--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/utils/Fasta/Fasta.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,325 @@
+// ***************************************************************************
+// FastaIndex.cpp (c) 2010 Erik Garrison <erik.garrison@bc.edu>
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 9 February 2010 (EG)
+// ---------------------------------------------------------------------------
+
+#include "Fasta.h"
+
+FastaIndexEntry::FastaIndexEntry(string name, int length, long long offset, int line_blen, int line_len)
+    : name(name)
+    , length(length)
+    , offset(offset)
+    , line_blen(line_blen)
+    , line_len(line_len)
+{}
+
+FastaIndexEntry::FastaIndexEntry(void) // empty constructor
+{ clear(); }
+
+FastaIndexEntry::~FastaIndexEntry(void)
+{}
+
+void FastaIndexEntry::clear(void)
+{
+    name = "";
+    length = NULL;
+    offset = -1;  // no real offset will ever be below 0, so this allows us to
+                  // check if we have already recorded a real offset
+    line_blen = NULL;
+    line_len  = NULL;
+}
+
+ostream& operator<<(ostream& output, const FastaIndexEntry& e) {
+    // just write the first component of the name, for compliance with other tools
+    output << split(e.name, ' ').at(0) << "\t" << e.length << "\t" << e.offset << "\t" <<
+        e.line_blen << "\t" << e.line_len;
+    return output;  // for multiple << operators.
+}
+
+FastaIndex::FastaIndex(void) 
+{}
+
+void FastaIndex::readIndexFile(string fname) {
+    string line;
+    long long linenum = 0;
+    indexFile.open(fname.c_str(), ifstream::in);
+    if (indexFile.is_open()) {
+        while (getline (indexFile, line)) {
+            ++linenum;
+            // the fai format defined in samtools is tab-delimited, every line being:
+            // fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len
+            vector<string> fields = split(line, '\t');
+            if (fields.size() == 5) {  // if we don't get enough fields then there is a problem with the file
+                // note that fields[0] is the sequence name
+                char* end;
+                string name = split(fields[0], " \t").at(0);  // key by first token of name
+                sequenceNames.push_back(name);
+                this->insert(make_pair(name, FastaIndexEntry(fields[0], atoi(fields[1].c_str()),
+                                                    strtoll(fields[2].c_str(), &end, 10),
+                                                    atoi(fields[3].c_str()),
+                                                    atoi(fields[4].c_str()))));
+            } else {
+                cerr << "Warning: malformed fasta index file " << fname << 
+                    "does not have enough fields @ line " << linenum << endl;
+                cerr << line << endl;
+                exit(1);
+            }
+        }
+    } else {
+        cerr << "could not open index file " << fname << endl;
+        exit(1);
+    }
+}
+
+// for consistency this should be a class method
+bool fastaIndexEntryCompare ( FastaIndexEntry a, FastaIndexEntry b) { return (a.offset<b.offset); }
+
+ostream& operator<<(ostream& output, FastaIndex& fastaIndex) {
+    vector<FastaIndexEntry> sortedIndex;
+    for(vector<string>::const_iterator it = fastaIndex.sequenceNames.begin(); it != fastaIndex.sequenceNames.end(); ++it)
+    {
+        sortedIndex.push_back(fastaIndex[*it]);
+    }
+    sort(sortedIndex.begin(), sortedIndex.end(), fastaIndexEntryCompare);
+    for( vector<FastaIndexEntry>::iterator fit = sortedIndex.begin(); fit != sortedIndex.end(); ++fit) {
+        output << *fit << endl;
+    }
+    return output;
+}
+
+void FastaIndex::indexReference(string refname) {
+    // overview:
+    //  for line in the reference fasta file
+    //  track byte offset from the start of the file
+    //  if line is a fasta header, take the name and dump the last sequnece to the index
+    //  if line is a sequence, add it to the current sequence
+    //cerr << "indexing fasta reference " << refname << endl;
+    string line;
+    FastaIndexEntry entry;  // an entry buffer used in processing
+    entry.clear();
+    int line_length = 0;
+    long long offset = 0;  // byte offset from start of file
+    long long line_number = 0; // current line number
+    bool mismatchedLineLengths = false; // flag to indicate if our line length changes mid-file
+                                        // this will be used to raise an error
+                                        // if we have a line length change at
+                                        // any line other than the last line in
+                                        // the sequence
+    bool emptyLine = false;  // flag to catch empty lines, which we allow for
+                             // index generation only on the last line of the sequence
+    ifstream refFile;
+    refFile.open(refname.c_str());
+    if (refFile.is_open()) {
+        while (getline(refFile, line)) {
+            ++line_number;
+            line_length = line.length();
+            if (line[0] == ';') {
+                // fasta comment, skip
+            } else if (line[0] == '+') {
+                // fastq quality header
+                getline(refFile, line);
+                line_length = line.length();
+                offset += line_length + 1;
+                // get and don't handle the quality line
+                getline(refFile, line);
+                line_length = line.length();
+            } else if (line[0] == '>' || line[0] == '@') { // fasta /fastq header
+                // if we aren't on the first entry, push the last sequence into the index
+                if (entry.name != "") {
+                    mismatchedLineLengths = false; // reset line length error tracker for every new sequence
+                    emptyLine = false;
+                    flushEntryToIndex(entry);
+                    entry.clear();
+                }
+                entry.name = line.substr(1, line_length - 1);
+            } else { // we assume we have found a sequence line
+                if (entry.offset == -1) // NB initially the offset is -1
+                    entry.offset = offset;
+                entry.length += line_length;
+                if (entry.line_len) {
+                    //entry.line_len = entry.line_len ? entry.line_len : line_length + 1;
+                    if (mismatchedLineLengths || emptyLine) {
+                        if (line_length == 0) {
+                            emptyLine = true; // flag empty lines, raise error only if this is embedded in the sequence
+                        } else {
+                            if (emptyLine) {
+                                cerr << "ERROR: embedded newline";
+                            } else {
+                                cerr << "ERROR: mismatched line lengths";
+                            }
+                            cerr << " at line " << line_number << " within sequence " << entry.name <<
+                                endl << "File not suitable for fasta index generation." << endl;
+                            exit(1);
+                        }
+                    }
+                    // this flag is set here and checked on the next line
+                    // because we may have reached the end of the sequence, in
+                    // which case a mismatched line length is OK
+                    if (entry.line_len != line_length + 1) {
+                        mismatchedLineLengths = true;
+                        if (line_length == 0) {
+                            emptyLine = true; // flag empty lines, raise error only if this is embedded in the sequence
+                        }
+                    }
+                } else {
+                    entry.line_len = line_length + 1; // first line
+                }
+                entry.line_blen = entry.line_len - 1;
+            }
+            offset += line_length + 1;
+        }
+        // we've hit the end of the fasta file!
+        // flush the last entry
+        flushEntryToIndex(entry);
+    } else {
+        cerr << "could not open reference file " << refname << " for indexing!" << endl;
+        exit(1);
+    }
+}
+
+void FastaIndex::flushEntryToIndex(FastaIndexEntry& entry) {
+    string name = split(entry.name, " \t").at(0);  // key by first token of name
+    sequenceNames.push_back(name);
+    this->insert(make_pair(name, FastaIndexEntry(entry.name, entry.length,
+                        entry.offset, entry.line_blen,
+                        entry.line_len)));
+
+}
+
+void FastaIndex::writeIndexFile(string fname) {
+    //cerr << "writing fasta index file " << fname << endl;
+    ofstream file;
+    file.open(fname.c_str()); 
+    if (file.is_open()) {
+        file << *this;
+    } else { 
+        cerr << "could not open index file " << fname << " for writing!" << endl;
+        exit(1);
+    }
+}
+
+FastaIndex::~FastaIndex(void) {
+    indexFile.close();
+}
+
+FastaIndexEntry FastaIndex::entry(string name) {
+    FastaIndex::iterator e = this->find(name);
+    if (e == this->end()) {
+        cerr << "unable to find FASTA index entry for '" << name << "'" << endl;
+        exit(1);
+    } else {
+        return e->second;
+    }
+}
+
+string FastaIndex::indexFileExtension() { return ".fai"; }
+
+void FastaReference::open(string reffilename, bool usemmap) {
+    filename = reffilename;
+    if (!(file = fopen(filename.c_str(), "r"))) {
+        cerr << "could not open " << filename << endl;
+        exit(1);
+    }
+    index = new FastaIndex();
+    struct stat stFileInfo; 
+    string indexFileName = filename + index->indexFileExtension(); 
+    // if we can find an index file, use it
+    if(stat(indexFileName.c_str(), &stFileInfo) == 0) { 
+        index->readIndexFile(indexFileName);
+    } else { // otherwise, read the reference and generate the index file in the cwd
+        cerr << "index file " << indexFileName << " not found, generating..." << endl;
+        index->indexReference(filename);
+        index->writeIndexFile(indexFileName);
+    }
+    if (usemmap) {
+        usingmmap = true;
+        int fd = fileno(file);
+        struct stat sb;
+        if (fstat(fd, &sb) == -1)
+            cerr << "could not stat file" << filename << endl;
+        filesize = sb.st_size;
+        // map the whole file
+        filemm = mmap(NULL, filesize, PROT_READ, MAP_SHARED, fd, 0);
+    }
+}
+
+FastaReference::~FastaReference(void) {
+    fclose(file);
+    if (usingmmap) {
+        munmap(filemm, filesize);
+    }
+    delete index;
+}
+
+string FastaReference::getSequence(string seqname) {
+    FastaIndexEntry entry = index->entry(seqname);
+    int newlines_in_sequence = entry.length / entry.line_blen;
+    int seqlen = newlines_in_sequence  + entry.length;
+    char* seq = (char*) calloc (seqlen + 1, sizeof(char));
+    if (usingmmap) {
+        memcpy(seq, (char*) filemm + entry.offset, seqlen);
+    } else {
+        fseek64(file, entry.offset, SEEK_SET);
+        fread(seq, sizeof(char), seqlen, file);
+    }
+    seq[seqlen] = '\0';
+    char* pbegin = seq;
+    char* pend = seq + (seqlen/sizeof(char));
+    pend = remove(pbegin, pend, '\n');
+    pend = remove(pbegin, pend, '\0');
+    string s = seq;
+    free(seq);
+    s.resize((pend - pbegin)/sizeof(char));
+    return s;
+}
+
+// TODO cleanup; odd function.  use a map
+string FastaReference::sequenceNameStartingWith(string seqnameStart) {
+    try {
+        return (*index)[seqnameStart].name;
+    } catch (exception& e) {
+        cerr << e.what() << ": unable to find index entry for " << seqnameStart << endl;
+        exit(1);
+    }
+}
+
+string FastaReference::getSubSequence(string seqname, int start, int length) {
+    FastaIndexEntry entry = index->entry(seqname);
+    if (start < 0 || length < 1) {
+        cerr << "Error: cannot construct subsequence with negative offset or length < 1" << endl;
+        exit(1);
+    }
+    // we have to handle newlines
+    // approach: count newlines before start
+    //           count newlines by end of read
+    //             subtracting newlines before start find count of embedded newlines
+    int newlines_before = start > 0 ? (start - 1) / entry.line_blen : 0;
+    int newlines_by_end = (start + length - 1) / entry.line_blen;
+    int newlines_inside = newlines_by_end - newlines_before;
+    int seqlen = length + newlines_inside;
+    char* seq = (char*) calloc (seqlen + 1, sizeof(char));
+    if (usingmmap) {
+        memcpy(seq, (char*) filemm + entry.offset + newlines_before + start, seqlen);
+    } else {
+        fseek64(file, (off_t) (entry.offset + newlines_before + start), SEEK_SET);
+        fread(seq, sizeof(char), (off_t) seqlen, file);
+    }
+    seq[seqlen] = '\0';
+    char* pbegin = seq;
+    char* pend = seq + (seqlen/sizeof(char));
+    pend = remove(pbegin, pend, '\n');
+    pend = remove(pbegin, pend, '\0');
+    string s = seq;
+    free(seq);
+    s.resize((pend - pbegin)/sizeof(char));
+    return s;
+}
+
+long unsigned int FastaReference::sequenceLength(string seqname) {
+    FastaIndexEntry entry = index->entry(seqname);
+    return entry.length;
+}
+