[med-svn] [last-align] 04/07: More manually written manpages

[Andreas Tille]

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tille pushed a commit to branch master
in repository last-align.

commit acf3a41e2171467c914dbbc6da20273980b87f64
Author: Andreas Tille <tille at debian.org>
Date:   Thu Dec 31 09:17:18 2015 +0100

    More manually written manpages
---
 debian/mans/last-map-probs.1 | 22 +++++++++++++++
 debian/mans/lastdb.1         | 64 ++++++++++++++++++++++++++++++++++++++++++++
 debian/rules                 | 16 ++++++-----
 3 files changed, 95 insertions(+), 7 deletions(-)

diff --git a/debian/mans/last-map-probs.1 b/debian/mans/last-map-probs.1
new file mode 100644
index 0000000..554d941
--- /dev/null
+++ b/debian/mans/last-map-probs.1
@@ -0,0 +1,22 @@
+.TH LAST-MAP-PROBS "1" "December 2015" "last-map-probs 712" "User Commands"
+.SH NAME
+last-map-probs \- Add extra column with mapping probabilities
+.SH SYNOPSIS
+.B last\-map\-probs
+[options] lastal\-alignments
+.SH DESCRIPTION
+Calculate a mismap probability for each alignment.  This is the probability
+that the alignment does not reflect the origin of the query sequence, assuming
+that one reported alignment does reflect the origin of each query.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-m\fR M, \fB\-\-mismap\fR=\fI\,M\/\fR
+don't write alignments with mismap probability > M
+(default: 0.01)
+.TP
+\fB\-s\fR S, \fB\-\-score\fR=\fI\,S\/\fR
+don't write alignments with score < S (default:
+e+t*ln[1000])
diff --git a/debian/mans/lastdb.1 b/debian/mans/lastdb.1
new file mode 100644
index 0000000..0c8b207
--- /dev/null
+++ b/debian/mans/lastdb.1
@@ -0,0 +1,64 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
+.TH LASTDB "1" "December 2015" "lastdb 712" "User Commands"
+.SH NAME
+lastdb \- genome-scale comparison of biological sequences
+.SH SYNOPSIS
+.B lastdb
+[\fI\,options\/\fR] \fI\,output-name fasta-sequence-file(s)\/\fR
+.SH DESCRIPTION
+Prepare sequences for subsequent alignment with lastal.
+.SH OPTIONS
+.SS Main Options
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show all options and their default settings, and exit
+.TP
+\fB\-p\fR
+interpret the sequences as proteins
+.TP
+\fB\-R\fR
+repeat\-marking options (default=10)
+.TP
+\fB\-c\fR
+soft\-mask lowercase letters
+.SS Advanced Options (default settings)
+.TP
+\fB\-Q\fR
+input format: 0=fasta, 1=fastq\-sanger, 2=fastq\-solexa, 3=fastq\-illumina (0)
+.TP
+\fB\-s\fR
+volume size (unlimited)
+.TP
+\fB\-m\fR
+seed pattern (non\-DNA: 1)
+.TP
+\fB\-u\fR
+seeding scheme (DNA: YASS)
+.TP
+\fB\-w\fR
+index step (1)
+.TP
+\fB\-a\fR
+user\-defined alphabet
+.TP
+\fB\-i\fR
+minimum limit on initial matches per query position (0)
+.TP
+\fB\-b\fR
+bucket depth
+.TP
+\fB\-C\fR
+child table type: 0=none, 1=byte\-size, 2=short\-size, 3=full (0)
+.TP
+\fB\-x\fR
+just count sequences and letters
+.TP
+\fB\-v\fR
+be verbose: write messages about what lastdb is doing
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+show version information, and exit
+.SH "REPORTING BUGS"
+Report bugs to: last\-align at googlegroups.com
+.br
+LAST home page: http://last.cbrc.jp/
diff --git a/debian/rules b/debian/rules
index c51a71a..61318c8 100755
--- a/debian/rules
+++ b/debian/rules
@@ -37,19 +37,21 @@ override_dh_auto_install:
 	         --name="genome-scale comparison of biological sequences" \
 	         --help-option="-h" \
                  $(CURDIR)/src/lastal > $(mandir)/lastal.1
-	$(HELP2MAN) \
-	         --name="genome-scale comparison of biological sequences" \
-	         --help-option="-h" \
-                 $(CURDIR)/src/lastdb > $(mandir)/lastdb.1
+        # help2man output needs manual postprocessing - see debian/mans
+	#$(HELP2MAN) \
+	#         --name="genome-scale comparison of biological sequences" \
+	#         --help-option="-h" \
+        #         $(CURDIR)/src/lastdb > $(mandir)/lastdb.1
 	$(HELP2MAN) \
                  --name="Sort MAF-format alignments by sequence name" \
                  $(CURDIR)/scripts/maf-sort > $(mandir)/maf-sort.1
 	$(HELP2MAN) \
                  --name="changes the order of the sequences in MAF-format alignments" \
                  $(CURDIR)/scripts/maf-swap > $(mandir)/maf-swap.1
-	$(HELP2MAN) \
-                 --name="Add extra column with mapping probabilities" \
-                 $(CURDIR)/scripts/last-map-probs > $(mandir)/last-map-probs.1
+        # help2man output needs manual postprocessing - see debian/mans
+	#$(HELP2MAN) \
+        #         --name="Add extra column with mapping probabilities" \
+        #         $(CURDIR)/scripts/last-map-probs > $(mandir)/last-map-probs.1
 	# This script has not enough to put in a manual page.
 	#$(HELP2MAN) \
         #         --name="Read files of lastal output, merge corresponding batches, and write them." \

-- 
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