[med-svn] [blat] 03/03: All command line tools now have manpages

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository blat.

commit 3866c08dc42cb1895bd7609239085a42fee67569
Author: Andreas Tille <tille at debian.org>
Date:   Mon Mar 3 13:19:59 2014 +0100

    All command line tools now have manpages
---
 debian/mans/pslReps.1    | 54 ++++++++++++++++++++++++++++++++++++++++++++++++
 debian/mans/pslSort.1    | 40 +++++++++++++++++++++++++++++++++++
 debian/mans/twoBitInfo.1 | 29 ++++++++++++++++++++++++++
 debian/mans/twoBitToFa.1 | 42 +++++++++++++++++++++++++++++++++++++
 4 files changed, 165 insertions(+)

diff --git a/debian/mans/pslReps.1 b/debian/mans/pslReps.1
new file mode 100644
index 0000000..47f8969
--- /dev/null
+++ b/debian/mans/pslReps.1
@@ -0,0 +1,54 @@
+.TH PSLREPS "1" "February 2014" "pslReps 35" "User Commands"
+.SH NAME
+pslReps \- analyse repeats and generate genome wide best
+.SH SYNOPSIS
+.B pslReps
+in.psl out.psl out.psr
+.SH DESCRIPTION
+.P
+Blat is an alignment tool like BLAST, but it is structured differently.
+The target database of BLAT is not  a  set  of  GenBank  sequences,  but
+instead an index derived from the assembly of the entire genome.
+.P
+The command line tool \fBpslReps\fR analyses repeats and generates genome
+wide best alignments from a sorted set of local alignments
+.SH OPTIONS
+.HP
+\fBin.psl\fR is an alignment file generated by psLayout and
+sorted by \fBpslSort\fR
+.HP
+\fBout.psl\fR is the best alignment output
+.HP
+\fBout.psr\fR contains repeat info
+.HP
+\fB\-nohead\fR don't add PSL header
+.HP
+\fB\-ignoreSize\fR Will not weigh in favor of larger alignments so much
+.HP
+\fB\-noIntrons\fR Will not penalize for not having introns when calculating
+size factor
+.TP
+\fB\-singleHit\fR
+Takes single best hit, not splitting into parts
+.TP
+\fB\-minCover\fR=\fI0\fR.N minimum coverage to output.
+Default is 0.
+.HP
+\fB\-ignoreNs\fR Ignore 'N's when calculating minCover.
+.HP
+\fB\-minAli\fR=\fI0\fR.N minimum alignment ratio
+.IP
+default is 0.93
+.HP
+\fB\-nearTop\fR=\fI0\fR.N how much can deviate from top and be taken
+.IP
+default is 0.01
+.TP
+\fB\-minNearTopSize\fR=\fIN\fR
+Minimum size of alignment that is near top for alignment to be kept.
+.IP
+Default 30.
+.TP
+\fB\-coverQSizes\fR=\fIfile\fR Tab\-separate file with effective query sizes.
+When used with \fB\-minCover\fR, this allows polyAs
+to be excluded from the coverage calculation
diff --git a/debian/mans/pslSort.1 b/debian/mans/pslSort.1
new file mode 100644
index 0000000..f980f3d
--- /dev/null
+++ b/debian/mans/pslSort.1
@@ -0,0 +1,40 @@
+.TH PSLSORT "1" "February 2014" "pslSort 35" "User Commands"
+.SH NAME
+pslSort \- merge and sort psCluster .psl output files
+.SH SYNOPSIS
+.B pslSort
+dirs[1|2] outFile tempDir inDir(s)
+.P
+.B pslSort
+g2g[1|2] outFile tempDir inDir(s)
+.SH DESCRIPTION
+.P
+Blat is an alignment tool like BLAST, but it is structured differently.
+The target database of BLAT is not  a  set  of  GenBank  sequences,  but
+instead an index derived from the assembly of the entire genome.
+.P
+The command line tool \fBpslSort\fR merges and sorts psCluster .psl output files
+.SH OPTIONS
+.P
+The command
+.IP
+\fBpslSort\fR dirs[1|2] outFile tempDir inDir(s)
+.P
+will sort all of the .psl files in the directories
+inDirs in two stages \- first into temporary files in tempDir
+and second into outFile.  The device on tempDir needs to have
+enough space (typically 15\-20 gigabytes if processing whole genome)
+.P
+The command
+.IP
+\fBpslSort\fR g2g[1|2] outFile tempDir inDir(s)
+.PP
+will sort a genome to genome alignment, reflecting the
+alignments across the diagonal.
+.PP
+Adding 1 or 2 after the dirs or g2g will limit the program to
+only the first or second pass respectively of the sort
+.HP
+\fB\-nohead\fR \- do not write psl header:
+.HP
+\fB\-verbose\fR=\fIN\fR Set verbosity level, higher for more output. Default 1
diff --git a/debian/mans/twoBitInfo.1 b/debian/mans/twoBitInfo.1
new file mode 100644
index 0000000..1802d75
--- /dev/null
+++ b/debian/mans/twoBitInfo.1
@@ -0,0 +1,29 @@
+.TH TWOBITINFO "1" "February 2014" "twoBitInfo 35" "User Commands"
+.SH NAME
+twoBitInfo \- get information about sequences in a .2bit file
+.SH SYNOPSIS
+.B twoBitInfo
+input.2bit output.tab
+.SH DESCRIPTION
+.P
+Blat is an alignment tool like BLAST, but it is structured differently.
+The target database of BLAT is not  a  set  of  GenBank  sequences,  but
+instead an index derived from the assembly of the entire genome.
+.P
+The command line tool \fBtwoBitInfo\fR gets information about sequences
+in a .2bit file.
+.SH OPTIONS
+.TP
+\fB\-nBed\fR
+instead of seq sizes, output BED records that define
+areas with N's in sequence
+.TP
+\fB\-noNs\fR
+outputs the length of each sequence, but does not count Ns
+.SS "Output file has the columns::"
+.IP
+seqName size
+.PP
+The 2bit file may be specified in the form path:seq or path:seq1,seq2,seqN...
+so that information is returned only on the requested sequence(s).
+If the form path:seq:start\-end is used, start\-end is ignored.
diff --git a/debian/mans/twoBitToFa.1 b/debian/mans/twoBitToFa.1
new file mode 100644
index 0000000..b332a36
--- /dev/null
+++ b/debian/mans/twoBitToFa.1
@@ -0,0 +1,42 @@
+.TH TWOBITTOFA "1" "February 2014" "twoBitToFa 35" "User Commands"
+.SH NAME
+twoBitToFa \- convert all or part of .2bit file to fasta
+.SH SYNOPSIS
+.B twoBitToFa
+input.2bit output.fa
+.SH DESCRIPTION
+.P
+Blat is an alignment tool like BLAST, but it is structured differently.
+The target database of BLAT is not  a  set  of  GenBank  sequences,  but
+instead an index derived from the assembly of the entire genome.
+.P
+The command line tool \fBtwoBitToFa\fR converts all or part of .2bit file to fasta
+.SH OPTIONS
+.HP
+\fB\-seq\fR=\fIname\fR \- restrict this to just one sequence
+.HP
+\fB\-start\fR=\fIX\fR  \- start at given position in sequence (zero\-based)
+.HP
+\fB\-end\fR=\fIX\fR \- end at given position in sequence (non\-inclusive)
+.TP
+\fB\-seqList\fR=\fIfile\fR \- file containing list of the desired sequence names
+in the format seqSpec[:start\-end], e.g. chr1 or chr1:0\-189
+where coordinates are half\-open zero\-based, i.e. [start,end)
+.HP
+\fB\-noMask\fR \- convert sequence to all upper case
+.HP
+\fB\-bpt\fR=\fIindex\fR.bpt \- use bpt index instead of built in one
+.HP
+\fB\-bed\fR=\fIinput\fR.bed \- grab sequences specified by input.bed. Will exclude introns
+Sequence and range may also be specified as part of the input
+file name using the syntax:
+.IP
+\fI/path/input\fP.2bit:name
+.IP
+or
+.IP
+\fI/path/input\fP.2bit:name
+.IP
+or
+.IP
+\fI/path/input\fP.2bit:name:start\-end

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