the new ticketing system at:
+.IP
+http://sourceforge.net/apps/trac/mira\-assembler/
+.SH AUTHOR
+The author of the mira code is Bastien Chevreux <bach at chevreux.org>
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
+distribution.

Modified: trunk/packages/mira/trunk/debian/scftool.1
===================================================================
--- trunk/packages/mira/trunk/debian/scftool.1	2013-06-07 06:56:11 UTC (rev 13861)
+++ trunk/packages/mira/trunk/debian/scftool.1	2013-06-07 07:15:58 UTC (rev 13862)
@@ -1,21 +1,50 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.42.1.
-.TH SCFTOOL: "1" "June 2013" "scftool" "User Commands"
+.TH SCFTOOL "1" "June 2013" "3.9.17" "User Commands"
 .SH NAME
 scftool \- provides a set of tools useful when working with SCF trace files.
-.SH AUTHOR
-Written by Bastien Chevreux (bach at chevreux.org)
+.SH SYNOPSIS
+.IP
+scftool
+<\fBtoolname\fR> <\fBtool parameters\fR>
+.SH OPTIONS
+Available tools:
+.IP convert
+Cuts the given range out of an SCF file and makes a new SCF out of it.
+.IP
+To get help more specific help please type \fIscftool convert\fR
+.IP cut
+Cuts a given range of a SCF file into a new SCF file.
+.IP remix
+Combines trace information of a SCF file with new bases, qualities and peak
+values (either in FASTA or PHD format) into a new SCF file.
+.SH EXAMPLES
+Example for cut:
+.IP
+scftool cut infile lower_base_bound upper_base_bound outfile
 .PP
-.SH "Usage:"
+Usage of remix (when using PHD files as input for bases, quals and peaks):
 .IP
-scftool <toolname> <tool parameters>
-.SS "Available tools:"
+scftool remix scf_infile phd_infile scf_outfile
+.PP
+Usage of remix (when using FASTA files as input for bases, quals and peaks):
 .IP
-convert Converts SCF file(s) to other formats.
+scftool remix scf_infile bases_infile quals_infile peaks_infile scf_outfile
+.SH "SEE ALSO"
+A more extensive documentation is provided in the mira-doc package and can be found at
+/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
+.PP
+You can also subscribe one of the MIRA mailing lists at
 .IP
-cut     Cuts a given range of a SCF file into a new SCF file.
+http://www.chevreux.org/mira_mailinglists.html
+.PP
+After subscribing, mail general questions to the MIRA talk mailing list:
 .IP
-remix   Combines trace information of a SCF file with new bases, qualities and
+mira_talk at freelists.org
+.SH BUGS
+To report bugs or ask for features, please use the new ticketing system at:
 .IP
-peak values.
+http://sourceforge.net/apps/trac/mira\-assembler/
+.SH AUTHOR
+The author of the mira code is Bastien Chevreux <bach at chevreux.org>
 .PP
-To get help on a specific tool, type 'scftool <toolname>'. E.g.: scftool remix
+This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
+distribution.


