RSEM v1.1.8

[rsem.git] / parseIt.cpp

diff --git a/parseIt.cpp b/parseIt.cpp
index 55dd954d3d1e2059911987ed5a8521748b16e9a1..e05585d43f5a6a897f874f90506a8add3bc3e571 100644 (file)
--- a/parseIt.cpp
+++ b/parseIt.cpp
@@ -14,8 +14,8 @@
 
 #include "GroupInfo.h"
 
-#include "Transcript.h"
-#include "Transcripts.h"
+#include "RefSeq.h"
+#include "Refs.h"
 
 #include "SingleRead.h"
 #include "SingleReadQ.h"
@@ -34,12 +34,12 @@ int N[3]; // note, N = N0 + N1 + N2 , but may not be equal to the total number o
 int nHits; // # of hits
 int nUnique, nMulti, nIsoMulti;
 char fn_list[STRLEN];
-char groupF[STRLEN], tiF[STRLEN];
+char refF[STRLEN], groupF[STRLEN];
 char imdName[STRLEN];
 char datF[STRLEN], cntF[STRLEN];
 
+Refs refs;
 GroupInfo gi;
-Transcripts transcripts;
 
 SamParser *parser;
 ofstream hit_out;
@@ -55,7 +55,7 @@ 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, transcripts, aux);
+       parser = new SamParser(alignFType, alignF, refs, aux);
 
        memset(cat, 0, sizeof(cat));
        memset(readOutFs, 0, sizeof(readOutFs));
@@ -96,6 +96,9 @@ void parseIt(SamParser *parser) {
                        if (record_val >= 0) {
                                record_read.write(n_os, cat[record_val]);
                                ++N[record_val];
+                       }
+                       // flush out previous read's hits if the read is alignable reads
+                       if (record_val == 1) {
                                hits.updateRI();
                                nHits += hits.getNHits();
                                nMulti += hits.calcNumGeneMultiReads(gi);
@@ -127,6 +130,9 @@ void parseIt(SamParser *parser) {
        if (record_val >= 0) {
                record_read.write(n_os, cat[record_val]);
                ++N[record_val];
+       }
+
+       if (record_val == 1) {
                hits.updateRI();
                nHits += hits.getNHits();
                nMulti += hits.calcNumGeneMultiReads(gi);
@@ -186,10 +192,10 @@ int main(int argc, char* argv[]) {
 
        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);
@@ -220,9 +226,11 @@ int main(int argc, char* argv[]) {
        fout<<N[0]<<" "<<N[1]<<" "<<N[2]<<" "<<(N[0] + N[1] + N[2])<<endl;
        fout<<nUnique<<" "<<nMulti<<" "<<nIsoMulti<<endl;
        fout<<nHits<<" "<<read_type<<endl;
+       fout<<"0\t"<<N[0]<<endl;
        for (iter = counter.begin(); iter != counter.end(); iter++) {
                fout<<iter->first<<'\t'<<iter->second<<endl;
        }
+       fout<<"Inf\t"<<N[2]<<endl;
        fout.close();
 
        release();