From 7a2a176bd8b22d69b680c65d83c3c783c13c682e Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Wed, 6 Nov 2013 16:09:29 -0500
Subject: [PATCH] Fixed a bug in BamRecord::printUnmapped, added a unit test
with with data file for unmapped Bam reads.
---
.../FileRecordTools/Records/BamRecord.cpp | 6 +-
test/intersect/a_with_bothUnmapped.bam | Bin 0 -> 2911 bytes
test/intersect/mapped_and_unmapped.sam | 4 -
test/intersect/new_test-intersect.sh | 210 +++++++++++++++++-
4 files changed, 212 insertions(+), 8 deletions(-)
create mode 100644 test/intersect/a_with_bothUnmapped.bam
delete mode 100644 test/intersect/mapped_and_unmapped.sam
diff --git a/src/utils/FileRecordTools/Records/BamRecord.cpp b/src/utils/FileRecordTools/Records/BamRecord.cpp
index fda5a28b..cde07329 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
@@ -148,10 +148,10 @@ void BamRecord::printRemainingBamFields(QuickString &outBuf, RecordKeyList *keyL
}
void BamRecord::printUnmapped(QuickString &outBuf) const {
- outBuf.append(_chrName);
+ outBuf.append(_chrName.empty() ? "." : _chrName);
outBuf.append("\t-1\t-1\t");
- outBuf.append(_name);
+ outBuf.append(_name.empty() ? "." : _name);
outBuf.append('\t');
- outBuf.append(_score);
+ outBuf.append(_score.empty() ? "." : _score);
outBuf.append("\t.\t-1\t-1\t-1\t0,0,0\t0\t.\t."); // dot for strand, -1 for blockStarts and blockEnd
}
diff --git a/test/intersect/a_with_bothUnmapped.bam b/test/intersect/a_with_bothUnmapped.bam
new file mode 100644
index 0000000000000000000000000000000000000000..c8959e5be8ce17babfed2100134abd8e575fbf1f
GIT binary patch
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diff --git a/test/intersect/mapped_and_unmapped.sam b/test/intersect/mapped_and_unmapped.sam
deleted file mode 100644
index 111b41d1..00000000
--- a/test/intersect/mapped_and_unmapped.sam
+++ /dev/null
@@ -1,4 +0,0 @@
-@HD VN:1.0 GO:none SO:coordinate
-@SQ SN:chr1 LN:249250621
-mapped 16 chr1 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50
-umapped 4 * 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50
diff --git a/test/intersect/new_test-intersect.sh b/test/intersect/new_test-intersect.sh
index 6f21ef16..e23ff4bf 100755
--- a/test/intersect/new_test-intersect.sh
+++ b/test/intersect/new_test-intersect.sh
@@ -12,10 +12,218 @@ check()
###########################################################
# Test intersection of a as bed from file vs b as bed from file
############################################################
-echo " intersect.t01...\c"
+echo " intersect.new.t01...\c"
echo \
"chr1 100 101 a2 2 -
chr1 100 110 a2 2 -" > exp
$BT intersect -a a.bed -b b.bed > obs
check obs exp
rm obs exp
+
+
+###########################################################
+# Test intersection of a as bed from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t02...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bed from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t03...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a.bed | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bed from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t04...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a.bed) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as gzipped from file vs b as bed from file
+############################################################
+echo " intersect.new.t05...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a a_gzipped.bed.gz -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as gzipped from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t06...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a_gzipped.bed.gz > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as gzipped from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t07...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a_gzipped.bed.gz | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as gzipped from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t08...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a_gzipped.bed.gz) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bgzipped from file vs b as bed from file
+############################################################
+echo " intersect.new.t09...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a a_bgzipped.bed.gz -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bgzipped from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t10...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a_bgzipped.bed.gz > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bgzipped from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t11...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a_bgzipped.bed.gz | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bgzipped from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t12...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a_bgzipped.bed.gz) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bam from file vs b as bed from file
+############################################################
+echo " intersect.new.t13...\c"
+$BT intersect -a a.bam -b b.bed> obs
+check obs aVSb.bam
+rm obs
+
+
+###########################################################
+# Test intersection of a as bam from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t14...\c"
+$BT intersect -a - -b b.bed < a.bam> obs
+check obs aVSb.bam
+rm obs
+
+
+###########################################################
+# Test intersection of a as bam from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t15...\c"
+cat a.bam | $BT intersect -a - -b b.bed> obs
+check obs aVSb.bam
+rm obs
+
+
+###########################################################
+# Test intersection of a as bam from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t16...\c"
+$BT intersect -a <(cat a.bam) -b b.bed > obs
+check obs aVSb.bam
+rm obs
+
+
+###########################################################
+# Test intersection of bam file containing both good reads
+# and those where both read and mate are unmapped vs b file
+# as bed.
+############################################################
+echo " intersect.new.t17...\c"
+echo \
+"chr1 100 101 a2 255 - 100 200 0,0,0 1 100, 0,
+chr1 100 110 a2 255 - 100 200 0,0,0 1 100, 0," > exp
+$BT intersect -a a_with_bothUnmapped.bam -b b.bed -bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of bam file containing both good reads
+# and those where both read and mate are unmapped vs b file
+# as bed, with noHit (-v) option.
+############################################################
+echo " intersect.new.t18...\c"
+echo \
+"chr1 10 20 a1 255 + 10 20 0,0,0 1 10, 0,
+. -1 -1 FCC1MK2ACXX:1:1101:5780:51632#/1 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1101:5780:51632#/2 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1101:8137:99409#/1 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1101:8137:99409#/2 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1102:6799:2633#/1 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1102:6799:2633#/2 0 . -1 -1 -1 0,0,0 0 . ." > exp
+$BT intersect -a a_with_bothUnmapped.bam -b b.bed -bed -v > obs
+check obs exp
+#rm obs exp
+
+
+
+
+
+
+
--
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