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commit e52075ef6f505c56fd8c2c6316a87dc633b727a5 Author: Afif Elghraoui <[email protected]> Date: Fri Jan 8 21:35:18 2016 -0800 Add manpages for new executables --- debian/daligner-doc/LAdump.1.md | 52 ++++++++++++++++++++++++++++++++++++++++ debian/daligner-doc/LAindex.1.md | 27 +++++++++++++++++++++ 2 files changed, 79 insertions(+) diff --git a/debian/daligner-doc/LAdump.1.md b/debian/daligner-doc/LAdump.1.md new file mode 100644 index 0000000..709f8d9 --- /dev/null +++ b/debian/daligner-doc/LAdump.1.md @@ -0,0 +1,52 @@ +% LAdump(1) 1.0+20151214 +% +% January 2016 + +# NAME + +LAdump - display daligner local alignments in a simple format + +# SYNOPSIS + +**LAdump** [**-cdt**] [**-o**] *src1:db|dam* [ *src2:db|dam* ] + *align:las* [ *reads:FILE* | *reads:range* ... ] + +# DESCRIPTION + +Like **LAshow**(1), **LAdump** allows one to display the local alignments (LAs) of a subset of the +piles in an .las file and select which information to show about them. The difference +is that the information is written in a very simple "1-code" ASCII format that makes it +easy for one to read and parse the information for further use. For each LA the pair of +reads is output on a line. **-c** requests that one further output the coordinates of the +LA segments be output. The **-d** option requests that the number of difference in the LA +be output, and **-t** requests that the tracepoint information be output. Finally, **-o** +requests that only LAs that are proper overlaps be output. + +The format is very simple. Each requested piece of information occurs on a line. The +first character of every line is a "1-code" character that tells you what information +to expect on the line. The rest of the line contains information where each item is +separated by a single blank space. The trace point line gives the number of trace +point intervals in the LA and is immediately followed by that many lines containing +a pair of integers giving the # of differences and b-displacement in each successive +trace point interval. + + P #a #b - (#a,#b) have an LA between them + C #ab #ae #bb #be - [#ab,#ae] aligns with [#bb,#be] + D # - there are # differences in the LA + T #n - there are #n trace point intervals for the LA + (#d #y )^#n - there are #d difference aligning the #y bp's of B with the + next fixed-size interval of A + + X # - Total amount of X (X = P or T) + % X # - Maximum amount of X in any pile (X = P or T) + @ T # - Maximum number of trace points in any trace + +1-code lines that begin with +, %, or @ are always the first lines in the output. +They give size information about what is contained in the output. Specifically, +'+ X #' gives the total number of LAs (X=P), or the total number of trace point +intervals (X=T) in the file . '% X #' gives the maximum number of LAs (X=P) or +the maximum number of trace point intervals (X=T) in a given *pile* (collection of +LAs all with the same a-read (applies only to sorted .las files). Finally @ T # +gives the maximum # of trace point intervals in any trace within the file. + +# SEE ALSO +**daligner**(1) diff --git a/debian/daligner-doc/LAindex.1.md b/debian/daligner-doc/LAindex.1.md new file mode 100644 index 0000000..b583a0d --- /dev/null +++ b/debian/daligner-doc/LAindex.1.md @@ -0,0 +1,27 @@ +% LAindex(1) 1.0+20151214 +% +% January 2016 + +# NAME + +LAindex - index Daligner alignment files + +# SYNOPSIS + +**LAindex** **-v** *source:las* ... + +# DESCRIPTION + +**LAindex** takes a series of one or more sorted .las files and produces a "pile +index" for each one. If the input file has name *X.las*, then the name of its +index file is *.X.las.idx*. For each A-read pile encoded in the .las file, +the index contains the offset to the first local alignment with A in the file. +The index starts with four 64-bit integers that encode the numbers % P, + T, % T, +and @ T described for **LAdump**(1), and then an offset for each pile beginning +with the first A-read in the file (which may not be read 0). The index is meant +to allow programs that process piles to more efficiently read just the piles +they need at any momment int time, as opposed to having to sequentially scan +through the .las file. + +# SEE ALSO +**daligner**(1) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/daligner.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
