[med-svn] r21052 - trunk/packages/aegean/trunk/debian/man

Sat Jan 9 13:34:36 UTC 2016

Author: sascha-guest
Date: 2016-01-09 13:34:35 +0000 (Sat, 09 Jan 2016)
New Revision: 21052

Added:
   trunk/packages/aegean/trunk/debian/man/tidygff3.1
Modified:
   trunk/packages/aegean/trunk/debian/man/canon-gff3.1
   trunk/packages/aegean/trunk/debian/man/gaeval.1
   trunk/packages/aegean/trunk/debian/man/locuspocus.1
   trunk/packages/aegean/trunk/debian/man/parseval.1
   trunk/packages/aegean/trunk/debian/man/pmrna.1
   trunk/packages/aegean/trunk/debian/man/xtractore.1
Log:
update man pages


Modified: trunk/packages/aegean/trunk/debian/man/canon-gff3.1
===================================================================

--- trunk/packages/aegean/trunk/debian/man/canon-gff3.1	2016-01-09 12:30:37 UTC (rev 21051)
+++ trunk/packages/aegean/trunk/debian/man/canon-gff3.1	2016-01-09 13:34:35 UTC (rev 21052)
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH CANON-GFF3 "1" "July 2015" "canon-gff3 0.13" "User Commands"
+.TH CANON-GFF3 "1" "January 2016" "canon-gff3 0.15.1" "User Commands"
 .SH NAME
 canon-gff3 \- create canonical GFF3
 .SH SYNOPSIS

Modified: trunk/packages/aegean/trunk/debian/man/gaeval.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/gaeval.1	2016-01-09 12:30:37 UTC (rev 21051)
+++ trunk/packages/aegean/trunk/debian/man/gaeval.1	2016-01-09 13:34:35 UTC (rev 21052)
@@ -1,12 +1,11 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH GAEVAL "1" "July 2015" "gaeval 0.13" "User Commands"
+.TH GAEVAL "1" "January 2016" "gaeval 0.15.1" "User Commands"
 .SH NAME
 gaeval \- calculate coverage and intergrity scores for gene models based on transcript alignments
 .SH SYNOPSIS
 .B gaeval
 [\fI\,options\/\fR] \fI\,alignments.gff3 genes.gff3 \/\fR[\fI\,moregenes.gff3 \/\fR...]
 .SH DESCRIPTION
-.IP
 Basic options:
 .TP
 \fB\-h\fR|\-\-help

Modified: trunk/packages/aegean/trunk/debian/man/locuspocus.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/locuspocus.1	2016-01-09 12:30:37 UTC (rev 21051)
+++ trunk/packages/aegean/trunk/debian/man/locuspocus.1	2016-01-09 13:34:35 UTC (rev 21052)
@@ -1,12 +1,11 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH LOCUSPOCUS "1" "July 2015" "locuspocus 0.13" "User Commands"
+.TH LOCUSPOCUS "1" "January 2016" "locuspocus 0.15.1" "User Commands"
 .SH NAME
 locuspocus \- calculate locus coordinates for the given gene annotation
 .SH SYNOPSIS
 .B locuspocus
 [\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 gff3file3 \/\fR...]
 .SH DESCRIPTION
-.IP
 Basic options:
 .TP
 \fB\-d\fR|\-\-debug
@@ -27,19 +26,37 @@
 regulatory regions; default is 500
 .TP
 \fB\-s\fR|\-\-skipends
-when enumerating interval loci, exclude gene\-less
-iLoci at either end of the sequence
+when enumerating interval loci, exclude
+unannotated (and presumably incomplete) iLoci at
+either end of the sequence
 .TP
 \fB\-e\fR|\-\-endsonly
-report only empty iLoci at the ends of sequences
-(complement of \fB\-\-skipends\fR)
+report only incomplete iLocus fragments at the
+unannotated ends of sequences (complement of
+\fB\-\-skipends\fR)
 .TP
-\fB\-y\fR|\-\-skipempty
-do not report empty iLoci
+\fB\-y\fR|\-\-skipiiloci
+do not report intergenic iLoci
 .IP
+Refinement options:
+.TP
+\fB\-r\fR|\-\-refine
+by default genes are grouped in the same iLocus
+if they have any overlap; 'refine' mode allows
+for a more nuanced handling of overlapping genes
+.TP
+\fB\-c\fR|\-\-cds
+use CDS rather than UTRs for determining gene
+overlap; implies 'refine' mode
+.TP
+\fB\-m\fR|\-\-minoverlap: INT
+the minimum number of nucleotides two genes must
+overlap to be grouped in the same iLocus; default
+is 1
+.IP
 Output options:
 .TP
-\fB\-I\fR|\-\-idformat: STR
+\fB\-n\fR|\-\-namefmt: STR
 provide a printf\-style format string to override
 the default ID format for newly created loci;
 default is 'locus%lu' (locus1, locus2, etc) for
@@ -48,6 +65,10 @@
 include a single %lu specifier to be filled in
 with a long unsigned integer value
 .TP
+\fB\-i\fR|\-\-ilens: FILE
+create a file with the lengths of each intergenic
+iLocus
+.TP
 \fB\-g\fR|\-\-genemap: FILE
 print a mapping from each gene annotation to its
 corresponding locus to the given file
@@ -56,6 +77,11 @@
 name of file to which results will be written;
 default is terminal (standard output)
 .TP
+\fB\-T\fR|\-\-retainids
+retain original feature IDs from input files;
+conflicts will arise if input contains duplicated
+ID values
+.TP
 \fB\-t\fR|\-\-transmap: FILE
 print a mapping from each transcript annotation
 to its corresponding locus to the given file

Modified: trunk/packages/aegean/trunk/debian/man/parseval.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/parseval.1	2016-01-09 12:30:37 UTC (rev 21051)
+++ trunk/packages/aegean/trunk/debian/man/parseval.1	2016-01-09 13:34:35 UTC (rev 21052)
@@ -1,12 +1,11 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH PARSEVAL "1" "July 2015" "parseval 0.13" "User Commands"
+.TH PARSEVAL "1" "January 2016" "parseval 0.15.1" "User Commands"
 .SH NAME
 parseval \- comparative analysis of two alternative sources of annotation
 .SH SYNOPSIS
 .B parseval
 [\fI\,options\/\fR] \fI\,reference.gff3 prediction.gff3\/\fR
 .SH DESCRIPTION
-.IP
 Basic options:
 .TP
 \fB\-d\fR|\-\-debug:
@@ -47,9 +46,9 @@
 File/directory to which output will be
 written; default is the terminal (STDOUT)
 .TP
-\fB\-p\fR|\-\-png:
-Generate individual PNG graphics for each
-gene locus (HTML mode only)
+\fB\-p\fR|\-\-nopng:
+In HTML output mode, skip generation of PNG
+graphics for each gene locus
 .TP
 \fB\-s\fR|\-\-summary:
 Only print summary statistics, do not print

Modified: trunk/packages/aegean/trunk/debian/man/pmrna.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/pmrna.1	2016-01-09 12:30:37 UTC (rev 21051)
+++ trunk/packages/aegean/trunk/debian/man/pmrna.1	2016-01-09 13:34:35 UTC (rev 21052)
@@ -1,12 +1,11 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH PMRNA "1" "July 2015" "pmrna 0.13" "User Commands"
+.TH PMRNA "1" "January 2016" "pmrna 0.15.1" "User Commands"
 .SH NAME
 pmrna \- filter out all but the primary isoform from each gene of the input
 .SH SYNOPSIS
 .B pmrna
 [\fI\,options\/\fR] \fI\,< annot.gff3 > new.gff3\/\fR
 .SH DESCRIPTION
-.IP
 Options:
 .TP
 \fB\-h\fR|\-\-help

Added: trunk/packages/aegean/trunk/debian/man/tidygff3.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/tidygff3.1	                        (rev 0)
+++ trunk/packages/aegean/trunk/debian/man/tidygff3.1	2016-01-09 13:34:35 UTC (rev 21052)
@@ -0,0 +1,11 @@
+.TH TIDYGFF3 "1" "January 2016" "tidygff3 0.15.1" "User Commands"
+.SH NAME
+tidygff3 \- tidy GFF3 file
+.SH SYNOPSIS
+.B tidygff3
+<
+.IR features.gff3
+.SH DESCRIPTION
+.IP
+Cleans up GFF3 format files read from stdin for further use in AEGeAn by
+printing the clean version on stdout.
\ No newline at end of file

Modified: trunk/packages/aegean/trunk/debian/man/xtractore.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/xtractore.1	2016-01-09 12:30:37 UTC (rev 21051)
+++ trunk/packages/aegean/trunk/debian/man/xtractore.1	2016-01-09 13:34:35 UTC (rev 21052)
@@ -1,14 +1,16 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH XTRACTORE "1" "July 2015" "xtractore 0.13" "User Commands"
+.TH XTRACTORE "1" "January 2016" "xtractore 0.15.1" "User Commands"
 .SH NAME
 xtractore \- extract sequences corresponding to annotated features from the given sequence file
 .SH SYNOPSIS
 .B xtractore
 [\fI\,options\/\fR] \fI\,features.gff3 sequences.fasta\/\fR
 .SH DESCRIPTION
-.IP
 Options:
 .TP
+\fB\-d\fR|\-\-debug
+print debugging output
+.TP
 \fB\-h\fR|\-\-help
 print this help message and exit
 .TP


