Notes on how to test tabix.

diff --git a/debian/README.test b/debian/README.test
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+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@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 edc00710471f58d7015469b1f7d9b1be59101cb6..c3f0f84c4053e218ce479f15eda977c552683b59 100644 (file)
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,2 @@
 NEWS
+debian/README.test