[med-svn] [snap-aligner] 01/01: ship docs; fix typo

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository snap-aligner.

commit 0c3107db637ee3a3dd28563641ad8d8caa5ebb27
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Tue Sep 29 20:09:52 2015 -0700

    ship docs; fix typo
---
 debian/doc-base.manual       | 16 ++++++++++++++++
 debian/doc-base.quickstart   | 16 ++++++++++++++++
 debian/docs                  |  3 +++
 debian/patches/finish-rename |  2 +-
 debian/rules                 |  4 ++++
 5 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/debian/doc-base.manual b/debian/doc-base.manual
new file mode 100644
index 0000000..8527746
--- /dev/null
+++ b/debian/doc-base.manual
@@ -0,0 +1,16 @@
+Document: snap-aligner-manual
+Title: Running SNAP: the snap-aligner manual
+Author: The SNAP team
+Abstract: Scalable Nucleotide Alignment Program
+ SNAP is a new sequence aligner that is 3-20x faster and just as accurate as
+ existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86
+ processors, and supports a rich error model that lets it cheaply match reads
+ with more differences from the reference than other tools. This gives SNAP up
+ to 2x lower error rates than existing tools (in some cases) and lets it match
+ larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or
+ gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting,
+ duplicate marking, and BAM indexing.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/snap-aligner/Manual.pdf.gz
diff --git a/debian/doc-base.quickstart b/debian/doc-base.quickstart
new file mode 100644
index 0000000..729e6ee
--- /dev/null
+++ b/debian/doc-base.quickstart
@@ -0,0 +1,16 @@
+Document: snap-aligner-quickstart
+Title: SNAP Quick Start: the snap-aligner quick start guide
+Author: The SNAP team
+Abstract: Scalable Nucleotide Alignment Program
+ SNAP is a new sequence aligner that is 3-20x faster and just as accurate as
+ existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86
+ processors, and supports a rich error model that lets it cheaply match reads
+ with more differences from the reference than other tools. This gives SNAP up
+ to 2x lower error rates than existing tools (in some cases) and lets it match
+ larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or
+ gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting,
+ duplicate marking, and BAM indexing.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/snap-aligner/QuickStart.pdf.gz
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..85e8190
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+docs/Manual.pdf
+docs/QuickStart.pdf
+README.md
diff --git a/debian/patches/finish-rename b/debian/patches/finish-rename
index 457f13d..b6156ad 100644
--- a/debian/patches/finish-rename
+++ b/debian/patches/finish-rename
@@ -50,7 +50,7 @@ Description: Change the name of program in docs
  {
  	WriteErrorMessage(
 -		"Usage: snap <command> [<options>]\n"
-+		"Usage: snap-alinger <command> [<options>]\n"
++		"Usage: snap-aligner <command> [<options>]\n"
  		"Commands:\n"
  		"   index    build a genome index\n"
  		"   single   align single-end reads\n"
diff --git a/debian/rules b/debian/rules
index 5511f2a..1b31a31 100755
--- a/debian/rules
+++ b/debian/rules
@@ -22,3 +22,7 @@ override_dh_auto_build:
 	help2man --no-discard-stderr --no-info --version-string="${VERSION}" \
 		--name "scalable nucleotide alignment program" \
 		--help-option=" " ./SNAPCommand > debian/SNAPCommand.1
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f debian/*.1

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