[med-svn] [last-align] 02/07: Add missing manpages

[Andreas Tille]

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

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

commit dcb550a527272f4e71c1313cdcefa9fb7e3f44f4
Author: Andreas Tille <tille at debian.org>
Date:   Thu Dec 31 08:59:41 2015 +0100

    Add missing manpages
---
 debian/changelog              |  1 +
 debian/manpages               |  1 +
 debian/mans/last-pair-probs.1 | 42 ++++++++++++++++++++++++++++++++++++++++++
 debian/rules                  | 26 ++++++++++++++++----------
 4 files changed, 60 insertions(+), 10 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 7c24be3..2dfe865 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,7 @@ last-align (712-1) UNRELEASED; urgency=medium
   [ Andreas Tille ]
   * New upstream version
   * Moved to Git
+  * Add missing manpages
 
   [ Julien Lamy ]
   * debian/rules:
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
diff --git a/debian/mans/last-pair-probs.1 b/debian/mans/last-pair-probs.1
new file mode 100644
index 0000000..7085735
--- /dev/null
+++ b/debian/mans/last-pair-probs.1
@@ -0,0 +1,42 @@
+.TH LAST-PAIR-PROBS "1" "December 2015" "last-pair-probs 712" "User Commands"
+.SH NAME
+last-pair-probs \- Read alignments of paired DNA reads to a genome, and do estimations
+.SH SYNOPSIS
+\fIlast\-pair\-probs\/\fP [options] interleaved\-alignments
+.P
+\fIlast\-pair\-probs\/\fP [options] alignments1 alignments2
+.SH DESCRIPTION
+Read alignments of paired DNA reads to a genome, and: (1) estimate the
+distribution of distances between paired reads, (2) estimate the probability
+that each alignment represents the genomic source of the read.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-r\fR, \fB\-\-rna\fR
+assume the reads are from potentially\-spliced RNA
+.TP
+\fB\-e\fR, \fB\-\-estdist\fR
+just estimate the distribution of distances
+.TP
+\fB\-m\fR M, \fB\-\-mismap\fR=\fI\,M\/\fR
+don't write alignments with mismap probability > M
+(default: 0.01)
+.TP
+\fB\-f\fR BP, \fB\-\-fraglen\fR=\fI\,BP\/\fR
+mean distance in bp
+.TP
+\fB\-s\fR BP, \fB\-\-sdev\fR=\fI\,BP\/\fR
+standard deviation of distance
+.TP
+\fB\-d\fR PROB, \fB\-\-disjoint\fR=\fI\,PROB\/\fR
+prior probability of disjoint mapping (default: 0.02
+if \fB\-r\fR, else 0.01)
+.TP
+\fB\-c\fR CHROM, \fB\-\-circular\fR=\fI\,CHROM\/\fR
+specifies that chromosome CHROM is circular (default:
+chrM)
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+show program's version number and exit
diff --git a/debian/rules b/debian/rules
index 6fc3e29..c51a71a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -41,10 +41,6 @@ override_dh_auto_install:
 	         --name="genome-scale comparison of biological sequences" \
 	         --help-option="-h" \
                  $(CURDIR)/src/lastdb > $(mandir)/lastdb.1
-#	$(HELP2MAN) \
-#		 --name="Calculate expected numbers of alignments for random sequences." \
-#	         --help-option="-h" \
-#                 $(CURDIR)/src/lastex > $(mandir)/lastex.1
 	$(HELP2MAN) \
                  --name="Sort MAF-format alignments by sequence name" \
                  $(CURDIR)/scripts/maf-sort > $(mandir)/maf-sort.1
@@ -74,12 +70,22 @@ override_dh_auto_install:
 	$(HELP2MAN) \
                  --name="Convert MAF-format alignments to tabular format" \
                  $(CURDIR)/scripts/maf-convert > $(mandir)/maf-convert.1
-#	$(HELP2MAN) \
-#                 --name="Cull alignments whose top\-sequence coordinates are contained in LIMIT or more" \
-#                 $(CURDIR)/scripts/maf-cull > $(mandir)/maf-cull.1
-#	$(HELP2MAN) \
-#                 --name="Read alignments of paired DNA reads to a genome" \
-#                 $(CURDIR)/scripts/last-pair-probs > $(mandir)/last-pair-probs.1
+	$(HELP2MAN) \
+                 --name="Read 2 fastq files, and write them interleaved" \
+                 $(CURDIR)/scripts/fastq-interleave > $(mandir)/fastq-interleave.1
+	$(HELP2MAN) \
+                 --name="Read files of lastal output, merge corresponding batches, and write them" \
+                 $(CURDIR)/src/last-merge-batches > $(mandir)/last-merge-batches.1
+        # help2man output needs manual postprocessing - see debian/mans
+	#$(HELP2MAN) \
+        #         --name="Read alignments of paired DNA reads to a genome, and do estimations" \
+        #         $(CURDIR)/src/last-pair-probs > $(mandir)/last-pair-probs.1
+	$(HELP2MAN) \
+                 --name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \
+                 $(CURDIR)/scripts/last-postmask > $(mandir)/last-postmask.1
+	$(HELP2MAN) \
+                 --name="Try to find suitable score parameters for aligning the given sequences" \
+                 $(CURDIR)/scripts/last-train > $(mandir)/last-train.1
 
 override_dh_installchangelogs:
 	dh_installchangelogs ChangeLog.txt

-- 
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