diff options
Diffstat (limited to 'reference.cpp')
| -rw-r--r-- | reference.cpp | 19 |
1 files changed, 10 insertions, 9 deletions
diff --git a/reference.cpp b/reference.cpp index 97a74ba..a1dc0c9 100644 --- a/reference.cpp +++ b/reference.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead <blangmea@jhsph.edu> + * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu> * * This file is part of Bowtie 2. * @@ -17,6 +17,7 @@ * along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>. */ +#include <string> #include <string.h> #include "reference.h" #include "mem_ids.h" @@ -52,7 +53,7 @@ BitPairReference::BitPairReference( #ifdef BOWTIE_MM int f3, f4; if((f3 = open(s3.c_str(), O_RDONLY)) < 0) { - cerr << "Could not open reference-string index file " << s3 << " for reading." << endl; + cerr << "Could not open reference-string index file " << s3.c_str() << " for reading." << endl; cerr << "This is most likely because your index was built with an older version" << endl << "(<= 0.9.8.1) of bowtie-build. Please re-run bowtie-build to generate a new" << endl << "index (or download one from the Bowtie website) and try again." << endl; @@ -60,14 +61,14 @@ BitPairReference::BitPairReference( return; } if((f4 = open(s4.c_str(), O_RDONLY)) < 0) { - cerr << "Could not open reference-string index file " << s4 << " for reading." << endl; + cerr << "Could not open reference-string index file " << s4.c_str() << " for reading." << endl; loaded_ = false; return; } char *mmFile = NULL; if(useMm_) { if(verbose_ || startVerbose) { - cerr << " Memory-mapping reference index file " << s4 << ": "; + cerr << " Memory-mapping reference index file " << s4.c_str() << ": "; logTime(cerr); } struct stat sbuf; @@ -128,7 +129,7 @@ BitPairReference::BitPairReference( uint32_t sz; sz = readU32(f3, swap); if(sz == 0) { - cerr << "Error: number of reference records is 0 in " << s3 << endl; + cerr << "Error: number of reference records is 0 in " << s3.c_str() << endl; throw 1; } @@ -193,7 +194,7 @@ BitPairReference::BitPairReference( sanityBuf_ = new uint8_t[cumsz >> 2]; size_t ret = fread(sanityBuf_, 1, cumsz >> 2, ftmp); if(ret != (cumsz >> 2)) { - cerr << "Only read " << ret << " bytes (out of " << (cumsz >> 2) << ") from reference index file " << s4 << endl; + cerr << "Only read " << ret << " bytes (out of " << (cumsz >> 2) << ") from reference index file " << s4.c_str() << endl; throw 1; } fclose(ftmp); @@ -226,7 +227,7 @@ BitPairReference::BitPairReference( // Open the bitpair-encoded reference file FILE *f4 = fopen(s4.c_str(), "rb"); if(f4 == NULL) { - cerr << "Could not open reference-string index file " << s4 << " for reading." << endl; + cerr << "Could not open reference-string index file " << s4.c_str() << " for reading." << endl; cerr << "This is most likely because your index was built with an older version" << endl << "(<= 0.9.8.1) of bowtie-build. Please re-run bowtie-build to generate a new" << endl << "index (or download one from the Bowtie website) and try again." << endl; @@ -237,7 +238,7 @@ BitPairReference::BitPairReference( size_t ret = fread(buf_, 1, cumsz >> 2, f4); // Didn't read all of it? if(ret != (cumsz >> 2)) { - cerr << "Only read " << ret << " bytes (out of " << (cumsz >> 2) << ") from reference index file " << s4 << endl; + cerr << "Only read " << ret << " bytes (out of " << (cumsz >> 2) << ") from reference index file " << s4.c_str() << endl; throw 1; } // Make sure there's no more @@ -593,7 +594,7 @@ BitPairReference::szsFromFasta( // hold the size records. ofstream fout3(file3.c_str(), ios::binary); if(!fout3.good()) { - cerr << "Could not open index file for writing: \"" << file3 << "\"" << endl + cerr << "Could not open index file for writing: \"" << file3.c_str() << "\"" << endl << "Please make sure the directory exists and that permissions allow writing by" << endl << "Bowtie." << endl; throw 1; |