[med-svn] r13855 - in trunk/packages/mira/trunk/debian: . patches
Thorsten Alteholz
alteholz at alioth.debian.org
Thu Jun 6 18:08:36 UTC 2013
Author: alteholz
Date: 2013-06-06 18:08:34 +0000 (Thu, 06 Jun 2013)
New Revision: 13855
Added:
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/mira-assembler.lintian-overrides
trunk/packages/mira/trunk/debian/mira-assembler.manpages
trunk/packages/mira/trunk/debian/mira-doc.doc-base
trunk/packages/mira/trunk/debian/miradiff.1
trunk/packages/mira/trunk/debian/miramer.1
trunk/packages/mira/trunk/debian/patches/spelling.patch
trunk/packages/mira/trunk/debian/scftool.1
Removed:
trunk/packages/mira/trunk/debian/patches/hardening-flags.patch
Modified:
trunk/packages/mira/trunk/debian/changelog
trunk/packages/mira/trunk/debian/control
trunk/packages/mira/trunk/debian/mira-doc.README.Debian
trunk/packages/mira/trunk/debian/patches/series
Log:
some progress on lintian complaints
Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog 2013-06-06 15:33:16 UTC (rev 13854)
+++ trunk/packages/mira/trunk/debian/changelog 2013-06-06 18:08:34 UTC (rev 13855)
@@ -6,14 +6,13 @@
* debian/control: DM-Upload-Allowed: removed
* debian/control: use dh 9
* debian/control: add dependency to libboost-iostreams-dev
+ * debian/control: improve extended descriptions
+ * debian/control: change VCS-tags according to new lintian
* debian/rules: get-orig-source added
* debian/watch: do not look at dev-versions
+ * debian/mira-doc.README.Debian: correct path to documentation
* TODO: lintian stuff: manpages
- spelling errors
- hardening flags for fastatool
- extended description
- docbase
- Up to now the new version builds with old gcc and old boost.
+ Up to now the new version builds with old gcc and old/new boost.
[ Dmitrijs Ledkovs ]
* Use dh-autoreconf
Modified: trunk/packages/mira/trunk/debian/control
===================================================================
--- trunk/packages/mira/trunk/debian/control 2013-06-06 15:33:16 UTC (rev 13854)
+++ trunk/packages/mira/trunk/debian/control 2013-06-06 18:08:34 UTC (rev 13855)
@@ -24,8 +24,8 @@
zlib1g-dev
Standards-Version: 3.9.4
Homepage: http://chevreux.org/projects_mira.html
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mira/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mira/trunk/
Package: mira-assembler
Architecture: any
@@ -74,7 +74,12 @@
Depends: ${misc:Depends}
Suggests: mira-assembler, mira-doc
Description: files to experiment with the mira assembler
- A series of files to exploit the functionality of mira.
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats.
+ .
+ This package contains a series of files to exploit the functionality
+ of mira.
Package: mira-doc
Section: doc
@@ -82,4 +87,8 @@
Depends: ${misc:Depends}
Suggests: mira-assembler
Description: documentation for the mira assembler
- An HTML book introducing to mira.
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats.
+ .
+ This package contains an HTML book introducing to mira.
Added: trunk/packages/mira/trunk/debian/convert_project.1
===================================================================
--- trunk/packages/mira/trunk/debian/convert_project.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/convert_project.1 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,554 @@
+.\" 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"
+.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
+[\-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.
+.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.
+.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
+.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
Added: trunk/packages/mira/trunk/debian/fasta2frag.1
===================================================================
--- trunk/packages/mira/trunk/debian/fasta2frag.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/fasta2frag.1 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,69 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.42.1.
+.TH FASTA2FRAG "1" "June 2013" "fasta2frag" "User Commands"
+.SH NAME
+.B fasta2frag \- splits a single fasta sequence into several overlapping fragments.
+.SH DESCRIPTION
+Usage:
+\fI<options> infile outfile\fR
+.TP
+\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
Added: trunk/packages/mira/trunk/debian/fastaselect.1
===================================================================
--- trunk/packages/mira/trunk/debian/fastaselect.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/fastaselect.1 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,19 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.42.1.
+.TH FASTASELECT "1" "June 2013" "fastaselect" "User Commands"
+.SH NAME
+.B fastaselect \- Select fasta sequences in a file according to names given
+.B in a name file.
+.SH DESCRIPTION
+Usage: fastaselect \fI<options>\fR
+.PP
+If fasta quality file is present (same basename, but with .qual appended),
+then also selects sequences from there.
+.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
Added: trunk/packages/mira/trunk/debian/fastatool.1
===================================================================
--- trunk/packages/mira/trunk/debian/fastatool.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/fastatool.1 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,19 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.42.1.
+.TH FASTATOOL "1" "June 2013" "fastatool" "User Commands"
+.SH NAME
+.B fastatool \- Provides a set of tools useful when working with FASTA files.
+.SH AUTHOR
+Written by Bastien Chevreux (bach at chevreux.org)
+.PP
+.SH "Usage:"
+.IP
+fastatool <toolname> <tool parameters>
+.SH "Available tools:"
+.TP
+clip
+Clip left and right parts of a FASTA sequence.
+.TP
+sanitize
+Deletes invalid sequences from FASTA files.
+.PP
+To get help on a specific tool, type 'fastatool <toolname>'. E.g.: fastatool cut
Added: trunk/packages/mira/trunk/debian/fastqselect.1
===================================================================
--- trunk/packages/mira/trunk/debian/fastqselect.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/fastqselect.1 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,15 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.42.1.
+.TH FASTQSELECT "1" "June 2013" "fastqselect" "User Commands"
+.SH NAME
+.B fastqselect \- Select fastq sequences in a file according to names given in a name file.
+.SH DESCRIPTION
+Usage: fastqselect \fI<options>\fR
+.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
Added: trunk/packages/mira/trunk/debian/mira-assembler.lintian-overrides
===================================================================
--- trunk/packages/mira/trunk/debian/mira-assembler.lintian-overrides (rev 0)
+++ trunk/packages/mira/trunk/debian/mira-assembler.lintian-overrides 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,6 @@
+# the CPPFLAGS are really used
+mira-assembler: hardening-no-fortify-functions usr/bin/fastatool
+# according to www.dict.cc transfering is American English spelling
+mira-assembler: spelling-error-in-binary usr/bin/mira Transfering Transferring
+mira-assembler: spelling-error-in-binary usr/bin/convert_project Transfering Transferring
+
Added: trunk/packages/mira/trunk/debian/mira-assembler.manpages
===================================================================
--- trunk/packages/mira/trunk/debian/mira-assembler.manpages (rev 0)
+++ trunk/packages/mira/trunk/debian/mira-assembler.manpages 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,8 @@
+debian/convert_project.1
+debian/fasta2frag.1
+debian/fastaselect.1
+debian/fastatool.1
+debian/fastqselect.1
+debian/miradiff.1
+debian/miramer.1
+debian/scftool.1
Modified: trunk/packages/mira/trunk/debian/mira-doc.README.Debian
===================================================================
--- trunk/packages/mira/trunk/debian/mira-doc.README.Debian 2013-06-06 15:33:16 UTC (rev 13854)
+++ trunk/packages/mira/trunk/debian/mira-doc.README.Debian 2013-06-06 18:08:34 UTC (rev 13855)
@@ -1,4 +1,4 @@
This package provides the Definitive Guide To MIRA book, which is included with
the default MIRA download, in HTML format.
-See: /usr/share/doc/mira/DefinitiveGuideToMIRA.html
+See: /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html
Added: trunk/packages/mira/trunk/debian/mira-doc.doc-base
===================================================================
--- trunk/packages/mira/trunk/debian/mira-doc.doc-base (rev 0)
+++ trunk/packages/mira/trunk/debian/mira-doc.doc-base 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,12 @@
+Document: mira-manual
+Title: Sequence assembly wirh mira3
+Author: Bastian Chevreux <bach at chevreux.org
+ Jacqueline Weber
+ Andrea Hoerster
+ Katrina Dlugosch
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/mira-assembler/*
+Index: /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html
+
Added: trunk/packages/mira/trunk/debian/miradiff.1
===================================================================
--- trunk/packages/mira/trunk/debian/miradiff.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/miradiff.1 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,21 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.42.1.
+.TH MIRADIFF "1" "June 2013" "miradiff 3.9.17 ()" "User Commands"
+.SH NAME
+miradiff \- manual page for version 3.9.17 ()
+.SH DESCRIPTION
+.PP
+mira MIRALIB version 3.9.17 ()
+.PP
+Author: Bastien Chevreux (bach at chevreux.org)
+.PP
+Purpose: diff two data sets
+.PP
+Usage:
+miradiff ...
+.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
Added: trunk/packages/mira/trunk/debian/miramer.1
===================================================================
--- trunk/packages/mira/trunk/debian/miramer.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/miramer.1 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,21 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.42.1.
+.TH MIRAMER "1" "June 2013" "miramer 3.9.17 ()" "User Commands"
+.SH NAME
+miramer \- manual page for version 3.9.17 ()
+.SH DESCRIPTION
+.PP
+mira MIRALIB version 3.9.17 ()
+.PP
+Author: Bastien Chevreux (bach at chevreux.org)
+.PP
+Purpose: diff two data sets
+.PP
+Usage:
+miramer ...
+.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
Deleted: trunk/packages/mira/trunk/debian/patches/hardening-flags.patch
===================================================================
--- trunk/packages/mira/trunk/debian/patches/hardening-flags.patch 2013-06-06 15:33:16 UTC (rev 13854)
+++ trunk/packages/mira/trunk/debian/patches/hardening-flags.patch 2013-06-06 18:08:34 UTC (rev 13855)
@@ -1,41 +0,0 @@
-Index: mira-3.9.17/src/progs/Makefile.in
-===================================================================
---- mira-3.9.17.orig/src/progs/Makefile.in 2013-05-21 20:17:52.000000000 +0200
-+++ mira-3.9.17/src/progs/Makefile.in 2013-06-05 15:58:01.000000000 +0200
-@@ -378,25 +378,29 @@
- rm -f $$list
- convert_project$(EXEEXT): $(convert_project_OBJECTS) $(convert_project_DEPENDENCIES) $(EXTRA_convert_project_DEPENDENCIES)
- @rm -f convert_project$(EXEEXT)
-- $(CXXLINK) $(convert_project_OBJECTS) $(convert_project_LDADD) $(LIBS)
-+ echo "XXX blubber $(LDFLAGS)"
-+ echo "XXX blubber $(CXXFLAGS)"
-+ echo "XXX blubber $(CPPFLAGS)"
-+ $(CXXLINK) $(LDFLAGS) $(convert_project_OBJECTS) $(convert_project_LDADD) $(LIBS)
-+ echo "XXX blubber ende"
- dbgreplay$(EXEEXT): $(dbgreplay_OBJECTS) $(dbgreplay_DEPENDENCIES) $(EXTRA_dbgreplay_DEPENDENCIES)
- @rm -f dbgreplay$(EXEEXT)
-- $(CXXLINK) $(dbgreplay_OBJECTS) $(dbgreplay_LDADD) $(LIBS)
-+ $(CXXLINK) $(LDFLAGS) $(dbgreplay_OBJECTS) $(dbgreplay_LDADD) $(LIBS)
- fastatool$(EXEEXT): $(fastatool_OBJECTS) $(fastatool_DEPENDENCIES) $(EXTRA_fastatool_DEPENDENCIES)
- @rm -f fastatool$(EXEEXT)
-- $(CXXLINK) $(fastatool_OBJECTS) $(fastatool_LDADD) $(LIBS)
-+ $(CXXLINK) $(LDFLAGS) $(fastatool_OBJECTS) $(fastatool_LDADD) $(LIBS)
- mira$(EXEEXT): $(mira_OBJECTS) $(mira_DEPENDENCIES) $(EXTRA_mira_DEPENDENCIES)
- @rm -f mira$(EXEEXT)
-- $(CXXLINK) $(mira_OBJECTS) $(mira_LDADD) $(LIBS)
-+ $(CXXLINK) $(LDFLAGS) $(mira_OBJECTS) $(mira_LDADD) $(LIBS)
- miramer$(EXEEXT): $(miramer_OBJECTS) $(miramer_DEPENDENCIES) $(EXTRA_miramer_DEPENDENCIES)
- @rm -f miramer$(EXEEXT)
-- $(CXXLINK) $(miramer_OBJECTS) $(miramer_LDADD) $(LIBS)
-+ $(CXXLINK) $(LDFLAGS) $(miramer_OBJECTS) $(miramer_LDADD) $(LIBS)
- miratest$(EXEEXT): $(miratest_OBJECTS) $(miratest_DEPENDENCIES) $(EXTRA_miratest_DEPENDENCIES)
- @rm -f miratest$(EXEEXT)
-- $(CXXLINK) $(miratest_OBJECTS) $(miratest_LDADD) $(LIBS)
-+ $(CXXLINK) $(LDFLAGS) $(miratest_OBJECTS) $(miratest_LDADD) $(LIBS)
- scftool$(EXEEXT): $(scftool_OBJECTS) $(scftool_DEPENDENCIES) $(EXTRA_scftool_DEPENDENCIES)
- @rm -f scftool$(EXEEXT)
-- $(CXXLINK) $(scftool_OBJECTS) $(scftool_LDADD) $(LIBS)
-+ $(CXXLINK) $(LDFLAGS) $(scftool_OBJECTS) $(scftool_LDADD) $(LIBS)
-
- mostlyclean-compile:
- -rm -f *.$(OBJEXT)
Modified: trunk/packages/mira/trunk/debian/patches/series
===================================================================
--- trunk/packages/mira/trunk/debian/patches/series 2013-06-06 15:33:16 UTC (rev 13854)
+++ trunk/packages/mira/trunk/debian/patches/series 2013-06-06 18:08:34 UTC (rev 13855)
@@ -1,4 +1,5 @@
xsltproc_nonet_for_doc_build
-hardening-flags.patch
add_shebang_lines
boost1.53
+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 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,67 @@
+Author: Thorsten Alteholz <debian at alteholz.de>
+Description: lintian complains about some spelling errors
+Index: mira-3.9.17/src/mira/assembly.C
+===================================================================
+--- mira-3.9.17.orig/src/mira/assembly.C 2013-05-21 20:10:33.000000000 +0200
++++ mira-3.9.17/src/mira/assembly.C 2013-06-06 11:20:57.000000000 +0200
+@@ -555,7 +555,7 @@
+ cerr << "\n\nOUCH! something strange ... tried more than 100 deletes of " << basename << " ... list size is " << AS_usedtmpfiles.size() << '\n';
+ }
+ if(numdeleted>1200) {
+- cerr << "\n\nOUCH! something wierd ... tried more than 1200 deletes of " << basename << " ... list size is " << AS_usedtmpfiles.size() << '\n';
++ cerr << "\n\nOUCH! something weird ... tried more than 1200 deletes of " << basename << " ... list size is " << AS_usedtmpfiles.size() << '\n';
+ cerr << "We'll stop that here.\n";
+ return numdeleted;
+ }
+Index: mira-3.9.17/src/mira/maf_parse.C
+===================================================================
+--- mira-3.9.17.orig/src/mira/maf_parse.C 2013-05-21 20:10:33.000000000 +0200
++++ mira-3.9.17/src/mira/maf_parse.C 2013-06-06 11:26:01.000000000 +0200
+@@ -985,7 +985,7 @@
+ MAF_read_seqtype=ReadGroupLib::stringToSeqType(actline);
+
+ if(MAF_read_seqtype==ReadGroupLib::SEQTYPE_END){
+- MIRANOTIFY(Notify::FATAL, "Error in " << MAF_read_name << " in tag " << acttoken << ": unkown sequencing type '" << actline << "'?");
++ MIRANOTIFY(Notify::FATAL, "Error in " << MAF_read_name << " in tag " << acttoken << ": unknown sequencing type '" << actline << "'?");
+ }
+ FUNCEND();
+ }
+Index: mira-3.9.17/src/progs/mira.C
+===================================================================
+--- mira-3.9.17.orig/src/progs/mira.C 2013-05-21 20:10:33.000000000 +0200
++++ mira-3.9.17/src/progs/mira.C 2013-06-06 11:20:16.000000000 +0200
+@@ -558,7 +558,7 @@
+ cout << "\nOptions:\n";
+ cout <<
+ " -c / --cwd=\t\tdirectory\tChange working directory\n"
+- " -r / --resume\t\t\t\tResume an interupted assembly\n"
++ " -r / --resume\t\t\t\tResume an interrupted assembly\n"
+ " -h / --help\t\t\t\tPrint short help and exit\n"
+ " -v / --version\t\t\tPrint version and exit\n"
+ ;
+Index: mira-3.9.17/src/io/gap4_ft_so_map.xxd
+===================================================================
+--- mira-3.9.17.orig/src/io/gap4_ft_so_map.xxd 2013-05-21 20:10:33.000000000 +0200
++++ mira-3.9.17/src/io/gap4_ft_so_map.xxd 2013-06-06 11:34:24.000000000 +0200
+@@ -46,7 +46,7 @@
+ Fm-R misc_RNA transcript SO:0000673 any transcript or RNA product that cannot be defined by other RNA keys (prim_transcript, precursor_RNA, mRNA, 5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS, sig_peptide, transit_peptide, mat_peptide, intron, polyA_site, rRNA, tRNA, scRNA, and snRNA); An RNA synthesized on a DNA or RNA template by an RNA polymerase.
+ Fm-b misc_binding binding_site SO:0000409 site in nucleic acid which covalently or non-covalently binds another moiety that cannot be described by any other binding key (primer_bind or protein_bind); A region on the surface of a molecule that may interact with another molecule.
+ Fm-d misc_difference sequence_difference SO:0000413 feature sequence is different from that presented in the entry and cannot be described by any other Difference key (conflict, unsure, old_sequence, variation, or modified_base); A region where the sequences differs from that of a specified sequence.
+-Fm-f misc_feature region SO:0000001 region of biological interest which cannot be described by any other feature key; a new or rare feature; Continous sequence.
++Fm-f misc_feature region SO:0000001 region of biological interest which cannot be described by any other feature key; a new or rare feature; Continuous sequence.
+ Fm-r misc_recomb recombination_feature SO:0000298 site of any generalized, site-specific or replicative recombination event where there is a breakage and reunion of duplex DNA that cannot be described by other recombination keys or qualifiers of source key (/insertion_seq, /transposon, /proviral);
+ Fm-S misc_signal regulatory_region SO:0005836 any region containing a signal controlling or altering gene function or expression that cannot be described by other signal keys (promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal, GC_signal, RBS, polyA_signal, enhancer, attenuator, terminator, and rep_origin). A DNA sequence that controls the expression of a gene.
+ Fm-s misc_structure sequence_secondary_structure SO:0000002 any secondary or tertiary nucleotide structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop); A folded sequence.
+Index: mira-3.9.17/src/mira/sam_collect.C
+===================================================================
+--- mira-3.9.17.orig/src/mira/sam_collect.C 2013-05-21 20:10:33.000000000 +0200
++++ mira-3.9.17/src/mira/sam_collect.C 2013-06-06 11:33:31.000000000 +0200
+@@ -445,7 +445,7 @@
+ SAMC_contiglengths.push_back(mafline.size());
+ }else if(maftoken==cpsEC){
+ if(actcontigid==0){
+- errorMsgMAFFormat(mafname,linenumber,mafline,"found EC token without preceeding CO token?");
++ errorMsgMAFFormat(mafname,linenumber,mafline,"found EC token without preceding CO token?");
+ }
+ actcontigid=0;
+ }else if(maftoken==cpsHReadGroupShort
Added: trunk/packages/mira/trunk/debian/scftool.1
===================================================================
--- trunk/packages/mira/trunk/debian/scftool.1 (rev 0)
+++ trunk/packages/mira/trunk/debian/scftool.1 2013-06-06 18:08:34 UTC (rev 13855)
@@ -0,0 +1,21 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.42.1.
+.TH SCFTOOL: "1" "June 2013" "scftool" "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)
+.PP
+.SH "Usage:"
+.IP
+scftool <toolname> <tool parameters>
+.SS "Available tools:"
+.IP
+convert Converts SCF file(s) to other formats.
+.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
+.IP
+peak values.
+.PP
+To get help on a specific tool, type 'scftool <toolname>'. E.g.: scftool remix
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