From db638be7e3f7c3b1f630200589657f70ac1d928c Mon Sep 17 00:00:00 2001
From: arq5x <arq5x@virginia.edu>
Date: Mon, 9 Dec 2013 17:14:39 -0500
Subject: [PATCH] [TST] cleanup sample test
---
src/bamToBed/bamToBed.cpp | 87 +++++++++++++++++++++-----------
test/bamtobed/test-bamtobed.sh | 63 +++++++++++++++++++++++
test/bamtobed/two_blocks_w_D.sam | 6 +++
test/sample/test-sample.sh | 6 +--
4 files changed, 129 insertions(+), 33 deletions(-)
create mode 100644 test/bamtobed/two_blocks_w_D.sam
diff --git a/src/bamToBed/bamToBed.cpp b/src/bamToBed/bamToBed.cpp
index c89441a0..16d61644 100644
--- a/src/bamToBed/bamToBed.cpp
+++ b/src/bamToBed/bamToBed.cpp
@@ -38,9 +38,9 @@ void bamtobed_help(void);
void ConvertBamToBed(const string &bamFile, bool useEditDistance,
const string &bamTag, bool writeBed12,
- bool obeySplits, const string &color,
- bool useCigar, bool useNovoalign,
- bool useBWA);
+ bool obeySplits, bool splitOnDeletions,
+ const string &color, bool useCigar,
+ bool useNovoalign, bool useBWA);
void ConvertBamToBedpe(const string &bamFile,
const bool &useEditDistance, bool mate1First);
@@ -49,11 +49,13 @@ string PrintTag(const BamAlignment &bam, const string &tag);
void PrintBed(const BamAlignment &bam, const RefVector &refs,
bool useEditDistance, const string &bamTag,
- bool obeySplits, bool useCigar,
- bool useNovoalign, bool useBWA);
+ bool obeySplits, bool splitOnDeletions,
+ bool useCigar, bool useNovoalign,
+ bool useBWA);
void PrintBed12(const BamAlignment &bam, const RefVector &refs,
- bool useEditDistance, const string &bamTag,
+ bool useEditDistance, const string &bamTag,
+ bool obeySplits, bool splitOnDeletions,
string color = "255,0,0");
void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2,
@@ -86,6 +88,7 @@ int bamtobed_main(int argc, char* argv[]) {
bool useAlignmentScore = false;
bool useCigar = false;
bool obeySplits = false;
+ bool splitOnDeletions = false;
bool mate1First = false;
bool useNovoalign = false; // custom for Quinlan/Hall research
bool useBWA = false; // custom for Quinlan/Hall research
@@ -115,32 +118,36 @@ int bamtobed_main(int argc, char* argv[]) {
}
}
else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) {
- writeBedPE = true;
+ writeBedPE = true;
}
else if(PARAMETER_CHECK("-bed12", 6, parameterLength)) {
- writeBed12 = true;
+ writeBed12 = true;
}
else if(PARAMETER_CHECK("-split", 6, parameterLength)) {
- obeySplits = true;
+ obeySplits = true;
+ }
+ else if(PARAMETER_CHECK("-splitD", 7, parameterLength)) {
+ obeySplits = true;
+ splitOnDeletions = true;
}
else if(PARAMETER_CHECK("-ed", 3, parameterLength)) {
- useEditDistance = true;
- tag = "NM";
+ useEditDistance = true;
+ tag = "NM";
}
else if(PARAMETER_CHECK("-cigar", 6, parameterLength)) {
- useCigar = true;
+ useCigar = true;
}
else if(PARAMETER_CHECK("-as", 3, parameterLength)) {
- useAlignmentScore = true;
+ useAlignmentScore = true;
}
else if(PARAMETER_CHECK("-novo", 5, parameterLength)) {
- useNovoalign = true;
+ useNovoalign = true;
}
else if(PARAMETER_CHECK("-bwa", 4, parameterLength)) {
- useBWA = true;
+ useBWA = true;
}
else if(PARAMETER_CHECK("-mate1", 6, parameterLength)) {
- mate1First = true;
+ mate1First = true;
}
else if(PARAMETER_CHECK("-color", 6, parameterLength)) {
if ((i+1) < argc) {
@@ -210,8 +217,8 @@ int bamtobed_main(int argc, char* argv[]) {
if (writeBedPE == false)
ConvertBamToBed(bamFile, useEditDistance,
tag, writeBed12,
- obeySplits, color,
- useCigar,
+ obeySplits, splitOnDeletions,
+ color, useCigar,
useNovoalign, useBWA);
else
ConvertBamToBedpe(bamFile, useEditDistance, mate1First);
@@ -239,10 +246,14 @@ void bamtobed_help(void) {
cerr << "\t-mate1\t" << "When writing BEDPE (-bedpe) format, " << endl;
cerr << "\t\talways report mate one as the first BEDPE \"block\"." << endl << endl;
- cerr << "\t-bed12\t" << "Write \"blocked\" BED format (aka \"BED12\")." << endl << endl;
+ cerr << "\t-bed12\t" << "Write \"blocked\" BED format (aka \"BED12\"). Forces -split." << endl << endl;
cerr << "\t\thttp://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1" << endl << endl;
- cerr << "\t-split\t" << "Report \"split\" BAM alignments as separate BED entries." << endl << endl;
+ cerr << "\t-split\t" << "Report \"split\" BAM alignments as separate BED entries." << endl ;
+ cerr << "\t\tSplits only on N CIGAR operations." << endl << endl;
+
+ cerr << "\t-splitD\t" << "Split alignments based on N and D CIGAR operators." << endl;
+ cerr << "\t\tForces -split." << endl << endl;
cerr << "\t-ed\t" << "Use BAM edit distance (NM tag) for BED score." << endl;
cerr << "\t\t- Default for BED is to use mapping quality." << endl;
@@ -267,8 +278,10 @@ void bamtobed_help(void) {
void ConvertBamToBed(const string &bamFile, bool useEditDistance, const string &bamTag,
- bool writeBed12, bool obeySplits, const string &color,
- bool useCigar, bool useNovoalign, bool useBWA) {
+ bool writeBed12, bool obeySplits, bool splitOnDeletions,
+ const string &color, bool useCigar, bool useNovoalign, bool useBWA)
+{
+
// open the BAM file
BamReader reader;
if (!reader.Open(bamFile)) {
@@ -285,9 +298,11 @@ void ConvertBamToBed(const string &bamFile, bool useEditDistance, const string &
while (reader.GetNextAlignment(bam)) {
if (bam.IsMapped() == true) {
if (writeBed12 == false) // BED
- PrintBed(bam, refs, useEditDistance, bamTag, obeySplits, useCigar, useNovoalign, useBWA);
+ PrintBed(bam, refs, useEditDistance, bamTag, obeySplits, splitOnDeletions,
+ useCigar, useNovoalign, useBWA);
else //"blocked" BED
- PrintBed12(bam, refs, useEditDistance, bamTag, color);
+ PrintBed12(bam, refs, useEditDistance, bamTag, obeySplits, splitOnDeletions,
+ color);
}
}
reader.Close();
@@ -379,8 +394,9 @@ string PrintTag(const BamAlignment &bam, const string &tag)
void PrintBed(const BamAlignment &bam, const RefVector &refs,
bool useEditDistance, const string &bamTag,
- bool obeySplits, bool useCigar,
- bool useNovoalign, bool useBWA)
+ bool obeySplits, bool splitOnDeletions,
+ bool useCigar, bool useNovoalign,
+ bool useBWA)
{
// set the strand
string strand = "+";
@@ -474,14 +490,18 @@ void PrintBed(const BamAlignment &bam, const RefVector &refs,
vector<BED> bedBlocks;
string chrom = refs.at(bam.RefID).RefName;
// extract the block starts and lengths from the CIGAR string
- GetBamBlocks(bam, chrom, bedBlocks, false, true);
+ if (!splitOnDeletions)
+ GetBamBlocks(bam, chrom, bedBlocks, false, true);
+ else
+ GetBamBlocks(bam, chrom, bedBlocks, true, true);
+
unsigned int i;
for (i = 0; i < bedBlocks.size(); ++i) {
BED curr = bedBlocks[i];
if (bamTag == "") {
- printf("%s\t%d\t%d\t\%s\t%d\t%s\n",
+ printf("%s\t%d\t%d\t%s\t%d\t%s\n",
chrom.c_str(),
curr.start,
curr.end,
@@ -504,7 +524,11 @@ void PrintBed(const BamAlignment &bam, const RefVector &refs,
}
-void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDistance, const string &bamTag, string color) {
+void PrintBed12(const BamAlignment &bam, const RefVector &refs,
+ bool useEditDistance, const string &bamTag,
+ bool obeySplits, bool splitOnDeletions,
+ string color)
+{
// set the strand
string strand = "+";
@@ -520,7 +544,10 @@ void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDist
string chrom = refs.at(bam.RefID).RefName;
CHRPOS alignmentEnd = bam.GetEndPosition();
// extract the block starts and lengths from the CIGAR string
- GetBamBlocks(bam, chrom, bedBlocks, false, true);
+ if (!splitOnDeletions)
+ GetBamBlocks(bam, chrom, bedBlocks, false, true);
+ else
+ GetBamBlocks(bam, chrom, bedBlocks, true, true);
if (bamTag == "") {
cout << refs.at(bam.RefID).RefName << "\t"
diff --git a/test/bamtobed/test-bamtobed.sh b/test/bamtobed/test-bamtobed.sh
index 358d8a7e..193a3c1e 100644
--- a/test/bamtobed/test-bamtobed.sh
+++ b/test/bamtobed/test-bamtobed.sh
@@ -18,6 +18,7 @@ samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null
+samtools view -Sb two_blocks_w_D.sam > two_blocks_w_D.bam 2>/dev/null
##################################################################
@@ -110,4 +111,66 @@ $BT bamtobed -i three_blocks.bam -bed12 | $BT bed12tobed6 > bed12
check split bed12
rm split bed12
+##################################################################
+# Test an alignment with a D operator and N operator -split option
+##################################################################
+echo " bamtobed.t9...\c"
+echo \
+"chr1 0 15 two_blocks_1_1/2 40 +
+chr1 25 40 two_blocks_1_1/2 40 +
+chr1 99 129 two_blocks_1_2/1 40 +
+chr1 0 15 two_blocks_2_1/2 40 +
+chr1 25 42 two_blocks_2_1/2 40 +
+chr1 99 129 two_blocks_2_2/1 40 +" > exp
+$BT bamtobed -i two_blocks_w_D.bam -split > obs
+check exp obs
+rm exp obs
+
+
+##################################################################
+# Test an alignment with a D operator and N operator -splitD option
+##################################################################
+echo " bamtobed.t10...\c"
+echo \
+"chr1 0 15 two_blocks_1_1/2 40 +
+chr1 25 40 two_blocks_1_1/2 40 +
+chr1 99 129 two_blocks_1_2/1 40 +
+chr1 0 15 two_blocks_2_1/2 40 +
+chr1 25 35 two_blocks_2_1/2 40 +
+chr1 37 42 two_blocks_2_1/2 40 +
+chr1 99 129 two_blocks_2_2/1 40 +" > exp
+$BT bamtobed -i two_blocks_w_D.bam -splitD > obs
+check exp obs
+rm exp obs
+
+
+##################################################################
+# Test an alignment with a D operator and N operator -bed12 option
+##################################################################
+echo " bamtobed.t9...\c"
+echo \
+"chr1 0 40 two_blocks_1_1/2 40 + 0 40 255,0,0 2 15,15 0,25
+chr1 99 129 two_blocks_1_2/1 40 + 99 129 255,0,0 1 30 0
+chr1 0 42 two_blocks_2_1/2 40 + 0 42 255,0,0 2 15,17 0,25
+chr1 99 129 two_blocks_2_2/1 40 + 99 129 255,0,0 1 30 0" > exp
+$BT bamtobed -i two_blocks_w_D.bam -bed12 > obs
+check exp obs
+rm exp obs
+
+
+##################################################################
+# Test an alignment with a D operator and N operator -bed12 option
+##################################################################
+echo " bamtobed.t11...\c"
+echo \
+"chr1 0 40 two_blocks_1_1/2 40 + 0 40 255,0,0 2 15,15 0,25
+chr1 99 129 two_blocks_1_2/1 40 + 99 129 255,0,0 1 30 0
+chr1 0 42 two_blocks_2_1/2 40 + 0 42 255,0,0 3 15,10,5 0,25,37
+chr1 99 129 two_blocks_2_2/1 40 + 99 129 255,0,0 1 30 0" > exp
+$BT bamtobed -i two_blocks_w_D.bam -bed12 -splitD > obs
+
+check exp obs
+rm exp obs
+
+
rm *.bam
diff --git a/test/bamtobed/two_blocks_w_D.sam b/test/bamtobed/two_blocks_w_D.sam
new file mode 100644
index 00000000..00ddff2b
--- /dev/null
+++ b/test/bamtobed/two_blocks_w_D.sam
@@ -0,0 +1,6 @@
+@HD VN:1.0 GO:none SO:coordinate
+@SQ SN:chr1 LN:249250621
+two_blocks_1_1 163 chr1 1 40 15M10N15M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 XA:i:2
+two_blocks_1_2 99 chr1 100 40 30M * 0 0 AGGCGATGCTAACGAAAAATTCGGAAATTT CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 XA:i:2
+two_blocks_2_1 163 chr1 1 40 15M10N10M2D5M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 XA:i:2
+two_blocks_2_2 99 chr1 100 40 30M * 0 0 AGGCGATGCTAACGAAAAATTCGGAAATTT CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 XA:i:2
diff --git a/test/sample/test-sample.sh b/test/sample/test-sample.sh
index 56254dce..9cae9bc0 100644
--- a/test/sample/test-sample.sh
+++ b/test/sample/test-sample.sh
@@ -91,10 +91,10 @@ rm obs exp
# Test that we get the requested number of records
############################################################
echo " sample.new.t07...\c"
-echo 10 > exp
-$BT sample -i mainFile.bed -n 10 | wc -l | cut -f1 -d ' '> obs
+echo " 10" > exp
+$BT sample -i mainFile.bed -n 10 | wc -l > obs
check obs exp
-rm obs exp
+#rm obs exp
###########################################################
--
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