# HG changeset patch
# User devteam
# Date 1426711430 14400
# Node ID c04bee391baad824c4843e7dc66fda0cc7580163
Uploaded
diff -r 000000000000 -r c04bee391baa macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Mar 18 16:43:50 2015 -0400
@@ -0,0 +1,21 @@
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+ samtools
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+ 10.1093/bioinformatics/btp352
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+ samtools --version | head -n 1 | awk '{ print $2 }'
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diff -r 000000000000 -r c04bee391baa samtools_bedcov.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_bedcov.xml Wed Mar 18 16:43:50 2015 -0400
@@ -0,0 +1,57 @@
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+ on BAM files
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+ macros.xml
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+ "${output}"
+ ]]>
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+**What it does**
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+This tool runs the ``samtools bedcov`` command in the SAMtools toolkit.
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+Show read depth per BED region.
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diff -r 000000000000 -r c04bee391baa test-data/eboVir3.1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eboVir3.1.bed Wed Mar 18 16:43:50 2015 -0400
@@ -0,0 +1,3 @@
+eboVir3 500 1500
+eboVir3 1500 2000
+eboVir3 1500 3000
diff -r 000000000000 -r c04bee391baa test-data/eboVir3.2.bam
Binary file test-data/eboVir3.2.bam has changed
diff -r 000000000000 -r c04bee391baa test-data/eboVir3.2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eboVir3.2.bed Wed Mar 18 16:43:50 2015 -0400
@@ -0,0 +1,3 @@
+eboVir3 500 1500
+eboVir3 1500 2000
+eboVir3 1500 3000
diff -r 000000000000 -r c04bee391baa test-data/eboVir3.bam
Binary file test-data/eboVir3.bam has changed
diff -r 000000000000 -r c04bee391baa test-data/samtools_bedcov_out1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_bedcov_out1.tab Wed Mar 18 16:43:50 2015 -0400
@@ -0,0 +1,3 @@
+eboVir3 500 1500 7919
+eboVir3 1500 2000 3009
+eboVir3 1500 3000 9986
diff -r 000000000000 -r c04bee391baa test-data/samtools_bedcov_out2.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_bedcov_out2.tab Wed Mar 18 16:43:50 2015 -0400
@@ -0,0 +1,3 @@
+eboVir3 500 1500 7919 2094
+eboVir3 1500 2000 3009 1064
+eboVir3 1500 3000 9986 3455
diff -r 000000000000 -r c04bee391baa tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Mar 18 16:43:50 2015 -0400
@@ -0,0 +1,6 @@
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