2 * Assume any read should have a name other than ""
15 #include "GroupInfo.h"
16 #include "Transcripts.h"
18 #include "SingleRead.h"
19 #include "SingleReadQ.h"
20 #include "PairedEndRead.h"
21 #include "PairedEndReadQ.h"
22 #include "SingleHit.h"
23 #include "PairedEndHit.h"
25 #include "HitContainer.h"
26 #include "SamParser.h"
30 int read_type; // 0 SingleRead, 1 SingleReadQ, 2 PairedEndRead, 3 PairedEndReadQ
31 READ_INT_TYPE N[3]; // note, N = N0 + N1 + N2 , but may not be equal to the total number of reads in data
32 HIT_INT_TYPE nHits; // # of hits
33 READ_INT_TYPE nUnique, nMulti, nIsoMulti;
35 char groupF[STRLEN], tiF[STRLEN];
36 char datF[STRLEN], cntF[STRLEN];
39 Transcripts transcripts;
44 int n_os; // number of ostreams
45 ostream *cat[3][2]; // cat : category 1-dim 0 N0 1 N1 2 N2; 2-dim 0 mate1 1 mate2
46 char readOutFs[3][2][STRLEN];
48 map<int, READ_INT_TYPE> counter;
49 map<int, READ_INT_TYPE>::iterator iter;
51 void init(const char* imdName, char alignFType, const char* alignF) {
54 if (strcmp(fn_list, "")) aux = fn_list;
55 parser = new SamParser(alignFType, alignF, aux, transcripts, imdName);
57 memset(cat, 0, sizeof(cat));
58 memset(readOutFs, 0, sizeof(readOutFs));
62 for (int i = 0; i < 3; i++) {
63 genReadFileNames(imdName, i, read_type, n_os, readOutFs[i]);
65 assert(tmp_n_os < 0 || tmp_n_os == n_os); tmp_n_os = n_os;
67 for (int j = 0; j < n_os; j++)
68 cat[i][j] = new ofstream(readOutFs[i][j]);
74 //Do not allow duplicate for unalignable reads and supressed reads in SAM input
75 template<class ReadType, class HitType>
76 void parseIt(SamParser *parser) {
77 // record_val & record_read are copies of val & read for record purpose
79 ReadType read, record_read;
81 HitContainer<HitType> hits;
84 nUnique = nMulti = nIsoMulti = 0;
85 memset(N, 0, sizeof(N));
87 READ_INT_TYPE cnt = 0;
89 record_val = -2; //indicate no recorded read now
90 while ((val = parser->parseNext(read, hit)) >= 0) {
91 if (val >= 0 && val <= 2) {
92 // flush out previous read's info if needed
93 if (record_val >= 0) {
94 record_read.write(n_os, cat[record_val]);
98 general_assert(record_val == 1 || hits.getNHits() == 0, "Read " + record_read.getName() + " is both unalignable and alignable according to the input SAM/BAM file!");
100 // flush out previous read's hits if the read is alignable reads
101 if (record_val == 1) {
103 nHits += hits.getNHits();
104 nMulti += hits.calcNumGeneMultiReads(gi);
105 nIsoMulti += hits.calcNumIsoformMultiReads();
108 iter = counter.find(hits.getNHits());
109 if (iter != counter.end()) {
113 counter[hits.getNHits()] = 1;
119 record_read = read; // no pointer, thus safe
122 if (val == 1 || val == 5) {
127 if (verbose && (cnt % 1000000 == 0)) { cout<< "Parsed "<< cnt<< " entries"<< endl; }
130 if (record_val >= 0) {
131 record_read.write(n_os, cat[record_val]);
135 if (record_val == 1) {
137 nHits += hits.getNHits();
138 nMulti += hits.calcNumGeneMultiReads(gi);
139 nIsoMulti += hits.calcNumIsoformMultiReads();
142 iter = counter.find(hits.getNHits());
143 if (iter != counter.end()) {
147 counter[hits.getNHits()] = 1;
151 nUnique = N[1] - nMulti;
155 for (int i = 0; i < 3; i++) {
156 for (int j = 0; j < n_os; j++) {
157 ((ofstream*)cat[i][j])->close();
160 if (N[i] > 0) continue;
161 for (int j = 0; j < n_os; j++) {
162 remove(readOutFs[i][j]); //delete if the file is empty
168 int main(int argc, char* argv[]) {
172 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");
179 for (int i = 6; i < argc; i++) {
180 if (!strcmp(argv[i], "-t")) {
181 read_type = atoi(argv[i + 1]);
183 if (!strcmp(argv[i], "-l")) {
184 strcpy(fn_list, argv[i + 1]);
186 if (!strcmp(argv[i], "-tag")) {
187 SamParser::setReadTypeTag(argv[i + 1]);
189 if (!strcmp(argv[i], "-q")) { quiet = true; }
195 sprintf(groupF, "%s.grp", argv[1]);
197 sprintf(tiF, "%s.ti", argv[1]);
198 transcripts.readFrom(tiF);
200 sprintf(datF, "%s.dat", argv[2]);
201 sprintf(cntF, "%s.cnt", argv[3]);
203 init(argv[2], argv[4][0], argv[5]);
207 string firstLine(99, ' ');
208 firstLine.append(1, '\n'); //May be dangerous!
212 case 0 : parseIt<SingleRead, SingleHit>(parser); break;
213 case 1 : parseIt<SingleReadQ, SingleHit>(parser); break;
214 case 2 : parseIt<PairedEndRead, PairedEndHit>(parser); break;
215 case 3 : parseIt<PairedEndReadQ, PairedEndHit>(parser); break;
218 hit_out.seekp(0, ios_base::beg);
219 hit_out<<N[1]<<" "<<nHits<<" "<<read_type;
223 //cntF for statistics of alignments file
225 fout<<N[0]<<" "<<N[1]<<" "<<N[2]<<" "<<(N[0] + N[1] + N[2])<<endl;
226 fout<<nUnique<<" "<<nMulti<<" "<<nIsoMulti<<endl;
227 fout<<nHits<<" "<<read_type<<endl;
228 fout<<"0\t"<<N[0]<<endl;
229 for (iter = counter.begin(); iter != counter.end(); iter++) {
230 fout<<iter->first<<'\t'<<iter->second<<endl;
232 fout<<"Inf\t"<<N[2]<<endl;
237 if (verbose) { printf("Done!\n"); }