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 <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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 (b...@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 <b...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> +.PP +This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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 (b...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@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 <ti...@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_t...@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 <b...@chevreux.org> -.PP -This manual page was written by Andreas Tille <ti...@debian.org> but can be freely used for any other -distribution. _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit