From be0639f742c5df63e830a6a4176ff964a04c0f06 Mon Sep 17 00:00:00 2001
From: Derek <derekwbarnett@gmail.com>
Date: Tue, 20 Jul 2010 16:25:48 -0400
Subject: [PATCH] Modified BamMultiReader::Open() to return bool. Still needs
some tweaks to handle all error cases correctly.
---
BamMultiReader.cpp | 19 +++++++++++--------
BamMultiReader.h | 4 ++--
2 files changed, 13 insertions(+), 10 deletions(-)
diff --git a/BamMultiReader.cpp b/BamMultiReader.cpp
index 75054a2..001df07 100644
--- a/BamMultiReader.cpp
+++ b/BamMultiReader.cpp
@@ -3,7 +3,7 @@
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 23 Februrary 2010 (EG)
+// Last modified: 20 July 2010 (DB)
// ---------------------------------------------------------------------------
// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
// Institute.
@@ -210,7 +210,7 @@ void BamMultiReader::UpdateAlignments(void) {
}
// opens BAM files
-void BamMultiReader::Open(const vector<string> filenames, bool openIndexes, bool coreMode, bool useDefaultIndex) {
+bool BamMultiReader::Open(const vector<string> filenames, bool openIndexes, bool coreMode, bool useDefaultIndex) {
// for filename in filenames
fileNames = filenames; // save filenames in our multireader
@@ -245,18 +245,21 @@ void BamMultiReader::Open(const vector<string> filenames, bool openIndexes, bool
make_pair(reader, alignment)));
} else {
cerr << "WARNING: could not read first alignment in " << filename << ", ignoring file" << endl;
+ // if only file available & could not be read, return failure
+ if ( filenames.size() == 1 ) return false;
}
}
- // TODO; error handling on openedOK == false
- else {
-
-
- }
+ // TODO; any more error handling on openedOK ??
+ else
+ return false;
}
-
+
+ // files opened ok, at least one alignment could be read,
+ // now need to check that all files use same reference data
ValidateReaders();
+ return true;
}
void BamMultiReader::PrintFilenames(void) {
diff --git a/BamMultiReader.h b/BamMultiReader.h
index 37ad765..bd36d71 100644
--- a/BamMultiReader.h
+++ b/BamMultiReader.h
@@ -3,7 +3,7 @@
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 22 February 2010 (EG)
+// Last modified: 20 July 2010 (DB)
// ---------------------------------------------------------------------------
// Functionality for simultaneously reading multiple BAM files
// ***************************************************************************
@@ -59,7 +59,7 @@ class BamMultiReader {
// indexes.
// @coreMode - setup our first alignments using GetNextAlignmentCore();
// also useful for merging
- void Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool useDefaultIndex = true);
+ bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool useDefaultIndex = true);
// performs random-access jump to reference, position
bool Jump(int refID, int position = 0);
--
2.39.5