This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository dazzdb.
commit 8c52c1a37b9d7b683a7ff133fde99bd98f664828 Author: Afif Elghraoui <a...@debian.org> Date: Tue Oct 11 21:41:02 2016 -0700 Drop manpages and refer to README for program documentation They are too time-intensive to maintain without upstream support. All the work is to re-apply changes to the README to the individual pages. --- debian/control | 1 - debian/man/Catrack.1.md | 22 --------------------- debian/man/DAM2fasta.1.md | 25 ------------------------ debian/man/DB2fasta.1.md | 27 -------------------------- debian/man/DB2quiva.1.md | 25 ------------------------ debian/man/DBdust.1.md | 34 -------------------------------- debian/man/DBrm.1.md | 21 -------------------- debian/man/DBshow.1.md | 48 ---------------------------------------------- debian/man/DBsplit.1.md | 30 ----------------------------- debian/man/DBstats.1.md | 25 ------------------------ debian/man/Makefile | 12 ------------ debian/man/dazzdb.1 | 11 +++++++++++ debian/man/dsimulator.1.md | 39 ------------------------------------- debian/man/fasta2DAM.1.md | 24 ----------------------- debian/man/fasta2DB.1.md | 28 --------------------------- debian/man/quiva2DB.1.md | 25 ------------------------ debian/rules | 15 ++++++++------- 17 files changed, 19 insertions(+), 393 deletions(-) diff --git a/debian/control b/debian/control index 42b91d6..a9e3bcd 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,6 @@ Uploaders: Afif Elghraoui <a...@debian.org> Section: science Priority: optional Build-Depends: debhelper (>= 9), - pandoc Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/dazzdb.git Vcs-Git: https://anonscm.debian.org/git/debian-med/dazzdb.git diff --git a/debian/man/Catrack.1.md b/debian/man/Catrack.1.md deleted file mode 100644 index 2d5fdc3..0000000 --- a/debian/man/Catrack.1.md +++ /dev/null @@ -1,22 +0,0 @@ -% CATRACK(1) 1.0 -% -% September 2015 - -# NAME - -Catrack - merge dazzler block tracks - -# SYNOPSIS - -**Catrack** [**-v**] *path:db|dam* *track:name* - -# DESCRIPTION - -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. - -# SEE ALSO - -**daligner**(1) diff --git a/debian/man/DAM2fasta.1.md b/debian/man/DAM2fasta.1.md deleted file mode 100644 index 8ec9a87..0000000 --- a/debian/man/DAM2fasta.1.md +++ /dev/null @@ -1,25 +0,0 @@ -% DAM2FASTA(1) 1.0 -% -% September 2015 - -# NAME - -DAM2fasta - get fasta files from Dazzler map DB - -# 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 - -**daligner**(1) diff --git a/debian/man/DB2fasta.1.md b/debian/man/DB2fasta.1.md deleted file mode 100644 index acb8fab..0000000 --- a/debian/man/DB2fasta.1.md +++ /dev/null @@ -1,27 +0,0 @@ -% 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 deleted file mode 100644 index 2323f9d..0000000 --- a/debian/man/DB2quiva.1.md +++ /dev/null @@ -1,25 +0,0 @@ -% DB2QUIVA(1) 1.0 -% -% September 2015 - -# NAME - -DB2quiva - get .quiva files from a Dazzler database - -# 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. - -# SEE ALSO - -**daligner**(1) diff --git a/debian/man/DBdust.1.md b/debian/man/DBdust.1.md deleted file mode 100644 index bb73a79..0000000 --- a/debian/man/DBdust.1.md +++ /dev/null @@ -1,34 +0,0 @@ -% DBDUST(1) 1.0 -% -% September 2015 - -# NAME - -DBdust - description - -# SYNOPSIS - -**DBdust** [**-b**] [**-w***int(64)*] [**-t***double(2.)*] [**-m***int(10)*] *path:db|dam* - -# DESCRIPTION - -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**(1), **DBstats**(1), and **daligner**(1). - -**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. - -# SEE ALSO - -**daligner**(1) diff --git a/debian/man/DBrm.1.md b/debian/man/DBrm.1.md deleted file mode 100644 index 05d0688..0000000 --- a/debian/man/DBrm.1.md +++ /dev/null @@ -1,21 +0,0 @@ -% DBRM(1) 1.0 -% -% September 2015 - -# NAME - -DBrm - delete a Dazzler database - -# SYNOPSIS - -**DBrm** *path:db|dam* ... - -# DESCRIPTION - -Delete all the files for the given databases. 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**. - -# SEE ALSO - -**daligner**(1) diff --git a/debian/man/DBshow.1.md b/debian/man/DBshow.1.md deleted file mode 100644 index cb54c8c..0000000 --- a/debian/man/DBshow.1.md +++ /dev/null @@ -1,48 +0,0 @@ -% DBSHOW(1) 1.0 -% -% September 2015 - -# NAME - -DBshow - display reads stored in a Dazzler database - -# SYNOPSIS - -**DBshow** [**-unqUQ**] [**-w***int(80)*] [**-m***track*]+ - *path:db|dam* [ *reads:FILE* | *reads:range* ... ] - -# DESCRIPTION - -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 may 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**(1) -and **quiva2DB**(1) (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. - -# SEE ALSO - -**daligner**(1) diff --git a/debian/man/DBsplit.1.md b/debian/man/DBsplit.1.md deleted file mode 100644 index 769b6db..0000000 --- a/debian/man/DBsplit.1.md +++ /dev/null @@ -1,30 +0,0 @@ -% DBSPLIT(1) 1.0 -% -% September 2015 - -# NAME - -DBsplit - divide a Dazzler database into a series of blocks - -# SYNOPSIS - -**DBsplit** [**-a**] [**-x***int*] [**-s***int(200)*] *path:db|dam* - -# DESCRIPTION - -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" **daligner**(1) 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. - -# SEE ALSO - -**daligner**(1) diff --git a/debian/man/DBstats.1.md b/debian/man/DBstats.1.md deleted file mode 100644 index 6f041ec..0000000 --- a/debian/man/DBstats.1.md +++ /dev/null @@ -1,25 +0,0 @@ -% DBSTATS(1) 1.0 -% -% September 2015 - -# NAME - -DBstats - show statistics for reads in a Dazzler database - -# SYNOPSIS - -**DBstats** [**-nu**] [**-b***int(1000)*] [**-m***track*]+ *path:db|dam* - -# DESCRIPTION - -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 histogram of read lengths -is not displayed. Any track such as a "dust" track that gives a series 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. - -# SEE ALSO - -**daligner**(1) diff --git a/debian/man/Makefile b/debian/man/Makefile deleted file mode 100644 index 7733e1b..0000000 --- a/debian/man/Makefile +++ /dev/null @@ -1,12 +0,0 @@ - -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/dazzdb.1 b/debian/man/dazzdb.1 new file mode 100644 index 0000000..fc450b2 --- /dev/null +++ b/debian/man/dazzdb.1 @@ -0,0 +1,11 @@ +.TH DAZZDB 1 "October 2016" +.SH NAME +dazzdb \- manage nucleotide sequencing read data for the Dazzler assembler +.SH DESCRIPTION +To facilitate the multiple phases of the dazzler assembler, all the read data +is organized into what is effectively a database of the +reads and their meta-information. +.SH OPTIONS +For a complete description of available commands and their options, see /usr/share/doc/dazzdb/README.md +.SH SEE ALSO +.BR daligner (1) diff --git a/debian/man/dsimulator.1.md b/debian/man/dsimulator.1.md deleted file mode 100644 index 66fe0a9..0000000 --- a/debian/man/dsimulator.1.md +++ /dev/null @@ -1,39 +0,0 @@ -% DSIMULATOR(1) 1.0 -% -% September 2015 - -# NAME - -dsimulator - generate synthetic reads for a random genome - -# SYNOPSIS - -**dsimulator** *genlen:double* [**-c***double(20.)*] [**-b***double(.5)*] - [**-r***int*] [**-m***int(10000)*] [**-s***int(2000)*] - [**-x***int(4000)*] [**-e***double(.15)*] - [**-M***file*] - -# DESCRIPTION - -**dsimulator** 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**(1). 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 - -**daligner**(1) diff --git a/debian/man/fasta2DAM.1.md b/debian/man/fasta2DAM.1.md deleted file mode 100644 index 582235a..0000000 --- a/debian/man/fasta2DAM.1.md +++ /dev/null @@ -1,24 +0,0 @@ -% FASTA2DAM(1) 1.0 -% -% September 2015 - -# NAME - -fasta2DAM - build a Dazzler map database from fasta files - -# 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. - -# SEE ALSO - -**DAM2fasta**(1) -**daligner**(1) diff --git a/debian/man/fasta2DB.1.md b/debian/man/fasta2DB.1.md deleted file mode 100644 index 1d06db6..0000000 --- a/debian/man/fasta2DB.1.md +++ /dev/null @@ -1,28 +0,0 @@ -% 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 deleted file mode 100644 index aa0d368..0000000 --- a/debian/man/quiva2DB.1.md +++ /dev/null @@ -1,25 +0,0 @@ -% QUIVA2DB(1) 1.0 -% -% September 2015 - -# NAME - -quiva2DB - add .quiva files to a Dazzler database - -# 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/rules b/debian/rules index 6064931..9bd03af 100755 --- a/debian/rules +++ b/debian/rules @@ -11,10 +11,11 @@ CFLAGS := $(CPPFLAGS) $(CFLAGS) %: dh $@ --parallel -override_dh_auto_build: - dh_auto_build - $(MAKE) -C debian/man - -override_dh_auto_clean: - dh_auto_clean - $(MAKE) -C debian/man clean +override_dh_auto_install: + dh_auto_install + mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1 + for command in $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/*; \ + do \ + ln -s dazzdb.1 \ + $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/$$(basename $$command).1; \ + done -- 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