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langmead committed Nov 26, 2009
1 parent 734a792 commit 8ce7539
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Showing 13 changed files with 718 additions and 814 deletions.
3 changes: 1 addition & 2 deletions NEWS
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,7 @@ Version 0.12.0 - November 25, 2009
crash toward the end of execution with -p > 1.
* bowtie -f now supports fasta files with reads split across
multiple lines
* New --suppress option allows user to suppress unwanted columns of
output
* New --suppress option suppresses unwanted columns of output
* DEPRECATED: --concise
* REMOVED: -z/--phased, -b/--binout, bowtie-maptool,
bowtie-maqconvert
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48 changes: 4 additions & 44 deletions ebwt_search.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -76,14 +76,8 @@ static bool randReadsNoSync; // true -> generate reads from per-thread random s
static int numRandomReads; // # random reads (see Random*PatternSource in pat.h)
static int lenRandomReads; // len of random reads (see Random*PatternSource in pat.h)
static bool noRefNames; // true -> print reference indexes; not names
static string dumpAlFaBase; // basename of FASTA files to dump aligned reads to
static string dumpAlFqBase; // basename of FASTQ files to dump aligned reads to
static string dumpAlBase; // basename of same-format files to dump aligned reads to
static string dumpUnalFaBase; // basename of FASTA files to dump unaligned reads to
static string dumpUnalFqBase; // basename of FASTQ files to dump unaligned reads to
static string dumpUnalBase; // basename of same-format files to dump unaligned reads to
static string dumpMaxFaBase; // basename of FASTA files to dump reads with more than -m valid alignments to
static string dumpMaxFqBase; // basename of FASTQ files to dump reads with more than -m valid alignments to
static string dumpMaxBase; // basename of same-format files to dump reads with more than -m valid alignments to
static uint32_t khits; // number of hits per read; >1 is much slower
static uint32_t mhits; // don't report any hits if there are > mhits
Expand Down Expand Up @@ -180,14 +174,8 @@ static void resetOptions() {
numRandomReads = 50000000; // # random reads (see Random*PatternSource in pat.h)
lenRandomReads = 35; // len of random reads (see Random*PatternSource in pat.h)
noRefNames = false; // true -> print reference indexes; not names
dumpAlFaBase = ""; // basename of FASTA files to dump aligned reads to
dumpAlFqBase = ""; // basename of FASTQ files to dump aligned reads to
dumpAlBase = ""; // basename of same-format files to dump aligned reads to
dumpUnalFaBase = ""; // basename of FASTA files to dump unaligned reads to
dumpUnalFqBase = ""; // basename of FASTQ files to dump unaligned reads to
dumpUnalBase = ""; // basename of same-format files to dump unaligned reads to
dumpMaxFaBase = ""; // basename of FASTA files to dump reads with more than -m valid alignments to
dumpMaxFqBase = ""; // basename of FASTQ files to dump reads with more than -m valid alignments to
dumpMaxBase = ""; // basename of same-format files to dump reads with more than -m valid alignments to
khits = 1; // number of hits per read; >1 is much slower
mhits = 0xffffffff; // don't report any hits if there are > mhits
Expand Down Expand Up @@ -337,7 +325,6 @@ static struct option long_options[] = {
{(char*)"orig", required_argument, 0, ARG_ORIG},
{(char*)"all", no_argument, 0, 'a'},
{(char*)"concise", no_argument, 0, ARG_CONCISE},
{(char*)"binout", no_argument, 0, 'b'},
{(char*)"noout", no_argument, 0, ARG_NOOUT},
{(char*)"solexa-quals", no_argument, 0, ARG_SOLEXA_QUALS},
{(char*)"integer-quals",no_argument, 0, ARG_integerQuals},
Expand Down Expand Up @@ -973,9 +960,7 @@ static void printLongUsage(ostream& out) {
" is specified, Bowtie gets the reads from stdin.\n"
"\n"
" <hit> File to write alignments to. By default,\n"
" alignments are written to stdout (the console),\n"
" but a <hits> file must be specified if the\n"
" -b/--binout option is also specified.\n"
" alignments are written to stdout (the console)\n"
"\n"
" Options:\n"
" ========\n"
Expand Down Expand Up @@ -1641,7 +1626,6 @@ static void parseOptions(int argc, const char **argv) {
case ARG_RANGE: rangeMode = true; break;
case ARG_CONCISE: outType = OUTPUT_CONCISE; break;
case ARG_CHAINOUT: outType = OUTPUT_CHAIN; break;
case 'b': outType = OUTPUT_BINARY; break;
case 'S': outType = OUTPUT_SAM; break;
case ARG_REFOUT: refOut = true; break;
case ARG_NOOUT: outType = OUTPUT_NONE; break;
Expand Down Expand Up @@ -2861,7 +2845,6 @@ static void twoOrThreeMismatchSearchFull(
bool two = true) /// true -> 2, false -> 3
{
// Global initialization
assert(fullIndex);
assert(!ebwtFw.isInMemory());
assert(!ebwtBw.isInMemory());
{
Expand Down Expand Up @@ -3270,7 +3253,6 @@ static void seededQualCutoffSearchFull(
vector<String<Dna5> >& os) /// text strings, if available (empty otherwise)
{
// Global intialization
assert(fullIndex);
assert_leq(seedMms, 3);

seededQualSearch_patsrc = &_patsrc;
Expand Down Expand Up @@ -3399,10 +3381,7 @@ patsrcFromStrings(int format, const vector<string>& qs) {
}
}

#define PASS_DUMP_FILES \
dumpAlFaBase, dumpAlFqBase, dumpAlBase, \
dumpUnalFaBase, dumpUnalFqBase, dumpUnalBase, \
dumpMaxFaBase, dumpMaxFqBase, dumpMaxBase
#define PASS_DUMP_FILES dumpAlBase, dumpUnalBase, dumpMaxBase

static string argstr;

Expand Down Expand Up @@ -3549,14 +3528,10 @@ static void driver(const char * type,
cerr << "Warning: ignoring alignment output file " << outfile << " because --refout was specified" << endl;
}
} else {
fout = new OutFileBuf(outfile.c_str(), outType == OUTPUT_BINARY);
fout = new OutFileBuf(outfile.c_str(), false);
}
} else {
if(outType == OUTPUT_BINARY && !refOut) {
cerr << "Error: Must specify an output file when output mode is binary" << endl;
throw 1;
}
else if(outType == OUTPUT_CHAIN) {
if(outType == OUTPUT_CHAIN && !refOut) {
cerr << "Error: Must specify an output file when output mode is --chain" << endl;
throw 1;
}
Expand Down Expand Up @@ -3703,21 +3678,6 @@ static void driver(const char * type,
table, refnames, reportOpps);
}
break;
case OUTPUT_BINARY:
if(refOut) {
sink = new BinaryHitSink(
ebwt.nPat(), offBase,
PASS_DUMP_FILES,
format == TAB_MATE,
table, refnames);
} else {
sink = new BinaryHitSink(
fout, offBase,
PASS_DUMP_FILES,
format == TAB_MATE,
table, refnames);
}
break;
case OUTPUT_CHAIN:
assert(stateful);
sink = new ChainingHitSink(
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