/**
* Takes a data stream compressed with bzip2, and writes it out to disk, uncompresses it, and deletes the
* compressed version.
*/
static bool DecompressBZipToDisk( const char *outFilename, const char *srcFilename, char *data, int bytesTotal )
{
if ( g_pFileSystem->FileExists( outFilename ) || !data || bytesTotal < 1 )
{
return false;
}
// Create the subdirs
char * tmpDir = CloneString( outFilename );
COM_CreatePath( tmpDir );
delete[] tmpDir;
// open the file for writing
char fullSrcPath[MAX_PATH];
Q_MakeAbsolutePath( fullSrcPath, sizeof( fullSrcPath ), srcFilename, com_gamedir );
if ( !g_pFileSystem->FileExists( fullSrcPath ) )
{
// Write out the .bz2 file, for simplest decompression
FileHandle_t ifp = g_pFileSystem->Open( fullSrcPath, "wb" );
if ( !ifp )
{
return false;
}
int bytesWritten = g_pFileSystem->Write( data, bytesTotal, ifp );
g_pFileSystem->Close( ifp );
if ( bytesWritten != bytesTotal )
{
// couldn't write out all of the .bz2 file
g_pFileSystem->RemoveFile( srcFilename );
return false;
}
}
// Prepare the uncompressed filehandle
FileHandle_t ofp = g_pFileSystem->Open( outFilename, "wb" );
if ( !ofp )
{
g_pFileSystem->RemoveFile( srcFilename );
return false;
}
// And decompress!
const int OutBufSize = 65536;
char buf[ OutBufSize ];
BZFILE *bzfp = BZ2_bzopen( fullSrcPath, "rb" );
while ( 1 )
{
int bytesRead = BZ2_bzread( bzfp, buf, OutBufSize );
if ( bytesRead < 0 )
{
break; // error out
}
if ( bytesRead > 0 )
{
int bytesWritten = g_pFileSystem->Write( buf, bytesRead, ofp );
if ( bytesWritten != bytesRead )
{
break; // error out
}
}
else
{
g_pFileSystem->Close( ofp );
BZ2_bzclose( bzfp );
g_pFileSystem->RemoveFile( srcFilename );
return true;
}
}
// We failed somewhere, so clean up and exit
g_pFileSystem->Close( ofp );
BZ2_bzclose( bzfp );
g_pFileSystem->RemoveFile( srcFilename );
g_pFileSystem->RemoveFile( outFilename );
return false;
}
int filter_pe_fastq_bz2(FLT_OPTS *opts){
int left1=0,left2=0;
int stat_single1 = 0;
int stat_single2 = 0;
int stat_paired = 0;
int index=1;
char fn[128];
char outfile[128];
SEQ_QUAL item1=init_read();
SEQ_QUAL item2=init_read();
BZFILE *fp1=bzopen_report(opts->r1,"r");
BZFILE *fp2=bzopen_report(opts->r2,"r");
file_name(outfile,opt->r1);
sprintf(fn,"%s/%s.flt",opts->output,outfile);
FILE *fo1=fopen_report(fn,"w+");
if(!fo1) return -1;
file_name(outfile,opts->r2);
sprintf(fn,"%s/%s.flt",opts->output,outfile);
FILE *fo2=fopen_report(fn,"w+");
if(!fo2) return -1;
sprintf(fn,"%s/%s.flt.s",opts->output,outfile);
FILE *fos=fopen_report(fn,"w+");
if(!fos) return -1;
while(read_fastq_bz2(fp1,&item1,index) >= 0 && read_fastq_bz2(fp2,&item2,index) >= 0)
{
left1=filter_all(&item1, opts);
left2=filter_all(&item2, opts);
if(left1 == 1 && left2 == 1){
output_fastq(fo1, &item1);
output_fastq(fo2, &item2);
stat_single1++;
stat_single2++;
stat_paired++;
}else{
if(left1 == 1){
output_fastq(fos, &item1);
stat_single1++;
}
if(left2 == 1){
output_fastq(fos, &item2);
stat_single2++;
}
}
index++;
}
printf("Totally %d reads were processed\n",(index-1)*2);
printf(" file [ %s ]: %d reads were left (%.2f%)\n",opts->r1,stat_paired+stat_single1,(float) (stat_paired+stat_single1)*100/(index-1));
printf(" file [ %s ]: %d reads were left (%.2f%)\n",opts->r2,stat_paired+stat_single2,(float) (stat_paired+stat_single2)*100/(index-1));
printf("After filtering %d reads are paired in each file (%.2f%)\n",stat_paired,(float) stat_paired*100/(index-1));
printf(" file [ %s ]: %d reads were left as single end\n",opts->r1,stat_single1);
printf(" file [ %s ]: %d reads were left as single end\n",opts->r2,stat_single2);
free_read(&item1);
free_read(&item2);
BZ2_bzclose(fp1);
BZ2_bzclose(fp2);
fclose(fo1);
fclose(fo2);
fclose(fos);
return 0;
}