[med-svn] [dazzdb] 07/10: Drop manpages and refer to README for program documentation
Afif Elghraoui
afif at moszumanska.debian.org
Wed Oct 12 09:04:24 UTC 2016
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 <afif at 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 <afif at 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
--
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