[med-svn] [SCM] tabix branch, master, updated. debian/0.2.4-1-7-gc2d7990

[Charles Plessy]

The following commit has been merged in the master branch:
commit 115f4508fb71ad7e60fa333ffe49de8c8d1bbd8c
Author: Charles Plessy <plessy at debian.org>
Date:   Tue May 10 19:13:26 2011 +0900

    Notes on how to test tabix.

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..a7b2e86
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,39 @@
+Notes on how to test tabix
+──────────────────────────
+
+The tabix package contains example data to test the tabix program.  It is
+already compressed and indexed.  The following instruction decompress,
+recompress, re-index and test the example data.
+
+# Create a temporary file
+TABIXDATA=$(mktemp)
+
+# Uncompress example data
+zcat /usr/share/doc/tabix/examples/example.gtf.gz > $TABIXDATA
+
+# Compress example data with bgzip
+bgzip $TABIXDATA
+
+# Index with tabix
+tabix $TABIXDATA.gz
+
+# Extract with tabix the he features on chromosome 1 whose coordinates overlap
+# the interval 150,309–150,309.
+tabix $TABIXDATA.gz chr1:150309-150309 > $TABIXDATA.out
+
+# Reference result at the bottom of this file
+grep H\AVANA /usr/share/doc/tabix/README.test > $TABIXDATA.ref
+
+# No difference ?
+diff $TABIXDATA.ref $TABIXDATA.out
+
+# Clean
+rm $TABIXDATA.gz $TABIXDATA.gz.tbi $TABIXDATA.out $TABIXDATA.ref
+
+ -- Charles Plessy <plessy at debian.org>  Tue, 10 May 2011 19:12:19 +0900
+
+
+
+chr1	HAVANA	exon	150309	150553	.	+	.	gene_id "ENSG00000241599"; transcript_id "ENST00000496488"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12-201"; level 2; havana_gene "OTTHUMG00000002525"; havana_transcript "OTTHUMT00000007169";
+chr1	HAVANA	gene	150309	151388	.	+	.	gene_id "ENSG00000241599"; transcript_id "ENSG00000241599"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12"; level 2; havana_gene "OTTHUMG00000002525";
+chr1	HAVANA	transcript	150309	151388	.	+	.	gene_id "ENSG00000241599"; transcript_id "ENST00000496488"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12-201"; level 2; havana_gene "OTTHUMG00000002525"; havana_transcript "OTTHUMT00000007169";
diff --git a/debian/docs b/debian/docs
index edc0071..c3f0f84 100644
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,2 @@
 NEWS
+debian/README.test

-- 
Generic indexer for TAB-delimited genome position files.