#include "utils.h"
#include "GroupInfo.h"
-
-#include "RefSeq.h"
-#include "Refs.h"
+#include "Transcripts.h"
#include "SingleRead.h"
#include "SingleReadQ.h"
using namespace std;
int read_type; // 0 SingleRead, 1 SingleReadQ, 2 PairedEndRead, 3 PairedEndReadQ
-int N[3]; // note, N = N0 + N1 + N2 , but may not be equal to the total number of reads in data
-int nHits; // # of hits
-int nUnique, nMulti, nIsoMulti;
+READ_INT_TYPE N[3]; // note, N = N0 + N1 + N2 , but may not be equal to the total number of reads in data
+HIT_INT_TYPE nHits; // # of hits
+READ_INT_TYPE nUnique, nMulti, nIsoMulti;
char fn_list[STRLEN];
-char refF[STRLEN], groupF[STRLEN];
-char imdName[STRLEN];
+char groupF[STRLEN], tiF[STRLEN];
char datF[STRLEN], cntF[STRLEN];
-Refs refs;
GroupInfo gi;
+Transcripts transcripts;
SamParser *parser;
ofstream hit_out;
ostream *cat[3][2]; // cat : category 1-dim 0 N0 1 N1 2 N2; 2-dim 0 mate1 1 mate2
char readOutFs[3][2][STRLEN];
-map<int, int> counter;
-map<int, int>::iterator iter;
+map<int, READ_INT_TYPE> counter;
+map<int, READ_INT_TYPE>::iterator iter;
void init(const char* imdName, char alignFType, const char* alignF) {
char* aux = 0;
if (strcmp(fn_list, "")) aux = fn_list;
- parser = new SamParser(alignFType, alignF, refs, aux);
+ parser = new SamParser(alignFType, alignF, transcripts, aux);
memset(cat, 0, sizeof(cat));
memset(readOutFs, 0, sizeof(readOutFs));
nUnique = nMulti = nIsoMulti = 0;
memset(N, 0, sizeof(N));
- long long cnt = 0;
+ READ_INT_TYPE cnt = 0;
record_val = -2; //indicate no recorded read now
while ((val = parser->parseNext(read, hit)) >= 0) {
}
++cnt;
- if (verbose && (cnt % 1000000 == 0)) { printf("Parsed %lld entries\n", cnt); }
+ if (verbose && (cnt % 1000000 == 0)) { cout<< "Parsed "<< cnt<< " entries"<< endl; }
}
if (record_val >= 0) {
bool quiet = false;
if (argc < 6) {
- printf("Usage : rsem-parse-alignments refName sampleName sampleToken alignFType('s' for sam, 'b' for bam) alignF [-t Type] [-l fn_list] [-tag tagName] [-q]\n");
+ printf("Usage : rsem-parse-alignments refName imdName statName alignFType('s' for sam, 'b' for bam) alignF [-t Type] [-l fn_list] [-tag tagName] [-q]\n");
exit(-1);
}
verbose = !quiet;
- sprintf(refF, "%s.seq", argv[1]);
- refs.loadRefs(refF, 1);
sprintf(groupF, "%s.grp", argv[1]);
gi.load(groupF);
+ sprintf(tiF, "%s.ti", argv[1]);
+ transcripts.readFrom(tiF);
- sprintf(imdName, "%s.temp/%s", argv[2], argv[3]);
- sprintf(datF, "%s.dat", imdName);
- sprintf(cntF, "%s.stat/%s.cnt", argv[2], argv[3]);
+ sprintf(datF, "%s.dat", argv[2]);
+ sprintf(cntF, "%s.cnt", argv[3]);
- init(imdName, argv[4][0], argv[5]);
+ init(argv[2], argv[4][0], argv[5]);
hit_out.open(datF);
- string firstLine(59, ' ');
+ string firstLine(99, ' ');
firstLine.append(1, '\n'); //May be dangerous!
hit_out<<firstLine;