Removed Mac ._* files from repo

[rsem.git] / parseIt.cpp

diff --git a/parseIt.cpp b/parseIt.cpp
index c266715b31693686f7db773155d01e7905321102..3373ef280979428230b74d77439d61bff3a96d47 100644 (file)
--- a/parseIt.cpp
+++ b/parseIt.cpp
@@ -8,10 +8,12 @@
 #include<iostream>
 #include<fstream>
 #include<string>
+#include<map>
 
 #include "utils.h"
 
 #include "GroupInfo.h"
+#include "Transcripts.h"
 
 #include "SingleRead.h"
 #include "SingleReadQ.h"
@@ -26,14 +28,15 @@
 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 groupF[STRLEN];
+char groupF[STRLEN], tiF[STRLEN];
 char datF[STRLEN], cntF[STRLEN];
 
 GroupInfo gi;
+Transcripts transcripts;
 
 SamParser *parser;
 ofstream hit_out;
@@ -42,14 +45,14 @@ int n_os; // number of ostreams
 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];
 
-void init(const char* imdName, char alignFType, const char* alignF) {
+map<int, READ_INT_TYPE> counter;
+map<int, READ_INT_TYPE>::iterator iter;
 
-       sprintf(datF, "%s.dat", imdName);
-       sprintf(cntF, "%s.cnt", imdName);
+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, aux);
+       parser = new SamParser(alignFType, alignF, transcripts, aux);
 
        memset(cat, 0, sizeof(cat));
        memset(readOutFs, 0, sizeof(readOutFs));
@@ -64,6 +67,8 @@ void init(const char* imdName, char alignFType, const char* alignF) {
                for (int j = 0; j < n_os; j++)
                        cat[i][j] = new ofstream(readOutFs[i][j]);
        }
+
+       counter.clear();
 }
 
 //Do not allow duplicate for unalignable reads and supressed reads in SAM input
@@ -79,7 +84,7 @@ void parseIt(SamParser *parser) {
        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) {
@@ -88,11 +93,22 @@ 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);
                                nIsoMulti += hits.calcNumIsoformMultiReads();
                                hits.write(hit_out);
+
+                               iter = counter.find(hits.getNHits());
+                               if (iter != counter.end()) {
+                                       iter->second++;
+                               }
+                               else {
+                                       counter[hits.getNHits()] = 1;
+                               }
                        }
 
                        hits.clear();
@@ -105,17 +121,28 @@ void parseIt(SamParser *parser) {
                }
 
                ++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) {
                record_read.write(n_os, cat[record_val]);
                ++N[record_val];
+       }
+
+       if (record_val == 1) {
                hits.updateRI();
                nHits += hits.getNHits();
                nMulti += hits.calcNumGeneMultiReads(gi);
                nIsoMulti += hits.calcNumIsoformMultiReads();
                hits.write(hit_out);
+
+               iter = counter.find(hits.getNHits());
+               if (iter != counter.end()) {
+                       iter->second++;
+               }
+               else {
+                       counter[hits.getNHits()] = 1;
+               }
        }
 
        nUnique = N[1] - nMulti;
@@ -138,15 +165,15 @@ void release() {
 int main(int argc, char* argv[]) {
        bool quiet = false;
 
-       if (argc < 5) {
-               printf("Usage : rsem-parse-alignments refName imdName alignFType('s' for sam, 'b' for bam) alignF [-t Type] [-l fn_list] [-tag tagName] [-q]\n");
+       if (argc < 6) {
+               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);
        }
 
        strcpy(fn_list, "");
        read_type = 0;
-       if (argc > 5) {
-               for (int i = 5; i < argc; i++) {
+       if (argc > 6) {
+               for (int i = 6; i < argc; i++) {
                        if (!strcmp(argv[i], "-t")) {
                                read_type = atoi(argv[i + 1]);
                        }
@@ -162,14 +189,19 @@ int main(int argc, char* argv[]) {
 
        verbose = !quiet;
 
-       init(argv[2], argv[3][0], argv[4]);
-
        sprintf(groupF, "%s.grp", argv[1]);
        gi.load(groupF);
+       sprintf(tiF, "%s.ti", argv[1]);
+       transcripts.readFrom(tiF);
+
+       sprintf(datF, "%s.dat", argv[2]);
+       sprintf(cntF, "%s.cnt", argv[3]);
+
+       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;
 
@@ -190,6 +222,11 @@ 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();