From be0e9cc45169465cbb93eb610ca7b0598e37e30f Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 18 Sep 2012 22:07:41 -0400
Subject: [PATCH] exit is inout BAM file is not found
---
src/coverageBed/coverageBed.cpp | 8 +++++---
src/genomeCoverageBed/genomeCoverageBed.cpp | 5 ++++-
src/intersectBed/intersectBed.cpp | 6 +++++-
src/pairToBed/pairToBed.cpp | 5 ++++-
src/tagBam/tagBam.cpp | 6 +++++-
src/utils/chromsweep/chromsweep.cpp | 6 +++---
src/windowBed/windowBed.cpp | 6 +++++-
7 files changed, 31 insertions(+), 11 deletions(-)
diff --git a/src/coverageBed/coverageBed.cpp b/src/coverageBed/coverageBed.cpp
index f5477262..4af2edb2 100644
--- a/src/coverageBed/coverageBed.cpp
+++ b/src/coverageBed/coverageBed.cpp
@@ -85,10 +85,12 @@ void BedCoverage::CollectCoverageBam(string bamFile) {
// that we can easily compare "A" to it for overlaps
_bedB->loadBedCovFileIntoMap();
- // open the BAM file
+ // open the BAM file
BamReader reader;
- reader.Open(bamFile);
-
+ if (!reader.Open(bamFile)) {
+ cerr << "Failed to open BAM file " << bamFile << endl;
+ exit(1);
+ }
// get header & reference information
string header = reader.GetHeaderText();
RefVector refs = reader.GetReferenceData();
diff --git a/src/genomeCoverageBed/genomeCoverageBed.cpp b/src/genomeCoverageBed/genomeCoverageBed.cpp
index cdb04446..621c461d 100644
--- a/src/genomeCoverageBed/genomeCoverageBed.cpp
+++ b/src/genomeCoverageBed/genomeCoverageBed.cpp
@@ -211,7 +211,10 @@ void BedGenomeCoverage::CoverageBam(string bamFile) {
// open the BAM file
BamReader reader;
- reader.Open(bamFile);
+ if (!reader.Open(bamFile)) {
+ cerr << "Failed to open BAM file " << bamFile << endl;
+ exit(1);
+ }
// get header & reference information
string header = reader.GetHeaderText();
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index 3382b2df..4f25c1b3 100644
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -308,7 +308,11 @@ void BedIntersect::IntersectBam(string bamFile) {
// open the BAM file
BamReader reader;
BamWriter writer;
- reader.Open(bamFile);
+ if (!reader.Open(bamFile)) {
+ cerr << "Failed to open BAM file " << bamFile << endl;
+ exit(1);
+ }
+
// get header & reference information
string bamHeader = reader.GetHeaderText();
RefVector refs = reader.GetReferenceData();
diff --git a/src/pairToBed/pairToBed.cpp b/src/pairToBed/pairToBed.cpp
index a08c6736..7db744fc 100644
--- a/src/pairToBed/pairToBed.cpp
+++ b/src/pairToBed/pairToBed.cpp
@@ -383,7 +383,10 @@ void BedIntersectPE::IntersectBamPE(string bamFile) {
// open the BAM file
BamReader reader;
BamWriter writer;
- reader.Open(bamFile);
+ if (!reader.Open(bamFile)) {
+ cerr << "Failed to open BAM file " << bamFile << endl;
+ exit(1);
+ }
// get header & reference information
string bamHeader = reader.GetHeaderText();
diff --git a/src/tagBam/tagBam.cpp b/src/tagBam/tagBam.cpp
index 384094d5..5c7590fb 100644
--- a/src/tagBam/tagBam.cpp
+++ b/src/tagBam/tagBam.cpp
@@ -64,7 +64,11 @@ void TagBam::Tag() {
// open the BAM file
BamReader reader;
BamWriter writer;
- reader.Open(_bamFile);
+ if (!reader.Open(_bamFile)) {
+ cerr << "Failed to open BAM file " << _bamFile << endl;
+ exit(1);
+ }
+
// get header & reference information
string bamHeader = reader.GetHeaderText();
RefVector refs = reader.GetReferenceData();
diff --git a/src/utils/chromsweep/chromsweep.cpp b/src/utils/chromsweep/chromsweep.cpp
index 88456f36..e3c4afad 100644
--- a/src/utils/chromsweep/chromsweep.cpp
+++ b/src/utils/chromsweep/chromsweep.cpp
@@ -169,9 +169,9 @@ bool ChromSweep::Next(pair<BED, vector<BED> > &next) {
{
if (IsValidHit(_curr_qy, _curr_db)) {
_hits.push_back(_curr_db);
- }
- _cache.push_back(_curr_db);
- _db->GetNextBed(_curr_db, true);
+ }
+ _cache.push_back(_curr_db);
+ _db->GetNextBed(_curr_db, true);
}
// add the hits for this query to the pump
_results.push(make_pair(_curr_qy, _hits));
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index 852a475b..55342db0 100644
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -158,7 +158,11 @@ void BedWindow::WindowIntersectBam(string bamFile) {
// open the BAM file
BamReader reader;
BamWriter writer;
- reader.Open(bamFile);
+ if (!reader.Open(bamFile)) {
+ cerr << "Failed to open BAM file " << bamFile << endl;
+ exit(1);
+ }
+
// get header & reference information
string bamHeader = reader.GetHeaderText();
--
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