From e940859f9b49b60ec4c536f39d7e715367303ed7 Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Wed, 25 Sep 2013 19:32:56 -0400
Subject: [PATCH] Shortened output buffer, corrected Chromsweep errors with
some print options due to early termination.
---
src/utils/FileRecordTools/RecordOutputMgr.cpp | 14 +++++++++++---
src/utils/FileRecordTools/RecordOutputMgr.h | 3 ++-
src/utils/NewChromsweep/NewChromsweep.cpp | 12 ++++++++++--
src/utils/NewChromsweep/NewChromsweep.h | 1 +
4 files changed, 24 insertions(+), 6 deletions(-)
diff --git a/src/utils/FileRecordTools/RecordOutputMgr.cpp b/src/utils/FileRecordTools/RecordOutputMgr.cpp
index 984d6aba..7595f3aa 100644
--- a/src/utils/FileRecordTools/RecordOutputMgr.cpp
+++ b/src/utils/FileRecordTools/RecordOutputMgr.cpp
@@ -28,14 +28,19 @@ RecordOutputMgr::RecordOutputMgr()
: _context(NULL),
_printable(true),
_bamWriter(NULL),
- _currBlockList(NULL)
+ _currBlockList(NULL),
+ _numWrites(0)
{
}
RecordOutputMgr::~RecordOutputMgr()
{
- flush();
+ if (_outBuf.size() > 0) {
+ flush();
+ _numWrites++;
+ }
+ cerr << "Total number of buffer writes was " << _numWrites << endl;
if (_bamWriter != NULL) {
_bamWriter->Close();
delete _bamWriter;
@@ -105,7 +110,10 @@ RecordOutputMgr::printBamType RecordOutputMgr::printBamRecord(RecordKeyList &key
void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockList)
{
- if (needsFlush()) flush();
+ if (needsFlush()) {
+ flush();
+ _numWrites++;
+ }
//The first time we print a record is when we print any header, because the header
//hasn't been read from the query file until after the first record has also been read.
diff --git a/src/utils/FileRecordTools/RecordOutputMgr.h b/src/utils/FileRecordTools/RecordOutputMgr.h
index b8f76630..fe54b3ea 100644
--- a/src/utils/FileRecordTools/RecordOutputMgr.h
+++ b/src/utils/FileRecordTools/RecordOutputMgr.h
@@ -40,6 +40,7 @@ private:
RecordKeyList *_currBlockList;
QuickString _outBuf;
+ int _numWrites;
//some helper functions to neaten the code.
void tab() { _outBuf.append('\t'); }
@@ -48,7 +49,7 @@ private:
void printKey(const Record *key);
void printKey(const Record *key, const QuickString & start, const QuickString & end);
- static const unsigned int MAX_OUTBUF_SIZE = 33554432; //32 Mb
+ static const unsigned int MAX_OUTBUF_SIZE = 16384; //16 K
bool needsFlush() const { return _outBuf.size() >= MAX_OUTBUF_SIZE *.9; }
void flush();
};
diff --git a/src/utils/NewChromsweep/NewChromsweep.cpp b/src/utils/NewChromsweep/NewChromsweep.cpp
index 6c441c4e..27cc4b92 100644
--- a/src/utils/NewChromsweep/NewChromsweep.cpp
+++ b/src/utils/NewChromsweep/NewChromsweep.cpp
@@ -24,7 +24,8 @@ NewChromSweep::NewChromSweep(Context *context,
_databaseRecordsTotalLength(0),
_wasInitialized(false),
_currQueryRec(NULL),
- _currDatabaseRec(NULL)
+ _currDatabaseRec(NULL),
+ _runToQueryEnd(false)
{
}
@@ -52,6 +53,13 @@ bool NewChromSweep::init() {
if (_currDatabaseRec == NULL) {
return false;
}
+
+ //determine whether to stop when the database end is hit, or keep going until the
+ //end of the query file is hit as well.
+
+ if (_context->getNoHit() || _context->getWriteCount() || _context->getWriteOverlap() || _context->getWriteAllOverlap() || _context->getLeftJoin()) {
+ _runToQueryEnd = true;
+ }
_wasInitialized = true;
return true;
}
@@ -155,7 +163,7 @@ bool NewChromSweep::next(RecordKeyList &next) {
return false;
}
- if (_currDatabaseRec == NULL && _cache.empty()) {
+ if (_currDatabaseRec == NULL && _cache.empty() && !_runToQueryEnd) {
return false;
}
_hits.clear();
diff --git a/src/utils/NewChromsweep/NewChromsweep.h b/src/utils/NewChromsweep/NewChromsweep.h
index abd20e92..2c0beb7f 100644
--- a/src/utils/NewChromsweep/NewChromsweep.h
+++ b/src/utils/NewChromsweep/NewChromsweep.h
@@ -81,6 +81,7 @@ private:
Record *_currDatabaseRec;
// a cache of the current chrom from the query. used to handle chrom changes.
QuickString _currChromName;
+ bool _runToQueryEnd;
void nextRecord(bool query); //true fetches next query record, false fetches next db record.
void nextDatabase();
--
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