[med-svn] r20629 - in trunk/packages/mira/trunk/debian: . mans patches
Andreas Tille
tille at moszumanska.debian.org
Fri Dec 4 12:24:44 UTC 2015
Author: tille
Date: 2015-12-04 12:24:43 +0000 (Fri, 04 Dec 2015)
New Revision: 20629
Added:
trunk/packages/mira/trunk/debian/mans/
trunk/packages/mira/trunk/debian/mans/convert_project.1
trunk/packages/mira/trunk/debian/mans/fasta2frag.1
trunk/packages/mira/trunk/debian/mans/fastaselect.1
trunk/packages/mira/trunk/debian/mans/fastatool.1
trunk/packages/mira/trunk/debian/mans/fastqselect.1
trunk/packages/mira/trunk/debian/mans/fixACE4consed.1
trunk/packages/mira/trunk/debian/mans/mira.1
trunk/packages/mira/trunk/debian/mans/miraSearchESTSNPs.1
trunk/packages/mira/trunk/debian/mans/mirabait.1
trunk/packages/mira/trunk/debian/mans/miraconvert.1
trunk/packages/mira/trunk/debian/mans/miradiff.1
trunk/packages/mira/trunk/debian/mans/miramem.1
trunk/packages/mira/trunk/debian/mans/miramer.1
trunk/packages/mira/trunk/debian/mans/scftool.1
trunk/packages/mira/trunk/debian/mira-examples.lintian-overrides
trunk/packages/mira/trunk/debian/patches/spelling.patch
Removed:
trunk/packages/mira/trunk/debian/convert_project.1
trunk/packages/mira/trunk/debian/fasta2frag.1
trunk/packages/mira/trunk/debian/fastaselect.1
trunk/packages/mira/trunk/debian/fastatool.1
trunk/packages/mira/trunk/debian/fastqselect.1
trunk/packages/mira/trunk/debian/fixACE4consed.1
trunk/packages/mira/trunk/debian/mira.1
trunk/packages/mira/trunk/debian/miraSearchESTSNPs.1
trunk/packages/mira/trunk/debian/mirabait.1
trunk/packages/mira/trunk/debian/miradiff.1
trunk/packages/mira/trunk/debian/miramem.1
trunk/packages/mira/trunk/debian/miramer.1
trunk/packages/mira/trunk/debian/scftool.1
Modified:
trunk/packages/mira/trunk/debian/changelog
trunk/packages/mira/trunk/debian/mira-assembler.manpages
trunk/packages/mira/trunk/debian/patches/series
Log:
Fix / override several lintian issues; wrote missing manpage
Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/changelog 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,3 +1,13 @@
+mira (4.9.5-2) unstable; urgency=medium
+
+ * Verify that package builds without problems with gcc-5
+ Closes: #793261
+ * override false lintian positives
+ * Fix spelling
+ * wrote missing manpage and moved manpages to separate dir
+
+ -- Andreas Tille <tille at debian.org> Fri, 04 Dec 2015 12:56:09 +0100
+
mira (4.9.5-1) unstable; urgency=medium
* New upstream version
Deleted: trunk/packages/mira/trunk/debian/convert_project.1
===================================================================
--- trunk/packages/mira/trunk/debian/convert_project.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/convert_project.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,302 +0,0 @@
-.TH CONVERT_PROJECT "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-convert_project \- convert assembly and sequencing file types
-.SH DESCRIPTION
-This program is part of the MIRA assembler package. It is used to convert
-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> ...]
-.SH OPTIONS
-.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.
-.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
-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
-.IP
-convert_project source.caf dest.fasta wig ace
-.IP
-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.
Deleted: trunk/packages/mira/trunk/debian/fasta2frag.1
===================================================================
--- trunk/packages/mira/trunk/debian/fasta2frag.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/fasta2frag.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,95 +0,0 @@
-.TH FASTA2FRAG "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-.B fasta2frag \- splits a single fasta sequence into several overlapping fragments.
-.SH DESCRIPTION
-This program is part of the MIRA assembler package. The purpose of fasta2frag
-is to fragment sequences into smaller, overlapping
-subsequences. It can be used for simulating shotgun sequences. It can create
-subsequences in both directions (/default) and also paired-end sequences.
-Please check out the
-documentation below for more detailed information about fasta2frag.
-.SH SYNOPSIS
-fasta2frag
-\fI<options> infile outfile\fR
-.SH OPTIONS
-\fB\-l\fR
-int Length of fragments (default=3000)
-.TP
-\fB\-i\fR
-int Increment of fragment start site (default=2500)
-.TP
-\fB\-p\fR
-int Paired end (default=0 is off, 1 is on)
-.TP
-\fB\-P\fR
-int In paired\-end mode, reverse one of the reads
-(0 is off, default=1 is on)
-.TP
-\fB\-s\fR
-int Strobe sequencing (default=0 is off, 1 is on)
-.TP
-\fB\-q\fR
-int Default quality when no quality data present (default=30)
-.TP
-\fB\-r\fR
-int Reverse every nth fragment (default=2)
-.TP
-\fB\-c\fR
-int Circularise fragments so that they form a ring
-.IP
-(default=0 is is off, 1 would be on)
-.TP
-\fB\-qualdivisor\fR
-int Divide quality values by this (default=1)
-.TP
-\fB\-minqual\fR
-int But give it at least this qual (default=0)
-.TP
-\fB\-insert_size\fR
-int paired\-end: insert size (default=3000)
-.TP
-\fB\-insert_stdev\fR int
-paired\-end: standard dev (default=900)
-this is not working at the moment
-.TP
-\fB\-pairednaming\fR string
-naming scheme for paired\-end:
-sanger, 454 (default) or solexa
-.TP
-\fB\-minmut\fR
-int min. number of mutations/seq. errors (def=0)
-.TP
-\fB\-maxmut\fR
-int max. number of mutations/seq. errors (def=0)
-.TP
-\fB\-strobeon\fR
-int number of bases read during strobe on
-.TP
-\fB\-strobeoff\fR
-int number of bases during strobe off
-.TP
-\fB\-startoffset\fR
-int start at offset position
-.TP
-\fB\-namesuffix\fR
-string suffix name with string
-.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.
Deleted: trunk/packages/mira/trunk/debian/fastaselect.1
===================================================================
--- trunk/packages/mira/trunk/debian/fastaselect.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/fastaselect.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,47 +0,0 @@
-.TH FASTASELECT "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-.B fastaselect \- select fasta sequences in a file
-.SH DESCRIPTION
-This script selects fasta sequences in a file according to names given
-in a name file. Given a FASTA file (and possibly a FASTA quality file) and
-a file with names of reads, select the sequences from the input FASTA (and
-quality file) and writes them to an output FASTA.
-.PP
-If fasta quality file is present (same basename, but with .qual appended),
-then also selects sequences from there.
-.PP
-Please check out the documentation below for more detailed information.
-.SH SYNOPSIS
-fastaselect \fI<options>\fR
-.SH OPTIONS
-.TP
-\fB\-infile\fR
-name filename containing all fasta sequences
-.TP
-\fB\-name\fR
-name filename containing all names of sequences to select
-.TP
-\fB\-outfile\fR name
-filename where to write selcted sequences to
-.SH "SEE ALSO"
-fastqselect(1)
-.PP
-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.
Deleted: trunk/packages/mira/trunk/debian/fastatool.1
===================================================================
--- trunk/packages/mira/trunk/debian/fastatool.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/fastatool.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,49 +0,0 @@
-.TH FASTATOOL "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-.B fastatool \- Provides a set of tools useful when working with FASTA files.
-.SH DESCRIPTION
-This program is part of the MIRA assembler package.
-Fastatool provides a set of tools useful when working with FASTA trace files.
-.PP
-Please check out the documentation below for more detailed information.
-.SH SYNOPSIS"
-fastatool \fI<toolname>\fR \fI<tool parameters>\fR
-.SH OPTIONS
-.TP
-clip
-Clips bases on the left and right of a FASTA sequence, writes result to STDOUT.
-.IP
-Usage:
-.TP
- clipFASTA \-l leftclip \-r rightclip fastainfile
-.TP
-sanitize
-Deletes sequences with non-IUPAC bases or empty sequences from a FASTA file,
-writes the 'surviving' sequences to a new file.
-If a quality file is given, a cleaned version of that is also written.
-The sequences in the quality files (if given) MUST be in the same order than
-in the fasta file.
-.IP
-Usage:
-.TP
- sanitizeFASTA fastainfile fastaoutfile [fastaqualin fastaqualoutfile]
-.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.
Deleted: trunk/packages/mira/trunk/debian/fastqselect.1
===================================================================
--- trunk/packages/mira/trunk/debian/fastqselect.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/fastqselect.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,47 +0,0 @@
-.TH FASTQSELECT "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-.B fastqselect \- select fastq sequences in a file
-.SH DESCRIPTION
-This script selects fastq sequences in a file according to names given
-in a name file. Given a FASTQ file (and possibly a FASTQ quality file) and
-a file with names of reads, select the sequences from the input FASTQ (and
-quality file) and writes them to an output FASTQ.
-.PP
-If fastq quality file is present (same basename, but with .qual appended),
-then also selects sequences from there.
-.PP
-Please check out the documentation below for more detailed information.
-.SH SYNOPSIS
-fastqselect \fI<options>\fR
-.SH OPTIONS
-.TP
-\fB\-infile\fR
-name filename containing all fastq sequences
-.TP
-\fB\-name\fR
-name filename containing all names of sequences to select
-.TP
-\fB\-outfile\fR name
-filename where to write selcted sequences to
-.SH "SEE ALSO"
-fastaselect(1)
-.PP
-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.
Deleted: trunk/packages/mira/trunk/debian/fixACE4consed.1
===================================================================
--- trunk/packages/mira/trunk/debian/fixACE4consed.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/fixACE4consed.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,32 +0,0 @@
-.TH fixACE4consed "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-fixACE4consed \- workaround to allow consed loading the ACE generated by MIRA
-.SH DESCRIPTION
-The ACE output of MIRA is conforming to the file specification given in the
-consed documentation. However, due to a bug in consed, consed cannot correctly
-load tags set by MIRA.
-.PP
-The script fixACE4consed implements a workaround to allow consed loading the
-ACE generated by MIRA.
-.SH SYNOPSIS
-fixACE4consed infile.ace >outfile.ace
-.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.
Added: trunk/packages/mira/trunk/debian/mans/convert_project.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/convert_project.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/convert_project.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,302 @@
+.TH CONVERT_PROJECT "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+convert_project \- convert assembly and sequencing file types
+.SH DESCRIPTION
+This program is part of the MIRA assembler package. It is used to convert
+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> ...]
+.SH OPTIONS
+.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.
+.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
+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
+.IP
+convert_project source.caf dest.fasta wig ace
+.IP
+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.
Added: trunk/packages/mira/trunk/debian/mans/fasta2frag.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/fasta2frag.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/fasta2frag.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,95 @@
+.TH FASTA2FRAG "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+.B fasta2frag \- splits a single fasta sequence into several overlapping fragments.
+.SH DESCRIPTION
+This program is part of the MIRA assembler package. The purpose of fasta2frag
+is to fragment sequences into smaller, overlapping
+subsequences. It can be used for simulating shotgun sequences. It can create
+subsequences in both directions (/default) and also paired-end sequences.
+Please check out the
+documentation below for more detailed information about fasta2frag.
+.SH SYNOPSIS
+fasta2frag
+\fI<options> infile outfile\fR
+.SH OPTIONS
+\fB\-l\fR
+int Length of fragments (default=3000)
+.TP
+\fB\-i\fR
+int Increment of fragment start site (default=2500)
+.TP
+\fB\-p\fR
+int Paired end (default=0 is off, 1 is on)
+.TP
+\fB\-P\fR
+int In paired\-end mode, reverse one of the reads
+(0 is off, default=1 is on)
+.TP
+\fB\-s\fR
+int Strobe sequencing (default=0 is off, 1 is on)
+.TP
+\fB\-q\fR
+int Default quality when no quality data present (default=30)
+.TP
+\fB\-r\fR
+int Reverse every nth fragment (default=2)
+.TP
+\fB\-c\fR
+int Circularise fragments so that they form a ring
+.IP
+(default=0 is is off, 1 would be on)
+.TP
+\fB\-qualdivisor\fR
+int Divide quality values by this (default=1)
+.TP
+\fB\-minqual\fR
+int But give it at least this qual (default=0)
+.TP
+\fB\-insert_size\fR
+int paired\-end: insert size (default=3000)
+.TP
+\fB\-insert_stdev\fR int
+paired\-end: standard dev (default=900)
+this is not working at the moment
+.TP
+\fB\-pairednaming\fR string
+naming scheme for paired\-end:
+sanger, 454 (default) or solexa
+.TP
+\fB\-minmut\fR
+int min. number of mutations/seq. errors (def=0)
+.TP
+\fB\-maxmut\fR
+int max. number of mutations/seq. errors (def=0)
+.TP
+\fB\-strobeon\fR
+int number of bases read during strobe on
+.TP
+\fB\-strobeoff\fR
+int number of bases during strobe off
+.TP
+\fB\-startoffset\fR
+int start at offset position
+.TP
+\fB\-namesuffix\fR
+string suffix name with string
+.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.
Added: trunk/packages/mira/trunk/debian/mans/fastaselect.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/fastaselect.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/fastaselect.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,47 @@
+.TH FASTASELECT "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+.B fastaselect \- select fasta sequences in a file
+.SH DESCRIPTION
+This script selects fasta sequences in a file according to names given
+in a name file. Given a FASTA file (and possibly a FASTA quality file) and
+a file with names of reads, select the sequences from the input FASTA (and
+quality file) and writes them to an output FASTA.
+.PP
+If fasta quality file is present (same basename, but with .qual appended),
+then also selects sequences from there.
+.PP
+Please check out the documentation below for more detailed information.
+.SH SYNOPSIS
+fastaselect \fI<options>\fR
+.SH OPTIONS
+.TP
+\fB\-infile\fR
+name filename containing all fasta sequences
+.TP
+\fB\-name\fR
+name filename containing all names of sequences to select
+.TP
+\fB\-outfile\fR name
+filename where to write selcted sequences to
+.SH "SEE ALSO"
+fastqselect(1)
+.PP
+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.
Added: trunk/packages/mira/trunk/debian/mans/fastatool.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/fastatool.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/fastatool.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,49 @@
+.TH FASTATOOL "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+.B fastatool \- Provides a set of tools useful when working with FASTA files.
+.SH DESCRIPTION
+This program is part of the MIRA assembler package.
+Fastatool provides a set of tools useful when working with FASTA trace files.
+.PP
+Please check out the documentation below for more detailed information.
+.SH SYNOPSIS"
+fastatool \fI<toolname>\fR \fI<tool parameters>\fR
+.SH OPTIONS
+.TP
+clip
+Clips bases on the left and right of a FASTA sequence, writes result to STDOUT.
+.IP
+Usage:
+.TP
+ clipFASTA \-l leftclip \-r rightclip fastainfile
+.TP
+sanitize
+Deletes sequences with non-IUPAC bases or empty sequences from a FASTA file,
+writes the 'surviving' sequences to a new file.
+If a quality file is given, a cleaned version of that is also written.
+The sequences in the quality files (if given) MUST be in the same order than
+in the fasta file.
+.IP
+Usage:
+.TP
+ sanitizeFASTA fastainfile fastaoutfile [fastaqualin fastaqualoutfile]
+.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.
Added: trunk/packages/mira/trunk/debian/mans/fastqselect.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/fastqselect.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/fastqselect.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,47 @@
+.TH FASTQSELECT "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+.B fastqselect \- select fastq sequences in a file
+.SH DESCRIPTION
+This script selects fastq sequences in a file according to names given
+in a name file. Given a FASTQ file (and possibly a FASTQ quality file) and
+a file with names of reads, select the sequences from the input FASTQ (and
+quality file) and writes them to an output FASTQ.
+.PP
+If fastq quality file is present (same basename, but with .qual appended),
+then also selects sequences from there.
+.PP
+Please check out the documentation below for more detailed information.
+.SH SYNOPSIS
+fastqselect \fI<options>\fR
+.SH OPTIONS
+.TP
+\fB\-infile\fR
+name filename containing all fastq sequences
+.TP
+\fB\-name\fR
+name filename containing all names of sequences to select
+.TP
+\fB\-outfile\fR name
+filename where to write selcted sequences to
+.SH "SEE ALSO"
+fastaselect(1)
+.PP
+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.
Added: trunk/packages/mira/trunk/debian/mans/fixACE4consed.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/fixACE4consed.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/fixACE4consed.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,32 @@
+.TH fixACE4consed "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+fixACE4consed \- workaround to allow consed loading the ACE generated by MIRA
+.SH DESCRIPTION
+The ACE output of MIRA is conforming to the file specification given in the
+consed documentation. However, due to a bug in consed, consed cannot correctly
+load tags set by MIRA.
+.PP
+The script fixACE4consed implements a workaround to allow consed loading the
+ACE generated by MIRA.
+.SH SYNOPSIS
+fixACE4consed infile.ace >outfile.ace
+.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.
Added: trunk/packages/mira/trunk/debian/mans/mira.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/mira.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/mira.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,53 @@
+.TH 3.9.17 "1" "June 2013" "User Commands"
+.SH NAME
+mira \- The Genome and EST Sequence Assembly System
+.SH DESCRIPTION
+The mira genome fragment assembler is a specialised assembler for
+sequencing projects classified as 'hard' due to high number of similar
+repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
+specialised on reconstructing pristine mRNA transcripts while
+detecting and classifying single nucleotide polymorphisms (SNP)
+occuring in different variations thereof.
+.PP
+The assembler is routinely used for such various tasks as mutation
+detection in different cell types, similarity analysis of transcripts
+between organisms, and pristine assembly of sequences from various
+sources for oligo design in clinical microarray experiments.
+.PP
+The purpose of the \fBmira\fR executable is to assemble sequencing data.
+.SH SYNOPSIS
+mira
+[\fIOPTION\fR] manifest_file [\fImanifest_file\fR] ...
+.SH OPTIONS
+.TP
+\fB\-c\fR / \fB\-\-cwd=\fRdirectory
+Change working directory
+.TP
+\fB\-r\fR / \fB\-\-resume\fR
+Resume an interrupted assembly
+.TP
+\fB\-h\fR / \fB\-\-help\fR
+Print short help and exit
+.TP
+\fB\-v\fR / \fB\-\-version\fR
+Print version and exit
+.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.
Added: trunk/packages/mira/trunk/debian/mans/miraSearchESTSNPs.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/miraSearchESTSNPs.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/miraSearchESTSNPs.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,43 @@
+.TH miraSearchESTSNPs "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+miraSearchESTSNPs \- Pipeline to discover SNPs in ESTs from different strains
+.SH DESCRIPTION
+The program miraSearchESTSNPs can be used for assembly of EST data from
+different strains (or organisms) and SNP detection within this assembly.
+This is the former miraEST program which was renamed as many people got
+confused regarding whether to use MIRA in est mode or miraEST.
+.PP
+miraSearchESTSNPs is a pipeline that reconstructs the pristine mRNA
+transcript sequences gathered in EST sequencing projects of more than
+one strain, which can be a reliable basis for subsequent analysis steps
+like clustering or exon analysis. This means that even genes that
+contain only one transcribed SNP on different alleles are first treated
+as different transcripts. The optional last step of the assembly process
+can be configured as a simple clusterer that can assemble transcripts
+containing the same exon sequence -- but only differ in SNP positions --
+into one consensus sequence. Such SNPs can then be analysed, classified
+and reliably assigned to their corresponding mRNA transcriptome
+sequence. However, it is important to note that miraSearchESTSNPs is an
+assembler and not a full blown clustering tool.
+.SH SYNOPSIS
+In version 3.9.17 this functionality is deactivated.
+.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.
Added: trunk/packages/mira/trunk/debian/mans/mirabait.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/mirabait.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/mirabait.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,131 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
+.TH MIRABAIT: "1" "August 2013" "MIRALIB version 3.9.18" "User Commands"
+.SH NAME
+mirabait \- select reads from a read collection
+.SH SYNOPSIS
+.B mirabait
+[\fI\-f <fromtype>\fR] [\fI\-t <totype> [\-t <totype> ...]\fR] [\fI\-iklor\fR] baitfile infile <basename_for_outfile(s)>
+.SH DESCRIPTION
+\fBmirabait\fR selects reads from a read collection which
+are partly similar or equal to sequences defined as target
+baits. Similarity is defined by finding a user-adjustable number of
+common k-mers (sequences of k consecutive bases) which are the same in
+the bait sequences and the screened sequences to be selected, either in forward
+or reverse complement direction.
+.SH OPTIONS
+.TP
+\fB\-f\fR <fromtype>
+load this type of project files, where fromtype is:
+.TP
+caf
+sequences from CAF
+.TP
+maf
+sequences from MAF
+.TP
+phd
+sequences from a PHD
+.TP
+gbf
+sequences from a GBF
+.TP
+fasta
+sequences from a FASTA
+.TP
+fastq
+sequences from a FASTQ
+.TP
+\fB\-t\fR <totype>
+write the sequences to this type (multiple mentions
+of \fB\-t\fR are allowed):
+.TP
+fasta
+sequences to FASTA
+.TP
+fastq
+sequences to FASTQ
+.TP
+caf
+sequences to CAF
+.TP
+maf
+sequences to MAF
+.TP
+txt
+sequence names to text file
+.TP
+\fB\-k\fR
+k\-mer, length of bait in bases (<32, default=31)
+.TP
+\fB\-n\fR
+Min. number of k\-mer baits needed (default=1)
+.TP
+\fB\-i\fR
+Inverse hit: writes only sequences that do not hit bait
+.TP
+\fB\-r\fR
+No checking of reverse complement direction
+.TP
+\fB\-o\fR
+fastq quality Offset (only for \fB\-f\fR = 'fastq')
+Offset of quality values in FASTQ file. Default: 33
+A value of 0 tries to automatically recognise.
+.TP
+\fB\-f\fR <fromtype>
+load this type of project files, where fromtype is:
+.TP
+caf
+sequences from CAF
+.TP
+maf
+sequences from MAF
+.TP
+phd
+sequences from a PHD
+.TP
+gbf
+sequences from a GBF
+.TP
+fasta
+sequences from a FASTA
+.TP
+fastq
+sequences from a FASTQ
+.TP
+\fB\-t\fR <totype>
+write the sequences to this type (multiple mentions
+of \fB\-t\fR are allowed):
+.TP
+fasta
+sequences to FASTA
+.TP
+fastq
+sequences to FASTQ
+.TP
+caf
+sequences to CAF
+.TP
+maf
+sequences to MAF
+.TP
+txt
+sequence names to text file
+.TP
+\fB\-k\fR
+k\-mer, length of bait in bases (<32, default=31)
+.TP
+\fB\-n\fR
+Min. number of k\-mer baits needed (default=1)
+.TP
+\fB\-i\fR
+Inverse hit: writes only sequences that do not hit bait
+.TP
+\fB\-r\fR
+No checking of reverse complement direction
+.TP
+\fB\-o\fR
+fastq quality Offset (only for \fB\-f\fR = 'fastq')
+Offset of quality values in FASTQ file. Default: 33
+A value of 0 tries to automatically recognise.
+.SH AUTHOR
+Bastien Chevreux (bach at chevreux.org)
Added: trunk/packages/mira/trunk/debian/mans/miraconvert.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/miraconvert.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/miraconvert.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,327 @@
+.TH MIRACONVERT "1" "December 2015" "miraconvert 4.9.5" "User Commands"
+.SH NAME
+miraconvert \- convert assembly and sequencing file types
+.SH SYNOPSIS
+.B miraconvert
+[\-f <fromtype>] [\-t <totype> [\-t <totype> ...]] [\-aAChimMsuZ] [\-cflnNoPqrtvxXyYz {...}] {infile} {outfile} [<totype> <totype> ...]
+.SH OPTIONS
+.TP
+\fB\-f\fR \fI<fromtype>\fR
+load this type of project files, where fromtype is:
+.IP
+\fIcaf\fR
+a complete assembly or single sequences from CAF
+.IP
+\fImaf\fR
+a complete assembly or single sequences from CAF
+.IP
+\fIfasta\fR
+sequences from a FASTA file
+.IP
+\fIfastq\fR
+sequences from a FASTQ file
+.IP
+\fIgb[f|k|ff]\fR
+sequences from a GenBank file
+.IP
+\fIphd\fR
+sequences from a PHD file
+.IP
+\fIfofnexp\fR
+sequences in EXP files from file of filenames
+.TP
+\fB\-t\fR \fI<totype>\fR
+write the sequences/assembly to this type (multiple
+mentions of \fB\-t\fR are allowed):
+.IP
+\fIace\fR
+sequences or complete assembly to ACE
+.IP
+\fIcaf\fR
+sequences or complete assembly to CAF
+.IP
+\fImaf\fR
+sequences or complete assembly to MAF
+.IP
+\fIsam\fR
+complete assembly to SAM
+.IP
+\fIsamnbb\fR
+like above, but leaving out reference (backbones) in mapping assemblies
+.IP
+\fIgb[f|k|ff]\fR
+sequences or consensus to GenBank
+.IP
+\fIgff3\fR
+consensus to GFF3
+.IP
+\fIwig\fR
+assembly coverage info to wiggle file
+.IP
+\fIgcwig\fR
+assembly gc content info to wiggle file
+.IP
+\fIfasta\fR
+sequences or consensus to FASTA file (qualities to \&.qual)
+.IP
+\fIfastq\fR
+sequences or consensus to FASTQ file
+.IP
+\fIexp\fR
+sequences or complete assembly to EXP files in
+directories. Complete assemblies are suited for gap4
+import as directed assembly.
+Note: using caf2gap to import into gap4 is recommended
+though
+.IP
+\fItext\fR
+complete assembly to text alignment (only when \fB\-f\fR is
+\fIcaf\fR, \fImaf\fR or \fIgbf\fR)
+.IP
+\fIhtml\fR
+complete assembly to HTML (only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR)
+.IP
+\fItcs\fR
+complete assembly to tcs
+.IP
+\fIhsnp\fR
+surrounding of SNP tags (SROc, SAOc, SIOc) to HTML
+(only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR)
+.IP
+\fIasnp\fR
+analysis of SNP tags
+(only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR)
+.IP
+\fIcstats\fR
+contig statistics file like from MIRA
+(only when source contains contigs)
+.IP
+\fIcrlist\fR
+contig read list file like from MIRA
+(only when source contains contigs)
+.IP
+\fImaskedfasta\fR
+reads where sequencing vector is masked out
+(with X) to FASTA file (qualities to .qual)
+.IP
+\fIscaf\fR
+sequences or complete assembly to single sequences CAF
+.TP
+\fB\-a\fR
+Append to target files instead of rewriting
+.TP
+\fB\-A\fR
+Do not Adjust sequence case
+.IP
+When reading formats which define clipping points,
+and saving to formats which do not have clipping
+information, miraconvert normally adjusts the case of
+read sequences: lower case for clipped parts, upper
+case for unclipped parts of reads.
+Use \fB\-A\fR if you do not want this. See also \fB\-C\fR.
+.IP
+Applies only to files/formats which do not contain
+contigs.
+.TP
+\fB\-b\fR
+Blind data
+.IP
+Replaces all bases in reads/contigs with a 'c'
+.TP
+\fB\-C\fR
+Perform hard clip to reads
+.IP
+When reading formats which define clipping points, will
+save only the unclipped part into the result file.
+.IP
+Applies only to files/formats which do not contain
+contigs.
+.TP
+\fB\-d\fR
+Delete gap only columns
+.IP
+When output is contigs: delete columns that are
+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 read groups to different files
+.IP
+Works only for input files with readgroups (CAF/MAF)
+3 (or 4) files generated: one or two for paired, one
+for unpaired and one for debris reads.
+.IP
+Reads in paired file are interlaced by default, use \fB\-F\fR
+twice to create separate files.
+.TP
+\fB\-m\fR
+Make contigs (only for \fB\-t\fR = \fIcaf\fR or \fImaf\fR)
+.IP
+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\-N\fR <filename>
+like \fB\-n\fR, but sorts output according to order given
+in file.
+.TP
+\fB\-i\fR
+when \fB\-n\fR is used, inverts the selection
+.TP
+\fB\-o\fR <quality>t
+FASTQ quality Offset (only for \fB\-f\fR = 'fastq')
+.IP
+Offset of quality values in FASTQ file. Default of 33
+loads Sanger/Phred style files, using 0 tries to
+automatically recognise.
+.TP
+\fB\-P\fR <string>
+String with MIRA parameters to be parsed
+.IP
+Useful when setting parameters affecting consensus
+calling like \fB\-CO\fR:mrpg etc.
+.IP
+E.g.: \fB\-P\fR "454_SETTINGS \fB\-CO\fR:mrpg=3"
+.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.
+.IP
+Known bug: will create duplicate names if input
+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.
+.TP
+\fB\-T\fR
+When converting single reads, trim/clip away stretches
+of N and X and ends of reads. Note: remember to use \fB\-C\fR to
+also perform a hard clip (e.g. with FASTA as output).
+.TP
+\fB\-v\fR
+Print version number and exit
+.TP
+\fB\-Y\fR <integer>
+Yield. Max (clipped/padded) bases to convert.
+.IP
+When used on reads: output will contain first reads of
+file where length of clipped bases totals at least \fB\-Y\fR.
+When used on contigs: output will contain first contigs
+of file where length of padded contigs totals at least
+\fB\-Y\fR.
+.P
+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
+sequence of the reads they are composed of.
+.TP
+\fB\-r\fR [\fIcCqf\fR]
+Recalculate consensus and / or consensus quality values
+and / or SNP feature tags.
+.IP
+\&'\fIc\fR' recalc cons & cons qualities (with IUPAC)
+.IP
+\&'\fIC\fR' recalc cons & cons qualities (forcing non\-IUPAC)
+.IP
+\&'\fIq\fR' recalc consensus qualities only
+.IP
+\&'\fIf\fR' recalc SNP features
+.IP
+Note: only the last of \fIcCq\fR is relevant, \fIf\fR works as a
+switch and can be combined with \fIcQq\fR (e.g. "\fB\-r\fR \fIC\fR \fB\-r\fR \fIf\fR")
+.IP
+Note: if the CAF/MAF contains multiple strains,
+recalculation of cons & cons qualities is forced, you
+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'
+.IP
+Fill holes in the genome of one strain (N or @)
+with sequence from a consensus of other strains
+.IP
+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
+.IP
+Only used with \fB\-r\fR, and \fB\-f\fR is caf/maf and \fB\-t\fR is (fasta
+or gbf)
+.TP
+\fB\-V\fR <integer>
+Defines minimum coverage a consensus base of a strain
+must have, bases with coverage below this will be 'N'
+Default: 0
+.IP
+Only used with \fB\-r\fR, and \fB\-t\fR is (fasta
+or gbf)
+.TP
+\fB\-x\fR <integer>
+Minimum contig or unclipped read length
+.IP
+When loading, discard all contigs / reads with a
+length less than this value. Default: 0 (=switched off)
+.IP
+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)
+.SH EXAMPLES
+.IP
+miraconvert source.maf dest.sam
+.IP
+miraconvert source.caf dest.fasta wig ace
+.IP
+miraconvert \-x 2000 \-y 10 source.caf dest.caf
+.IP
+miraconvert \-x 40 \-C \-F \-F source.maf .fastq
+.IP
+miraconvert: Missing infile and out\-basename as arguments!
+.SH AUTHOR
+The program \fBmiraconvert\fR was written by Bastien Chevreux <bach at chevreux.org>.
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/mira/trunk/debian/mans/miradiff.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/miradiff.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/miradiff.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,36 @@
+.TH MIRADIFF "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+miradiff \- diff two data sets of mira(1)
+.SH DESCRIPTION
+This program is part of the MIRA assembler package. Please check out the
+documentation below for more detailed information about miradiff.
+.SH SYNOPSIS
+miradiff
+[\fIOPTION\fR]
+.SH OPTIONS
+.TP
+\fB\-h\fR / \fB\-\-help\fR
+Print short help and exit
+.TP
+\fB\-v\fR / \fB\-\-version\fR
+Print version and exit
+.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.
Added: trunk/packages/mira/trunk/debian/mans/miramem.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/miramem.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/miramem.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,33 @@
+.TH MIRAMEM "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+miramem \- estimating needed memory for a MIRA assembly project
+.SH DESCRIPTION
+When called from the command line, it will ask a number of questions and
+then print out an estimate of the amount of RAM needed to assemble the
+project. Take this estimate with a grain of salt, depending on the
+sequences properties, variations in the estimate can be +/- 30% for
+bacteria and 'simple' eukaryotes. The higher the number of repeats is,
+the more likely you will need to restrict memory usage in some way or
+another.
+.SH SYNOPSIS
+miramem
+.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.
Added: trunk/packages/mira/trunk/debian/mans/miramer.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/miramer.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/miramer.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,36 @@
+.TH MIRAMER "1" "June 2013" "3.9.17" "User Commands"
+.SH NAME
+miramer \- handle k-mer statistics of a data set
+.SH DESCRIPTION
+This program is part of the MIRA assembler package. Please check out the
+documentation below for more detailed information about miramer.
+.SH SYNOPSIS
+miramer
+[\fIOPTION\fR]
+.SH OPTIONS
+.TP
+\fB\-h\fR / \fB\-\-help\fR
+Print short help and exit
+.TP
+\fB\-v\fR / \fB\-\-version\fR
+Print version and exit
+.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.
Added: trunk/packages/mira/trunk/debian/mans/scftool.1
===================================================================
--- trunk/packages/mira/trunk/debian/mans/scftool.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/mans/scftool.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,50 @@
+.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 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
+Usage of remix (when using PHD files as input for bases, quals and peaks):
+.IP
+scftool remix scf_infile phd_infile scf_outfile
+.PP
+Usage of remix (when using FASTA files as input for bases, quals and peaks):
+.IP
+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
+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/mira-assembler.manpages
===================================================================
--- trunk/packages/mira/trunk/debian/mira-assembler.manpages 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/mira-assembler.manpages 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1 +1 @@
-debian/*.1
+debian/mans/*.1
Added: trunk/packages/mira/trunk/debian/mira-examples.lintian-overrides
===================================================================
--- trunk/packages/mira/trunk/debian/mira-examples.lintian-overrides (rev 0)
+++ trunk/packages/mira/trunk/debian/mira-examples.lintian-overrides 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,3 @@
+# Exclude false positives that are verbose copies from upstream tarball
+mira-examples: package-contains-timestamped-gzip usr/share/doc/mira-examples/examples/minidemo/data/scf/*.scf.gz
+
Deleted: trunk/packages/mira/trunk/debian/mira.1
===================================================================
--- trunk/packages/mira/trunk/debian/mira.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/mira.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,53 +0,0 @@
-.TH 3.9.17 "1" "June 2013" "User Commands"
-.SH NAME
-mira \- The Genome and EST Sequence Assembly System
-.SH DESCRIPTION
-The mira genome fragment assembler is a specialised assembler for
-sequencing projects classified as 'hard' due to high number of similar
-repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
-specialised on reconstructing pristine mRNA transcripts while
-detecting and classifying single nucleotide polymorphisms (SNP)
-occuring in different variations thereof.
-.PP
-The assembler is routinely used for such various tasks as mutation
-detection in different cell types, similarity analysis of transcripts
-between organisms, and pristine assembly of sequences from various
-sources for oligo design in clinical microarray experiments.
-.PP
-The purpose of the \fBmira\fR executable is to assemble sequencing data.
-.SH SYNOPSIS
-mira
-[\fIOPTION\fR] manifest_file [\fImanifest_file\fR] ...
-.SH OPTIONS
-.TP
-\fB\-c\fR / \fB\-\-cwd=\fRdirectory
-Change working directory
-.TP
-\fB\-r\fR / \fB\-\-resume\fR
-Resume an interrupted assembly
-.TP
-\fB\-h\fR / \fB\-\-help\fR
-Print short help and exit
-.TP
-\fB\-v\fR / \fB\-\-version\fR
-Print version and exit
-.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.
Deleted: trunk/packages/mira/trunk/debian/miraSearchESTSNPs.1
===================================================================
--- trunk/packages/mira/trunk/debian/miraSearchESTSNPs.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/miraSearchESTSNPs.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,43 +0,0 @@
-.TH miraSearchESTSNPs "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-miraSearchESTSNPs \- Pipeline to discover SNPs in ESTs from different strains
-.SH DESCRIPTION
-The program miraSearchESTSNPs can be used for assembly of EST data from
-different strains (or organisms) and SNP detection within this assembly.
-This is the former miraEST program which was renamed as many people got
-confused regarding whether to use MIRA in est mode or miraEST.
-.PP
-miraSearchESTSNPs is a pipeline that reconstructs the pristine mRNA
-transcript sequences gathered in EST sequencing projects of more than
-one strain, which can be a reliable basis for subsequent analysis steps
-like clustering or exon analysis. This means that even genes that
-contain only one transcribed SNP on different alleles are first treated
-as different transcripts. The optional last step of the assembly process
-can be configured as a simple clusterer that can assemble transcripts
-containing the same exon sequence -- but only differ in SNP positions --
-into one consensus sequence. Such SNPs can then be analysed, classified
-and reliably assigned to their corresponding mRNA transcriptome
-sequence. However, it is important to note that miraSearchESTSNPs is an
-assembler and not a full blown clustering tool.
-.SH SYNOPSIS
-In version 3.9.17 this functionality is deactivated.
-.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.
Deleted: trunk/packages/mira/trunk/debian/mirabait.1
===================================================================
--- trunk/packages/mira/trunk/debian/mirabait.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/mirabait.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,131 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
-.TH MIRABAIT: "1" "August 2013" "MIRALIB version 3.9.18" "User Commands"
-.SH NAME
-mirabait \- select reads from a read collection
-.SH SYNOPSIS
-.B mirabait
-[\fI\-f <fromtype>\fR] [\fI\-t <totype> [\-t <totype> ...]\fR] [\fI\-iklor\fR] baitfile infile <basename_for_outfile(s)>
-.SH DESCRIPTION
-\fBmirabait\fR selects reads from a read collection which
-are partly similar or equal to sequences defined as target
-baits. Similarity is defined by finding a user-adjustable number of
-common k-mers (sequences of k consecutive bases) which are the same in
-the bait sequences and the screened sequences to be selected, either in forward
-or reverse complement direction.
-.SH OPTIONS
-.TP
-\fB\-f\fR <fromtype>
-load this type of project files, where fromtype is:
-.TP
-caf
-sequences from CAF
-.TP
-maf
-sequences from MAF
-.TP
-phd
-sequences from a PHD
-.TP
-gbf
-sequences from a GBF
-.TP
-fasta
-sequences from a FASTA
-.TP
-fastq
-sequences from a FASTQ
-.TP
-\fB\-t\fR <totype>
-write the sequences to this type (multiple mentions
-of \fB\-t\fR are allowed):
-.TP
-fasta
-sequences to FASTA
-.TP
-fastq
-sequences to FASTQ
-.TP
-caf
-sequences to CAF
-.TP
-maf
-sequences to MAF
-.TP
-txt
-sequence names to text file
-.TP
-\fB\-k\fR
-k\-mer, length of bait in bases (<32, default=31)
-.TP
-\fB\-n\fR
-Min. number of k\-mer baits needed (default=1)
-.TP
-\fB\-i\fR
-Inverse hit: writes only sequences that do not hit bait
-.TP
-\fB\-r\fR
-No checking of reverse complement direction
-.TP
-\fB\-o\fR
-fastq quality Offset (only for \fB\-f\fR = 'fastq')
-Offset of quality values in FASTQ file. Default: 33
-A value of 0 tries to automatically recognise.
-.TP
-\fB\-f\fR <fromtype>
-load this type of project files, where fromtype is:
-.TP
-caf
-sequences from CAF
-.TP
-maf
-sequences from MAF
-.TP
-phd
-sequences from a PHD
-.TP
-gbf
-sequences from a GBF
-.TP
-fasta
-sequences from a FASTA
-.TP
-fastq
-sequences from a FASTQ
-.TP
-\fB\-t\fR <totype>
-write the sequences to this type (multiple mentions
-of \fB\-t\fR are allowed):
-.TP
-fasta
-sequences to FASTA
-.TP
-fastq
-sequences to FASTQ
-.TP
-caf
-sequences to CAF
-.TP
-maf
-sequences to MAF
-.TP
-txt
-sequence names to text file
-.TP
-\fB\-k\fR
-k\-mer, length of bait in bases (<32, default=31)
-.TP
-\fB\-n\fR
-Min. number of k\-mer baits needed (default=1)
-.TP
-\fB\-i\fR
-Inverse hit: writes only sequences that do not hit bait
-.TP
-\fB\-r\fR
-No checking of reverse complement direction
-.TP
-\fB\-o\fR
-fastq quality Offset (only for \fB\-f\fR = 'fastq')
-Offset of quality values in FASTQ file. Default: 33
-A value of 0 tries to automatically recognise.
-.SH AUTHOR
-Bastien Chevreux (bach at chevreux.org)
Deleted: trunk/packages/mira/trunk/debian/miradiff.1
===================================================================
--- trunk/packages/mira/trunk/debian/miradiff.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/miradiff.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,36 +0,0 @@
-.TH MIRADIFF "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-miradiff \- diff two data sets of mira(1)
-.SH DESCRIPTION
-This program is part of the MIRA assembler package. Please check out the
-documentation below for more detailed information about miradiff.
-.SH SYNOPSIS
-miradiff
-[\fIOPTION\fR]
-.SH OPTIONS
-.TP
-\fB\-h\fR / \fB\-\-help\fR
-Print short help and exit
-.TP
-\fB\-v\fR / \fB\-\-version\fR
-Print version and exit
-.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.
Deleted: trunk/packages/mira/trunk/debian/miramem.1
===================================================================
--- trunk/packages/mira/trunk/debian/miramem.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/miramem.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,33 +0,0 @@
-.TH MIRAMEM "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-miramem \- estimating needed memory for a MIRA assembly project
-.SH DESCRIPTION
-When called from the command line, it will ask a number of questions and
-then print out an estimate of the amount of RAM needed to assemble the
-project. Take this estimate with a grain of salt, depending on the
-sequences properties, variations in the estimate can be +/- 30% for
-bacteria and 'simple' eukaryotes. The higher the number of repeats is,
-the more likely you will need to restrict memory usage in some way or
-another.
-.SH SYNOPSIS
-miramem
-.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.
Deleted: trunk/packages/mira/trunk/debian/miramer.1
===================================================================
--- trunk/packages/mira/trunk/debian/miramer.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/miramer.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,36 +0,0 @@
-.TH MIRAMER "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-miramer \- handle k-mer statistics of a data set
-.SH DESCRIPTION
-This program is part of the MIRA assembler package. Please check out the
-documentation below for more detailed information about miramer.
-.SH SYNOPSIS
-miramer
-[\fIOPTION\fR]
-.SH OPTIONS
-.TP
-\fB\-h\fR / \fB\-\-help\fR
-Print short help and exit
-.TP
-\fB\-v\fR / \fB\-\-version\fR
-Print version and exit
-.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/patches/series
===================================================================
--- trunk/packages/mira/trunk/debian/patches/series 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/patches/series 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1 +1,2 @@
fix_strange_link_issue.patch
+spelling.patch
Added: trunk/packages/mira/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/mira/trunk/debian/patches/spelling.patch (rev 0)
+++ trunk/packages/mira/trunk/debian/patches/spelling.patch 2015-12-04 12:24:43 UTC (rev 20629)
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 04 Dec 2015 12:15:04 +0100
+Description: Fix spelling
+ Remark: Lintian found another issue ressize -> resize but I can not find
+ this inside the code
+
+--- a/src/util/fileanddisk.C
++++ b/src/util/fileanddisk.C
+@@ -866,7 +866,7 @@ bool globWalkPath(string dn, list<fnft_t
+ getCanonicalFileAndZipType(tmptype,dummypathto,dummystem,overridetype,ziptype);
+ if(overridetype.empty()){
+ tmptype=tmptype.substr(1,999);
+- MIRANOTIFY(Notify::FATAL,"You tried to explicitely define a file type via " << tmptype << "::" << dn << ", however the type '" << tmptype << "' is not known to MIRA.");
++ MIRANOTIFY(Notify::FATAL,"You tried to explicitly define a file type via " << tmptype << "::" << dn << ", however the type '" << tmptype << "' is not known to MIRA.");
+ }
+ //cout << "###" << overridetype << "###\n";
+ }
Deleted: trunk/packages/mira/trunk/debian/scftool.1
===================================================================
--- trunk/packages/mira/trunk/debian/scftool.1 2015-12-04 12:22:55 UTC (rev 20628)
+++ trunk/packages/mira/trunk/debian/scftool.1 2015-12-04 12:24:43 UTC (rev 20629)
@@ -1,50 +0,0 @@
-.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 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
-Usage of remix (when using PHD files as input for bases, quals and peaks):
-.IP
-scftool remix scf_infile phd_infile scf_outfile
-.PP
-Usage of remix (when using FASTA files as input for bases, quals and peaks):
-.IP
-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
-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.
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