1 #include "twoPassRunPass1.h"
2 #include "mapThreadsSpawn.h"
3 #include "ReadAlignChunk.h"
4 #include "Stats.h"
5 #include "GlobalVariables.h"
6 #include "outputSJ.h"
7 #include "sjdbInsertJunctions.h"
8
twoPassRunPass1(Parameters & P,Genome & genomeMain,Transcriptome * transcriptomeMain,SjdbClass & sjdbLoci)9 void twoPassRunPass1(Parameters &P, Genome &genomeMain, Transcriptome *transcriptomeMain, SjdbClass &sjdbLoci) //2-pass: 1st pass
10 {
11 if (!P.twoPass.yes)
12 return;
13
14 //re-define P and genomeMain for the pass1
15 Genome genomeMain1=genomeMain;
16
17 Parameters P1=P;
18 //turn off unnecessary calculations
19 P1.outSAMtype[0]="None";
20 P1.outSAMbool=false;
21 P1.outBAMunsorted=false;
22 P1.outBAMcoord=false;
23
24 P1.pCh.segmentMin=0;
25
26 P1.quant.yes=false;
27 P1.quant.trSAM.yes=false;
28 P1.quant.trSAM.bamYes=false;
29 P1.quant.geneFull.yes=false;
30 P1.quant.geCount.yes=false;
31 P1.quant.gene.yes=false;
32
33 P1.outSAMunmapped.within=false;
34
35 P1.outFilterBySJoutStage=0;
36
37 P1.outReadsUnmapped="None";
38
39 P1.outFileNamePrefix=P.twoPass.dir;
40
41 P1.readMapNumber=min(P.twoPass.pass1readsN, P.readMapNumber);
42 // P1.inOut->logMain.open((P1.outFileNamePrefix + "Log.out").c_str());
43
44 P1.wasp.outputMode="None"; //no WASP filtering on the 1st pass
45 P1.pSolo.type=P1.pSolo.SoloTypes::None; //no solo in the first pass
46
47 g_statsAll.resetN();
48 time(&g_statsAll.timeStartMap);
49 P.inOut->logProgress << timeMonthDayTime(g_statsAll.timeStartMap) <<"\tStarted 1st pass mapping\n" <<flush;
50 *P.inOut->logStdOut << timeMonthDayTime(g_statsAll.timeStartMap) << " ..... started 1st pass mapping\n" <<flush;
51
52 //run mapping for Pass1
53 ReadAlignChunk *RAchunk1[P.runThreadN];
54 for (int ii=0;ii<P1.runThreadN;ii++) {
55 RAchunk1[ii]=new ReadAlignChunk(P1, genomeMain, transcriptomeMain, ii);
56 };
57 mapThreadsSpawn(P1, RAchunk1);
58 outputSJ(RAchunk1,P1); //collapse and output junctions
59 // for (int ii=0;ii<P1.runThreadN;ii++) {
60 // delete [] RAchunk[ii];
61 // };
62
63 time_t rawtime; time (&rawtime);
64 P.inOut->logProgress << timeMonthDayTime(rawtime) <<"\tFinished 1st pass mapping\n";
65 *P.inOut->logStdOut << timeMonthDayTime(rawtime) << " ..... finished 1st pass mapping\n" <<flush;
66 ofstream logFinal1 ( (P.twoPass.dir + "/Log.final.out").c_str());
67 g_statsAll.reportFinal(logFinal1);
68
69 P.twoPass.pass2=true;//starting the 2nd pass
70 P.twoPass.pass1sjFile=P.twoPass.dir+"/SJ.out.tab";
71
72 sjdbInsertJunctions(P, genomeMain, genomeMain1, sjdbLoci);
73
74 //reopen reads files
75 P.closeReadsFiles();
76 P.openReadsFiles();
77 };