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commit a4e0884de3568954a4e470b4153706ad2ece0732 Author: Afif Elghraoui <a...@ghraoui.name> Date: Sun Sep 13 22:38:34 2015 -0700 Create manpage stubs from README contents --- debian/man/Catrack.1.md | 20 ++++++++++++++++++++ debian/man/DAM2fasta.1.md | 21 +++++++++++++++++++++ debian/man/DB2fasta.1.md | 27 +++++++++++++++++++++++++++ debian/man/DB2quiva.1.md | 24 ++++++++++++++++++++++++ debian/man/DBdust.1.md | 32 ++++++++++++++++++++++++++++++++ debian/man/DBrm.1.md | 19 +++++++++++++++++++ debian/man/DBshow.1.md | 46 ++++++++++++++++++++++++++++++++++++++++++++++ debian/man/DBsplit.1.md | 28 ++++++++++++++++++++++++++++ debian/man/DBstats.1.md | 23 +++++++++++++++++++++++ debian/man/Makefile | 12 ++++++++++++ debian/man/fasta2DAM.1.md | 21 +++++++++++++++++++++ debian/man/fasta2DB.1.md | 28 ++++++++++++++++++++++++++++ debian/man/quiva2DB.1.md | 25 +++++++++++++++++++++++++ debian/man/simulator.1.md | 37 +++++++++++++++++++++++++++++++++++++ 14 files changed, 363 insertions(+) diff --git a/debian/man/Catrack.1.md b/debian/man/Catrack.1.md new file mode 100644 index 0000000..41adc6a --- /dev/null +++ b/debian/man/Catrack.1.md @@ -0,0 +1,20 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +# DESCRIPTION + +Catrack [-v] <path:db|dam> <track:name> + +Find all block tracks of the form .<path>.#.<track>... and merge them into a single +track, .<path>.<track>..., for the given DB or DAM. The block track files must all +encode the same kind of track data (this is checked), and the files must exist for +block 1, 2, 3, ... up to the last block number. + +# OPTIONS + +# SEE ALSO diff --git a/debian/man/DAM2fasta.1.md b/debian/man/DAM2fasta.1.md new file mode 100644 index 0000000..aaac72c --- /dev/null +++ b/debian/man/DAM2fasta.1.md @@ -0,0 +1,21 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +DAM2fasta [-vU] [-w<int(80)>] <path:dam> + +# DESCRIPTION + +The set of .fasta files for the given map DB or DAM are recreated from the DAM +exactly as they were input. That is, this is a perfect inversion, including the +reconstitution of the proper .fasta headers and the concatenation of contigs with +the proper number of N's between them. By default the output sequences are in lower +case and 80 chars per line. The -U option specifies upper case should be used, and +the characters per line, or line width, can be set to any positive value with +the -w option. + +# SEE ALSO diff --git a/debian/man/DB2fasta.1.md b/debian/man/DB2fasta.1.md new file mode 100644 index 0000000..acb8fab --- /dev/null +++ b/debian/man/DB2fasta.1.md @@ -0,0 +1,27 @@ +% DB2FASTA(1) 1.0 +% +% September 2015 + +# NAME + +DB2fasta - create fasta files from a Dazzler database + +# SYNOPSIS + +**DB2fasta** [**-vU**] [**-w***int(80)*] *path:db* + +# DESCRIPTION + +The set of .fasta files for the given DB are recreated from the DB exactly as +they were input. That is, this is a perfect inversion, including the +reconstitution of the proper .fasta headers. Because of this property, one can, +if desired, delete the .fasta source files once they are in the DB as they can +always be recreated from it. By default the output sequences are in lower case +and 80 chars per line. The **-U** option specifies upper case should be used, +and the characters per line, or line width, can be set to any positive value +with the **-w** option. + +# SEE ALSO + +**daligner**(1) +**fasta2DB**(1) diff --git a/debian/man/DB2quiva.1.md b/debian/man/DB2quiva.1.md new file mode 100644 index 0000000..4b1a03b --- /dev/null +++ b/debian/man/DB2quiva.1.md @@ -0,0 +1,24 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +DB2quiva [-vU] <path:db> + +# DESCRIPTION + +The set of .quiva files within the given DB are recreated from the DB exactly as they +were input. That is, this is a perfect inversion, including the reconstitution of the +proper .quiva headers. Because of this property, one can, if desired, delete the +.quiva source files once they are in the DB as they can always be recreated from it. +By .fastq convention each QV vector is output as a line without new-lines, and by +default the Deletion Tag entry is in lower case letters. The -U option specifies +upper case letters should be used instead. + + +# OPTIONS + +# SEE ALSO diff --git a/debian/man/DBdust.1.md b/debian/man/DBdust.1.md new file mode 100644 index 0000000..383707d --- /dev/null +++ b/debian/man/DBdust.1.md @@ -0,0 +1,32 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +# DESCRIPTION + +DBdust [-b] [-w<int(64)>] [-t<double(2.)>] [-m<int(10)>] <path:db|dam> + +Runs the symmetric DUST algorithm over the reads in the untrimmed DB <path>.db or +<path>.dam producing a track .<path>.dust[.anno,.data] that marks all intervals of low +complexity sequence, where the scan window is of size -w, the threshold for being a +low-complexity interval is -t, and only perfect intervals of size greater than -m are +recorded. If the -b option is set then the definition of low complexity takes into +account the frequency of a given base. The command is incremental if given a DB to +which new data has been added since it was last run on the DB, then it will extend +the track to include the new reads. It is important to set this flag for genomes with +a strong AT/GC bias, albeit the code is a tad slower. The dust track, if present, +is understood and used by DBshow, DBstats, and dalign. + +DBdust can also be run over an untriimmed DB block in which case it outputs a track +encoding where the trace file names contain the block number, e.g. .FOO.3.dust.anno +and .FOO.3.dust.data, given FOO.3 on the command line. We call this a *block track*. +This permits job parallelism in block-sized chunks, and the resulting sequence of +block tracks can then be merged into a track for the entire untrimmed DB with Catrack. + +# OPTIONS + +# SEE ALSO diff --git a/debian/man/DBrm.1.md b/debian/man/DBrm.1.md new file mode 100644 index 0000000..c923cd9 --- /dev/null +++ b/debian/man/DBrm.1.md @@ -0,0 +1,19 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +# DESCRIPTION + +DBrm <path:db|dam> ... + +Delete all the files for the given data bases. Do not use **rm**(1) to remove a database, as +there are at least two and often several secondary files for each DB including track +files, and all of these are removed by DBrm. + +# OPTIONS + +# SEE ALSO diff --git a/debian/man/DBshow.1.md b/debian/man/DBshow.1.md new file mode 100644 index 0000000..c163fa9 --- /dev/null +++ b/debian/man/DBshow.1.md @@ -0,0 +1,46 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +# DESCRIPTION + +DBshow [-unqUQ] [-w<int(80)>] [-m<track>]+ + <path:db|dam> [ <reads:FILE> | <reads:range> ... ] + +Displays the requested reads in the database <path>.db or <path>.dam. By default the +command applies to the trimmed database, but if -u is set then the entire DB is used. +If no read arguments are given then every read in the database or database block is +displayed. Otherwise the input file or the list of supplied integer ranges give the +ordinal positions in the actively loaded portion of the db. In the case of a file, it +should simply contain a read index, one per line. In the other case, a read range is +either a lone integer or the symbol $, in which case the read range consists of just +that read (the last read in the database if $). One may also give two positive +integers separated by a dash to indicate a range of integers, where again a $ +represents the index of the last read in the actively loaded db. For example, +1 3-5 $ displays reads 1, 3, 4, 5, and the last read in the active db. As another +example, 1-$ displays every read in the active db (the default). + +By default a .fasta file of the read sequences is displayed. If the -q option is +set, then the QV streams are also displayed in a non-standard modification of the +fasta format. If the -n option is set then the DNA sequence is *not* displayed. +If the -Q option is set then a .quiva file is displayed and in this case the -n +and -m options mayt not be set (and the -q and -w options have no effect). + +If one or more masks are set with the -m option then the track intervals are also +displayed in an additional header line and the bases within an interval are displayed +in the case opposite that used for all the other bases. By default the output +sequences are in lower case and 80 chars per line. The -U option specifies upper +case should be used, and the characters per line, or line width, can be set to any +positive value with the -w option. + +The .fasta or .quiva files that are output can be converted into a DB by fasta2DB +and quiva2DB (if the -q and -n options are not set and no -m options are set), +giving one a simple way to make a DB of a subset of the reads for testing purposes. + +# OPTIONS + +# SEE ALSO diff --git a/debian/man/DBsplit.1.md b/debian/man/DBsplit.1.md new file mode 100644 index 0000000..2a60e26 --- /dev/null +++ b/debian/man/DBsplit.1.md @@ -0,0 +1,28 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +# DESCRIPTION + + DBsplit [-a] [-x<int>] [-s<int(200)>] <path:db|dam> + +Divide the database <path>.db or <path>.dam conceptually into a series of blocks +referable to on the command line as <path>.1, <path>.2, ... If the -x option is set +then all reads less than the given length are ignored, and if the -a option is not +set then secondary reads from a given well are also ignored. The remaining reads, +constituting what we call the trimmed DB, are split amongst the blocks so that each +block is of size -s * 1Mbp except for the last which necessarily contains a smaller +residual. The default value for -s is 200Mbp because blocks of this size can be +compared by our "overlapper" dalign in roughly 16Gb of memory. The blocks are very +space efficient in that their sub-index of the master .idx is computed on the fly +when loaded, and the .bps and .qvs files (if a .db) of base pairs and quality values, +respectively, is shared with the master DB. Any relevant portions of tracks +associated with the DB are also computed on the fly when loading a database block. + +# OPTIONS + +# SEE ALSO diff --git a/debian/man/DBstats.1.md b/debian/man/DBstats.1.md new file mode 100644 index 0000000..c240a33 --- /dev/null +++ b/debian/man/DBstats.1.md @@ -0,0 +1,23 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +# DESCRIPTION + +DBstats [-nu] [-b<int(1000)] [-m<track>]+ <path:db|dam> + +Show overview statistics for all the reads in the trimmed data base <path>.db or +<path>.dam, including a histogram of read lengths where the bucket size is set +with the -b option (default 1000). If the -u option is given then the untrimmed +database is summarized. If the -n option is given then the histogran of read lengths +is not displayed. Any track such as a "dust" track that gives a seried of +intervals along the read can be specified with the -m option in which case a summary +and a histogram of the interval lengths is displayed. + +# OPTIONS + +# SEE ALSO diff --git a/debian/man/Makefile b/debian/man/Makefile new file mode 100644 index 0000000..7733e1b --- /dev/null +++ b/debian/man/Makefile @@ -0,0 +1,12 @@ + +MANPAGES = $(basename $(wildcard *.1.md)) + +all: $(MANPAGES) + +%.1: %.1.md + pandoc -s -f markdown -t man $< > $@ + +clean: + $(RM) $(MANPAGES) + +.PHONY: clean diff --git a/debian/man/fasta2DAM.1.md b/debian/man/fasta2DAM.1.md new file mode 100644 index 0000000..2b64f93 --- /dev/null +++ b/debian/man/fasta2DAM.1.md @@ -0,0 +1,21 @@ +% (1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +fasta2DAM [-v] <path:dam> ( -f<file> | <input:fasta> ... ) + +# DESCRIPTION + +Builds a map DB or DAM from the list of .fasta files following the map database name +argument, or if the -f option is used, the list of .fasta files in <file>. Any .fasta +entry that has a run of N's in it will be split into separate "contig" entries and +the interval of the contig in the original entry recorded. The header for each .fasta +entry is saved with the contigs created from it. + +# OPTIONS + +# SEE ALSO diff --git a/debian/man/fasta2DB.1.md b/debian/man/fasta2DB.1.md new file mode 100644 index 0000000..c1d8713 --- /dev/null +++ b/debian/man/fasta2DB.1.md @@ -0,0 +1,28 @@ +% FASTA2DB(1) 1.0 +% +% September 2015 + +# NAME + +fasta2DB - create a Dazzler database from fasta files + +# SYNOPSIS + +**fasta2DB** [**-v**] *path:db* {**-f***file* | *input:fasta* ...} + +# DESCRIPTION + +Builds an initial database, or adds to an existing database, the list of +.fasta files following the database name argument, or if the **-f** option is +used, the list of .fasta files in *file*. A given .fasta file can only be +added once to the DB (this is checked by the command). The .fasta headers must +be in the "Pacbio" format (i.e. the output of the Pacbio tools or our +**dextract**(1) program) and the well, pulse interval, and read quality are +extracted from the header and kept with each read record. If the files are +being added to an existing database, and the partition settings of the DB have +already been set (see **DBsplit**(1)), then the partitioning of the database +is updated to include the new data. + +# SEE ALSO + +**daligner**(1) diff --git a/debian/man/quiva2DB.1.md b/debian/man/quiva2DB.1.md new file mode 100644 index 0000000..4d46eef --- /dev/null +++ b/debian/man/quiva2DB.1.md @@ -0,0 +1,25 @@ +% QUIVA2DB(1) 1.0 +% +% September 2015 + +# NAME + +quiva2DB - + +# SYNOPSIS + +**quiva2DB** [**-vl**] *path:db* (**-f***file* | **input:quiva** ... ) + +# DESCRIPTION + +Adds the given .quiva files on the command line or in the file specified by the +**-f** option to an existing DB "path". The input files must be added in the +same order as the .fasta files were and have the same root names, +e.g. FOO.fasta and FOO.quiva. The files can be added incrementally but must be +added in the same order as the .fasta files. This is enforced by the program. +With the **-l** option set the compression scheme is a bit lossy to get more +compression (see the description of dexqv in the DEXTRACTOR module). + +# SEE ALSO + +**daligner**(1) diff --git a/debian/man/simulator.1.md b/debian/man/simulator.1.md new file mode 100644 index 0000000..aec8a14 --- /dev/null +++ b/debian/man/simulator.1.md @@ -0,0 +1,37 @@ +% SIMULATOR(1) 1.0 +% +% September 2015 + +# NAME + +# SYNOPSIS + +# DESCRIPTION + +simulator <genlen:double> [-c<double(20.)>] [-b<double(.5)] [-r<int>] + [-m<int(10000)>] [-s<int(2000)>] + [-x<int(4000)>] [-e<double(.15)>] + [-M<file>] + +In addition to the DB commands we include here, somewhat tangentially, a simple +simulator that generates synthetic reads for a random genome. simulator first +generates a fake genome of size genlen*1Mb long, that has an AT-bias of -b. It then +generates sample reads of mean length -m from a log-normal length distribution with +standard deviation -s, but ignores reads of length less than -x. It collects enough +reads to cover the genome -c times and introduces -e fraction errors into each read +where the ratio of insertions, deletions, and substitutions are set by defined +constants INS_RATE (default 73%) and DEL_RATE (default 20%) within generate.c. One +can also control the rate at which reads are picked from the forward and reverse +strands by setting the defined constant FLIP_RATE (default 50/50). The -r option seeds +the random number generator for the generation of the genome so that one can +reproducibly generate the same underlying genome to sample from. If this parameter is +missing, then the job id of the invocation seeds the random number generator. The +output is sent to the standard output (i.e. it is a UNIX pipe). The output is in +Pacbio .fasta format suitable as input to fasta2DB. Finally, the -M option requests +that the coordinates from which each read has been sampled are written to the indicated +file, one line per read, ASCII encoded. This "map" file essentially tells one where +every read belongs in an assembly and is very useful for debugging and testing +purposes. If a read pair is say b,e then if b < e the read was sampled from [b,e] in +the forward direction, and if b > e from [e,b] in the reverse direction. + +# SEE ALSO -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/dazzdb.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit