*** empty log message ***

NEWS

@@ -5,7 +5,7 @@ Bowtie NEWS
 
    Bowtie is now available for download.  0.9.0 is the first version to
 be released under the OSI Artistic License (see `COPYING') and freely
-available to the public for download.  The current version is 0.12.3.
+available to the public for download.  The current version is 0.12.4.
 
 Reporting Issues
 ================
@@ -26,6 +26,19 @@ our mailing list:
 Version Release History
 =======================
 
+Version 0.12.4 - April 5, 2010
+   * Periods in read sequences are now treated as Ns instead of
+     ignored.  This should help with some problems where Bowtie
+     erroneously reports "Reads file contained a pattern with more than
+     1024 quality values..." for data from recent versions of the
+     Illumina GA pipeline.
+   * Fixed a bug whereby some error and warning messages would be
+     printed on top of each other in -p mode.
+   * Chunk-exhaustion warnings messages are now suppressed when --quiet
+     is specified.
+   * Fixed small issue in quality decoding whereby no-confidence colors
+     would incorrectly influence decoded quality of adjacent bases.
+
 Version 0.12.3 - February 17, 2010
    * Fixed a significant bug in -C/--color mode whereby quality values
      for SNP nucleotide positions were erroneously penalized.

VERSION

@@ -1 +1 @@
-0.12.3
+0.12.4

ebwt.h

@@ -1275,8 +1275,9 @@ class EbwtSearchParams {
 						} else {
 							hit.quals[destpos] += qual[i-1];
 						}
+					} else if((int)hit.colSeq[i-1] != 4) {
+						hit.quals[destpos] -= qual[i-1];
 					}
-					else hit.quals[destpos] -= qual[i-1];
 				}
 				if(i < qlen) {
 					if(cmm[i] == 'M') {
@@ -1285,8 +1286,9 @@ class EbwtSearchParams {
 						} else {
 							hit.quals[destpos] += qual[i];
 						}
+					} else if((int)hit.patSeq[i] != 4) {
+						hit.quals[destpos] -= qual[i];
 					}
-					else hit.quals[destpos] -= qual[i];
 				}
 				if(hit.quals[destpos] < '!') {
 					hit.quals[destpos] = '!';

ebwt_search.cpp

@@ -43,7 +43,7 @@ static vector<string> mates12; // mated reads (1st/2nd interleaved in 1 file)
 static string adjustedEbwtFileBase;
 static bool verbose;      // be talkative
 static bool startVerbose; // be talkative at startup
-static bool quiet;        // print nothing but the alignments
+bool quiet;        // print nothing but the alignments
 static int sanityCheck;   // enable expensive sanity checks
 static int format;        // default read format is FASTQ
 static string origString; // reference text, or filename(s)
@@ -143,6 +143,7 @@ bool showSeed;
 static vector<string> qualities;
 static vector<string> qualities1;
 static vector<string> qualities2;
+MUTEX_T gLock;
 
 static void resetOptions() {
 	mates1.clear();
@@ -251,6 +252,7 @@ static void resetOptions() {
 	qualities.clear();
 	qualities1.clear();
 	qualities2.clear();
+	MUTEX_INIT(gLock);
 }
 
 // mating constraints
@@ -2769,9 +2771,9 @@ static void driver(const char * type,
 				cerr << "Invalid output type: " << outType << endl;
 				throw 1;
 		}
-    	if(verbose || startVerbose) {
-    		cerr << "Dispatching to search driver: "; logTime(cerr, true);
-    	}
+		if(verbose || startVerbose) {
+			cerr << "Dispatching to search driver: "; logTime(cerr, true);
+		}
 		if(maqLike) {
 			seededQualCutoffSearchFull(seedLen,
 									   qualThresh,

ebwt_search_backtrack.h

@@ -115,6 +115,7 @@ class GreedyDFSRangeSource {
 				_chars = new char[_qlen];
 				assert(_pairs != NULL && _elims != NULL && _chars != NULL);
 			} catch(std::bad_alloc& e) {
+				ThreadSafe _ts(&gLock);
 				cerr << "Unable to allocate memory for depth-first "
 				     << "backtracking search; new length = " << length(*_qry)
 				     << endl;
@@ -1953,6 +1954,7 @@ class EbwtRangeSource : public RangeSource {
 			if(offRev2_ != offRev3_) maxmms = 3;
 			if(qlen_ <= maxmms) {
 				if(!quiet_) {
+					ThreadSafe _ts(&gLock);
 					cerr << "Warning: Read (" << (*name_) << ") is less than " << (maxmms+1) << " characters long; skipping..." << endl;
 				}
 				this->done = true;

filebuf.h

@@ -299,6 +299,20 @@ class FileBuf {
 		return _lastn_cur;
 	}
 
+	/**
+	 * Get const pointer to the last-N-chars buffer.
+	 */
+	const char *lastN() const {
+		return _lastn_buf;
+	}
+
+	/**
+	 * Get current size of the last-N-chars buffer.
+	 */
+	const size_t lastNLen() const {
+		return _lastn_cur;
+	}
+
 private:
 
 	void init() {
@@ -451,7 +465,10 @@ class OutFileBuf {
 		if(cur_ + slen > BUF_SZ) {
 			if(cur_ > 0) flush();
 			if(slen >= BUF_SZ) {
-				fwrite(s.c_str(), slen, 1, out_);
+				if(fwrite(s.c_str(), slen, 1, out_) != slen) {
+					std::cerr << "Error while writing string output; not all characters written" << std::endl;
+					throw 1;
+				}
 			} else {
 				memcpy(&buf_[cur_], s.data(), slen);
 				assert_eq(0, cur_);
@@ -472,7 +489,10 @@ class OutFileBuf {
 		if(cur_ + len > BUF_SZ) {
 			if(cur_ > 0) flush();
 			if(len >= BUF_SZ) {
-				fwrite(s, len, 1, out_);
+				if(fwrite(s, len, 1, out_) != len) {
+					std::cerr << "Error while writing string output; not all characters written" << std::endl;
+					throw 1;
+				}
 			} else {
 				memcpy(&buf_[cur_], s, len);
 				assert_eq(0, cur_);

pat.h

@@ -2257,8 +2257,8 @@ class TabbedPatternSource : public BufferedFilePatternSource {
 		while(c != upto) {
 			if(color_) {
 				if(c >= '0' && c <= '4') c = "ACGTN"[(int)c - '0'];
-				if(c == '.') c = 'N';
 			}
+			if(c == '.') c = 'N';
 			if(isalpha(c)) {
 				assert_in(toupper(c), "ACGTN");
 				if(begin++ >= trim5) {
@@ -2660,8 +2660,8 @@ class FastqPatternSource : public BufferedFilePatternSource {
 			// Convert color numbers to letters if necessary
 			if(color_) {
 				if(c >= '0' && c <= '4') c = "ACGTN"[(int)c - '0'];
-				if(c == '.') c = 'N';
 			}
+			if(c == '.') c = 'N';
 			if(fuzzy_ && c == '-') c = 'A';
 			if(isalpha(c)) {
 				// If it's past the 5'-end trim point
@@ -2971,8 +2971,8 @@ class RawPatternSource : public BufferedFilePatternSource {
 		while(!isspace(c) && c >= 0) {
 			if(color_) {
 				if(c >= '0' && c <= '4') c = "ACGTN"[(int)c - '0'];
-				if(c == '.') c = 'N';
 			}
+			if(c == '.') c = 'N';
 			if(isalpha(c) && dstLen >= mytrim5) {
 				size_t len = dstLen - mytrim5;
 				if(len >= 1024) tooManyQualities(String<char>("(no name)"));

pool.h

@@ -12,6 +12,7 @@
 #include <stdlib.h>
 #include "bitset.h"
 #include "log.h"
+#include "search_globals.h"
 
 /**
  * Very simple allocator for fixed-size chunks of memory.  Chunk size
@@ -36,6 +37,7 @@ class ChunkPool {
 				throw std::bad_alloc();
 			}
 		} catch(std::bad_alloc& e) {
+			ThreadSafe _ts(&gLock);
 			std::cerr << "Error: Could not allocate ChunkPool of "
 			          << totSz << " bytes" << std::endl;
 			exhausted();
@@ -141,14 +143,18 @@ class ChunkPool {
 	 */
 	void exhausted() {
 		if(patid != lastSkippedRead_) {
-			if(!exhaustCrash_) {
-				std::cerr << "Warning: ";
+			if(!exhaustCrash_ && !quiet) std::cerr << "Warning: ";
+			if(!quiet) {
+				std::cerr << "Exhausted best-first chunk memory for read "
+				          << (*readName_) << " (patid " << patid
+				          << "); skipping read" << std::endl;
+			}
+			if(exhaustCrash_) {
+				if(!quiet) {
+					std::cerr << "Please try specifying a larger --chunkmbs <int> (default is 32)" << std::endl;
+				}
+				throw 1;
 			}
-			std::cerr << "Exhausted best-first chunk memory for read " << (*readName_) << " (patid " << patid << "); skipping read" << std::endl;
-		}
-		if(exhaustCrash_) {
-			std::cerr << "Please try specifying a larger --chunkmbs <int> (default is 32)" << std::endl;
-			throw 1;
 		}
 		lastSkippedRead_ = patid;
 	}
@@ -334,7 +340,7 @@ class AllocOnlyPool {
 				throw std::bad_alloc();
 			}
 		} catch(std::bad_alloc& e) {
-			//std::cerr << "Error: Could not allocate " << name_ << " pool #" << (curPool_+1) << " of " << (lim_ * sizeof(T)) << " bytes" << std::endl;
+			ThreadSafe _ts(&gLock);
 			pool_->exhausted();
 			return false;
 		}
@@ -354,7 +360,7 @@ class AllocOnlyPool {
 					throw std::bad_alloc();
 				}
 			} catch(std::bad_alloc& e) {
-				//std::cerr << "Error: Could not allocate " << name_ << " pool #1" << std::endl;
+				ThreadSafe _ts(&gLock);
 				pool_->exhausted();
 				return false;
 			}

search_globals.h

@@ -8,12 +8,17 @@
 #ifndef SEARCH_GLOBALS_H_
 #define SEARCH_GLOBALS_H_
 
+#include "threading.h"
+
 // declared in ebwt_search.cpp
 extern bool color;
 extern bool colorExEnds;
 extern bool colorSeq;
 extern bool colorQual;
 extern int  snpPhred;
 extern bool showSeed;
+extern bool quiet;
+
+extern MUTEX_T gLock;
 
 #endif /* SEARCH_GLOBALS_H_ */

threading.h

@@ -14,8 +14,8 @@
 #  include "spinlock.h"
 #  define MUTEX_T SpinLock
 #  define MUTEX_INIT(l)
-#  define MUTEX_LOCK(l) l.Enter()
-#  define MUTEX_UNLOCK(l) l.Leave()
+#  define MUTEX_LOCK(l) (l).Enter()
+#  define MUTEX_UNLOCK(l) (l).Leave()
 #else
 #  ifdef BOWTIE_PTHREADS
 #    define MUTEX_T pthread_mutex_t
@@ -57,4 +57,18 @@ static inline void createThread(pthread_t* th,
 }
 #endif
 
+/**
+ * Wrap a lock; obtain lock upon construction, release upon destruction.
+ */
+class ThreadSafe {
+public:
+	ThreadSafe(MUTEX_T* lock) {
+		lock_ = lock;
+		MUTEX_LOCK(*lock_);
+	}
+	~ThreadSafe() { MUTEX_UNLOCK(*lock_); }
+private:
+	MUTEX_T *lock_;
+};
+
 #endif

tokenize.h

@@ -1,3 +1,10 @@
+/*
+ * tokenize.h
+ *
+ *  Created on: Jul 21, 2009
+ *      Author: Ben Langmead
+ */
+
 #ifndef TOKENIZE_H_
 #define TOKENIZE_H_