[med-svn] [daligner] 05/09: Add manpages for new executables

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
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commit e52075ef6f505c56fd8c2c6316a87dc633b727a5
Author: Afif Elghraoui <afif at ghraoui.name>
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)

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