From d819c40d4768c2bfe83d042abd3c1583172899f9 Mon Sep 17 00:00:00 2001
From: Neil Kindlon <nek3d@d-128-109-67.bootp.Virginia.EDU>
Date: Sat, 6 Dec 2014 18:38:58 -0500
Subject: [PATCH] Fix for bug 150, closest hangs with -d and tie first mode
---
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 17 ++++++++++-------
src/utils/general/ParseTools.h | 8 +++++++-
2 files changed, 17 insertions(+), 8 deletions(-)
diff --git a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
index fcde1907..4f33b211 100644
--- a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
@@ -137,20 +137,23 @@ void RecordOutputMgr::printRecord(const Record *record, const QuickString & valu
}
void RecordOutputMgr::printClosest(RecordKeyVector &keyList, const vector<int> *dists) {
+
const ContextClosest *context = static_cast<const ContextClosest *>(_context);
bool deleteBlocks = false;
- RecordKeyVector blockList(keyList.getKey());
- if (keyList.getKey()->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
+ const Record *keyRec = keyList.getKey();
+ RecordKeyVector blockList(keyRec);
+ if (keyRec->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
_bamBlockMgr->getBlocks(blockList, deleteBlocks);
_currBamBlockList = &blockList;
}
if (!keyList.empty()) {
int distCount = 0;
for (RecordKeyVector::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
- printKey(keyList.getKey());
+ const Record *hitRec = *iter;
+ printKey(keyRec, keyRec->getStartPosStr(), keyRec->getEndPosStr());
tab();
- addDbFileId((*iter)->getFileIdx());
- (*iter)->print(_outBuf);
+ addDbFileId(hitRec->getFileIdx());
+ printKey(hitRec, hitRec->getStartPosStr(), hitRec->getEndPosStr());
if (dists != NULL) {
tab();
_outBuf.append((*dists)[distCount]);
@@ -160,9 +163,9 @@ void RecordOutputMgr::printClosest(RecordKeyVector &keyList, const vector<int> *
if (needsFlush()) flush();
}
} else {
- printKey(keyList.getKey());
+ printKey(keyRec, keyRec->getStartPosStr(), keyRec->getEndPosStr());
tab();
- null(true, false);
+ null(false, true);
if (context->reportDistance()) {
tab();
_outBuf.append(-1);
diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h
index 2ba28df3..a58495d1 100644
--- a/src/utils/general/ParseTools.h
+++ b/src/utils/general/ParseTools.h
@@ -12,6 +12,8 @@
#include <string>
#include <vector>
#include "QuickString.h"
+#include <cstdio>
+#include <cstdlib>
using namespace std;
@@ -35,7 +37,11 @@ int str2chrPos(const QuickString &str);
template<class T>
void int2str(int number, T& buffer, bool appendToBuf = false)
{
-
+ int maxVal = (1 << 31) -1;
+ if (((int)(abs(number))) > maxVal) {
+ fprintf(stderr, "ERROR: number out of bounds.\n");
+ exit(1);
+ }
register int useNum = number;
if (useNum == 0) {
if (appendToBuf) {
--
GitLab