# HG changeset patch
# User peterjc
# Date 1416581038 18000
# Node ID d1fdfaae5dbe6c2ca87d6368cdb10987d9bd2933
# Parent  ca8f63f2f7d43ed2f22267ca559c734ba957c0e3
Uploaded v0.0.1b with warning about samtools 8000 coverage limit

diff -r ca8f63f2f7d4 -r d1fdfaae5dbe tools/coverage_stats/coverage_stats.xml
--- a/tools/coverage_stats/coverage_stats.xml	Fri Nov 21 09:28:29 2014 -0500
+++ b/tools/coverage_stats/coverage_stats.xml	Fri Nov 21 09:43:58 2014 -0500
@@ -75,6 +75,12 @@
 plus the final row (labelled with an asterisk) representing 950320 unmapped reads.
 In this BAM file, the fourth column was otherwise zero.
 
+.. class:: warningmark
+
+**Note**. There is an internal hard limit of 8000 for the pileup routine in
+samtools, meaning the reported coverage from ``samtools depth`` will show
+maximum coverage depths *around* 8000.
+
 
 **Citation**