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 (b...@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 (b...@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 <b...@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 (b...@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 (b...@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 <deb...@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 (b...@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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit