void scan_libInfo ( char * libfile )
{
FILE * fp;
char line[1024], ch;
int i, j, index;
int libCounter;
boolean flag;
boolean * pe;
fp = ckopen ( libfile, "r" );
num_libs = 0;
while ( fgets ( line, 1024, fp ) )
{
ch = line[5];
line[5] = '\0';
if ( strcmp ( line, "[LIB]" ) == 0 )
{
num_libs++;
}
if ( !num_libs )
{
line[5] = ch;
flag = splitColumn ( line );
if ( !flag )
{
continue;
}
if ( strcmp ( tabs[0], "max_rd_len" ) == 0 )
{
maxReadLen = atoi ( tabs[1] );
}
}
}
if ( num_libs == 0 )
{
fprintf ( stderr, "Config file error: no [LIB] in file\n" );
exit ( -1 );
}
//count file numbers of each type
lib_array = ( LIB_INFO * ) ckalloc ( num_libs * sizeof ( LIB_INFO ) );
pe = ( boolean * ) ckalloc ( num_libs * sizeof ( boolean ) );
for ( i = 0; i < num_libs; i++ )
{
lib_array[i].asm_flag = 3;
lib_array[i].rank = 0;
lib_array[i].pair_num_cut = 0;
lib_array[i].rd_len_cutoff = 0;
lib_array[i].map_len = 0;
lib_array[i].num_s_a_file = 0;
lib_array[i].num_s_q_file = 0;
lib_array[i].num_p_file = 0;
lib_array[i].num_a1_file = 0;
lib_array[i].num_a2_file = 0;
lib_array[i].num_q1_file = 0;
lib_array[i].num_q2_file = 0;
lib_array[i].num_b_file = 0; //init
pe[i] = false;
}
libCounter = -1;
rewind ( fp );
i = -1;
while ( fgets ( line, 1024, fp ) )
{
ch = line[5];
line[5] = '\0';
if ( strcmp ( line, "[LIB]" ) == 0 )
{
i++;
continue;
}
line[5] = ch;
flag = splitColumn ( line );
if ( !flag )
{
continue;
}
if ( strcmp ( tabs[0], "f1" ) == 0 )
{
lib_array[i].num_a1_file++;
pe[i] = true;
}
else if ( strcmp ( tabs[0], "q1" ) == 0 )
{
lib_array[i].num_q1_file++;
pe[i] = true;
}
else if ( strcmp ( tabs[0], "f2" ) == 0 )
{
lib_array[i].num_a2_file++;
pe[i] = true;
}
else if ( strcmp ( tabs[0], "q2" ) == 0 )
{
lib_array[i].num_q2_file++;
pe[i] = true;
}
else if ( strcmp ( tabs[0], "f" ) == 0 )
{
lib_array[i].num_s_a_file++;
}
else if ( strcmp ( tabs[0], "q" ) == 0 )
{
lib_array[i].num_s_q_file++;
}
else if ( strcmp ( tabs[0], "p" ) == 0 )
{
lib_array[i].num_p_file++;
pe[i] = true;
}
else if ( strcmp ( tabs[0], "b" ) == 0 ) // the bam file
{
lib_array[i].num_b_file++;
pe[i] = true;
}
}
//allocate memory for filenames
for ( i = 0; i < num_libs; i++ )
{
if ( lib_array[i].num_a2_file != lib_array[i].num_a1_file )
{
fprintf ( stderr, "Config file error: the number of mark \"f1\" is not the same as \"f2\"!\n" );
exit ( -1 );
}
if ( lib_array[i].num_q2_file != lib_array[i].num_q1_file )
{
fprintf ( stderr, "Config file error: the number of mark \"q1\" is not the same as \"q2\"!\n" );
exit ( -1 );
}
if ( lib_array[i].num_s_a_file )
{
lib_array[i].s_a_fname = ( char ** ) ckalloc ( lib_array[i].num_s_a_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_s_a_file; j++ )
{
lib_array[i].s_a_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) );
}
}
if ( lib_array[i].num_s_q_file )
{
lib_array[i].s_q_fname = ( char ** ) ckalloc ( lib_array[i].num_s_q_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_s_q_file; j++ )
{
lib_array[i].s_q_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) );
}
}
if ( lib_array[i].num_p_file )
{
lib_array[i].p_fname = ( char ** ) ckalloc ( lib_array[i].num_p_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_p_file; j++ )
{
lib_array[i].p_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) );
}
}
if ( lib_array[i].num_a1_file )
{
lib_array[i].a1_fname = ( char ** ) ckalloc ( lib_array[i].num_a1_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_a1_file; j++ )
{
lib_array[i].a1_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) );
}
}
if ( lib_array[i].num_a2_file )
{
lib_array[i].a2_fname = ( char ** ) ckalloc ( lib_array[i].num_a2_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_a2_file; j++ )
{
lib_array[i].a2_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) );
}
}
if ( lib_array[i].num_q1_file )
{
lib_array[i].q1_fname = ( char ** ) ckalloc ( lib_array[i].num_q1_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_q1_file; j++ )
{
lib_array[i].q1_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) );
}
}
if ( lib_array[i].num_q2_file )
{
lib_array[i].q2_fname = ( char ** ) ckalloc ( lib_array[i].num_q2_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_q2_file; j++ )
{
lib_array[i].q2_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) );
}
}
if ( lib_array[i].num_b_file ) //allot memory for bam file name
{
lib_array[i].b_fname = ( char ** ) ckalloc ( lib_array[i].num_b_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_b_file; j++ )
{ lib_array[i].b_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) ); }
}
}
// get file names
for ( i = 0; i < num_libs; i++ )
{
lib_array[i].curr_type = 1;
lib_array[i].curr_index = 0;
lib_array[i].fp1 = NULL;
lib_array[i].fp2 = NULL;
lib_array[i].num_s_a_file = 0;
lib_array[i].num_s_q_file = 0;
lib_array[i].num_p_file = 0;
lib_array[i].num_a1_file = 0;
lib_array[i].num_a2_file = 0;
lib_array[i].num_q1_file = 0;
lib_array[i].num_q2_file = 0;
lib_array[i].num_b_file = 0; //init
lib_array[i].fp3 = NULL;
}
libCounter = -1;
rewind ( fp );
i = -1;
while ( fgets ( line, 1024, fp ) )
{
ch = line[5];
line[5] = '\0';
if ( strcmp ( line, "[LIB]" ) == 0 )
{
i++;
continue;
}
line[5] = ch;
flag = splitColumn ( line );
if ( !flag )
{
continue;
}
if ( strcmp ( tabs[0], "f1" ) == 0 )
{
index = lib_array[i].num_a1_file++;
strcpy ( lib_array[i].a1_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "q1" ) == 0 )
{
index = lib_array[i].num_q1_file++;
strcpy ( lib_array[i].q1_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "f2" ) == 0 )
{
index = lib_array[i].num_a2_file++;
strcpy ( lib_array[i].a2_fname[index], tabs[1] );
if ( strcmp ( lib_array[i].a2_fname[index], lib_array[i].a1_fname[index] ) == 0 )
{
fprintf ( stderr, "Config file error: f2 file is the same as f1 file\n" );
fprintf ( stderr, "f1=%s\n", lib_array[i].a1_fname[index] );
fprintf ( stderr, "f2=%s\n", lib_array[i].a2_fname[index] );
exit ( -1 );
}
}
else if ( strcmp ( tabs[0], "q2" ) == 0 )
{
index = lib_array[i].num_q2_file++;
strcpy ( lib_array[i].q2_fname[index], tabs[1] );
if ( strcmp ( lib_array[i].q2_fname[index], lib_array[i].q1_fname[index] ) == 0 )
{
fprintf ( stderr, "Config file error: q2 file is the same as q1 file\n" );
fprintf ( stderr, "q1=%s\n", lib_array[i].q1_fname[index] );
fprintf ( stderr, "q2=%s\n", lib_array[i].q2_fname[index] );
exit ( -1 );
}
}
else if ( strcmp ( tabs[0], "f" ) == 0 )
{
index = lib_array[i].num_s_a_file++;
strcpy ( lib_array[i].s_a_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "q" ) == 0 )
{
index = lib_array[i].num_s_q_file++;
strcpy ( lib_array[i].s_q_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "p" ) == 0 )
{
index = lib_array[i].num_p_file++;
strcpy ( lib_array[i].p_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "b" ) == 0 )
{
//bam file
index = lib_array[i].num_b_file++;
strcpy ( lib_array[i].b_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "min_ins" ) == 0 )
{
lib_array[i].min_ins = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "max_ins" ) == 0 )
{
lib_array[i].max_ins = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "avg_ins" ) == 0 )
{
lib_array[i].avg_ins = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "rd_len_cutoff" ) == 0 )
{
lib_array[i].rd_len_cutoff = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "reverse_seq" ) == 0 )
{
lib_array[i].reverse = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "asm_flags" ) == 0 )
{
lib_array[i].asm_flag = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "rank" ) == 0 )
{
lib_array[i].rank = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "pair_num_cutoff" ) == 0 )
{
lib_array[i].pair_num_cut = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "rd_len_cutoff" ) == 0 )
{
lib_array[i].rd_len_cutoff = atoi ( tabs[1] );
}
else if ( strcmp ( tabs[0], "map_len" ) == 0 )
{
lib_array[i].map_len = atoi ( tabs[1] );
}
}
for ( i = 0; i < num_libs; i++ )
{
if ( pe[i] && lib_array[i].avg_ins == 0 )
{
fprintf ( stderr, "Config file error: PE reads need avg_ins in [LIB] %d\n", i + 1 );
exit ( -1 );
}
}
fclose ( fp );
qsort ( &lib_array[0], num_libs, sizeof ( LIB_INFO ), cmp_lib );
}
// Inserts column(s) such that a note can start at ts and end at te
// Sets current position to starting column
// Returns note duration in columns
// Ignores bar structure, therefore use only in last bar
int TabTrack::insertColumn(int ts, int te)
{
// cout << "TabTrack::insertColumn("
// << ts << ", " << te << ")" << endl;
int cstart;
int cend;
int dur;
int res = 0;
if ((ts<0) || (te<=ts)) {
// LVIFIX: report error ?
// cout << "TabTrack::insertColumn() -> input error" << endl;
return -1;
}
int td = trackDuration();
// cout << "td=" << td << endl;
if (ts > td) {
// cout << "TabTrack::insertColumn() ->"
// << " ts > td, append rest: " << ts - td
// << endl;
x = c.size();
insertColumn(1);
c[x].flags = 0;
c[x].setFullDuration(ts - td);
// cout << "stop ringing:";
for (int j = 0; j < MAX_STRINGS; j++) {
if (isRingingAt(j, x)) {
// cout << " " << j;
c[x].e[j] = EFFECT_STOPRING;
}
}
// cout << endl;
// cout << "after append: ";
// dumpCols(this);
td = ts;
}
if (te > td) {
// cout << "TabTrack::insertColumn() ->"
// << " te > td, append column: " << te - td
// << endl;
x = c.size();
insertColumn(1);
c[x].flags = 0;
c[x].setFullDuration(te - td);
// cout << "stop ringing:";
for (int j = 0; j < MAX_STRINGS; j++) {
if (isRingingAt(j, x)) {
// cout << " " << j;
c[x].e[j] = EFFECT_STOPRING;
}
}
// cout << endl;
// cout << "after append: ";
// dumpCols(this);
td = te;
}
// find starting column
// cout << "TabTrack::insertColumn() ->"
// << " find starting column";
cstart = findCStart(ts, dur);
// cout
// << " cstart=" << cstart
// << " dur=" << dur
// << endl;
if (dur > 0) {
splitColumn(cstart, dur);
cstart++;
// cout << "after split start: ";
// dumpCols(this);
}
// find ending column
// cout << "TabTrack::insertColumn() ->"
// << " find ending column";
cend = findCEnd(te, dur);
// cout
// << " cend=" << cend
// << " dur=" << dur
// << endl;
if (dur < c[cend].fullDuration()) {
splitColumn(cend, dur);
// cout << "after split end: ";
// dumpCols(this);
}
x = cstart;
res = cend - cstart + 1;
// cout << "TabTrack::insertColumn() ->"
// << " x=" << x
// << " res=" << res
// << endl;
return res;
}
void scan_libInfo ( char * libfile )
{
FILE * fp;
char line[1024], ch;
int i, j, index;
int libCounter;
boolean flag;
fp = ckopen ( libfile, "r" );
num_libs = 0;
while ( fgets ( line, 1024, fp ) )
{
ch = line[5];
line[5] = '\0';
if ( strcmp ( line, "[LIB]" ) == 0 )
{ num_libs++; }
if ( !num_libs )
{
line[5] = ch;
flag = splitColumn ( line );
if ( !flag )
{ continue; }
if ( strcmp ( tabs[0], "max_rd_len" ) == 0 )
{ maxReadLen = atoi ( tabs[1] ); }
}
}
//count file numbers of each type
lib_array = ( LIB_INFO * ) ckalloc ( num_libs * sizeof ( LIB_INFO ) );
for ( i = 0; i < num_libs; i++ )
{
lib_array[i].asm_flag = 3;
lib_array[i].rd_len_cutoff = 0;
lib_array[i].rank = 0;
lib_array[i].pair_num_cut = 0;
lib_array[i].map_len = 0;
lib_array[i].num_s_a_file = 0;
lib_array[i].num_s_q_file = 0;
lib_array[i].num_p_file = 0;
lib_array[i].num_a1_file = 0;
lib_array[i].num_a2_file = 0;
lib_array[i].num_q1_file = 0;
lib_array[i].num_q2_file = 0;
}
libCounter = -1;
rewind ( fp );
i = -1;
while ( fgets ( line, 1024, fp ) )
{
ch = line[5];
line[5] = '\0';
if ( strcmp ( line, "[LIB]" ) == 0 )
{
i++;
continue;
}
line[5] = ch;
flag = splitColumn ( line );
if ( !flag )
{ continue; }
if ( strcmp ( tabs[0], "f1" ) == 0 )
{
lib_array[i].num_a1_file++;
}
else if ( strcmp ( tabs[0], "q1" ) == 0 )
{
lib_array[i].num_q1_file++;
}
else if ( strcmp ( tabs[0], "f2" ) == 0 )
{
lib_array[i].num_a2_file++;
}
else if ( strcmp ( tabs[0], "q2" ) == 0 )
{
lib_array[i].num_q2_file++;
}
else if ( strcmp ( tabs[0], "f" ) == 0 )
{
lib_array[i].num_s_a_file++;
}
else if ( strcmp ( tabs[0], "q" ) == 0 )
{
lib_array[i].num_s_q_file++;
}
else if ( strcmp ( tabs[0], "p" ) == 0 )
{
lib_array[i].num_p_file++;
}
}
//allocate memory for filenames
for ( i = 0; i < num_libs; i++ )
{
if ( lib_array[i].num_s_a_file )
{
lib_array[i].s_a_fname = ( char ** ) ckalloc ( lib_array[i].num_s_a_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_s_a_file; j++ )
{ lib_array[i].s_a_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) ); }
}
if ( lib_array[i].num_s_q_file )
{
lib_array[i].s_q_fname = ( char ** ) ckalloc ( lib_array[i].num_s_q_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_s_q_file; j++ )
{ lib_array[i].s_q_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) ); }
}
if ( lib_array[i].num_p_file )
{
lib_array[i].p_fname = ( char ** ) ckalloc ( lib_array[i].num_p_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_p_file; j++ )
{ lib_array[i].p_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) ); }
}
if ( lib_array[i].num_a1_file )
{
lib_array[i].a1_fname = ( char ** ) ckalloc ( lib_array[i].num_a1_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_a1_file; j++ )
{ lib_array[i].a1_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) ); }
}
if ( lib_array[i].num_a2_file )
{
lib_array[i].a2_fname = ( char ** ) ckalloc ( lib_array[i].num_a2_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_a2_file; j++ )
{ lib_array[i].a2_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) ); }
}
if ( lib_array[i].num_q1_file )
{
lib_array[i].q1_fname = ( char ** ) ckalloc ( lib_array[i].num_q1_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_q1_file; j++ )
{ lib_array[i].q1_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) ); }
}
if ( lib_array[i].num_q2_file )
{
lib_array[i].q2_fname = ( char ** ) ckalloc ( lib_array[i].num_q2_file * sizeof ( char * ) );
for ( j = 0; j < lib_array[i].num_q2_file; j++ )
{ lib_array[i].q2_fname[j] = ( char * ) ckalloc ( 1024 * sizeof ( char ) ); }
}
}
// get file names
for ( i = 0; i < num_libs; i++ )
{
lib_array[i].curr_type = 1;
lib_array[i].curr_index = 0;
lib_array[i].fp1 = NULL;
lib_array[i].fp2 = NULL;
lib_array[i].num_s_a_file = 0;
lib_array[i].num_s_q_file = 0;
lib_array[i].num_p_file = 0;
lib_array[i].num_a1_file = 0;
lib_array[i].num_a2_file = 0;
lib_array[i].num_q1_file = 0;
lib_array[i].num_q2_file = 0;
}
libCounter = -1;
rewind ( fp );
i = -1;
while ( fgets ( line, 1024, fp ) )
{
ch = line[5];
line[5] = '\0';
if ( strcmp ( line, "[LIB]" ) == 0 )
{
i++;
continue;
}
line[5] = ch;
flag = splitColumn ( line );
if ( !flag )
{ continue; }
if ( strcmp ( tabs[0], "f1" ) == 0 )
{
index = lib_array[i].num_a1_file++;
strcpy ( lib_array[i].a1_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "q1" ) == 0 )
{
index = lib_array[i].num_q1_file++;
strcpy ( lib_array[i].q1_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "f2" ) == 0 )
{
index = lib_array[i].num_a2_file++;
strcpy ( lib_array[i].a2_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "q2" ) == 0 )
{
index = lib_array[i].num_q2_file++;
strcpy ( lib_array[i].q2_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "f" ) == 0 )
{
index = lib_array[i].num_s_a_file++;
strcpy ( lib_array[i].s_a_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "q" ) == 0 )
{
index = lib_array[i].num_s_q_file++;
strcpy ( lib_array[i].s_q_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "p" ) == 0 )
{
index = lib_array[i].num_p_file++;
strcpy ( lib_array[i].p_fname[index], tabs[1] );
}
else if ( strcmp ( tabs[0], "min_ins" ) == 0 )
{ lib_array[i].min_ins = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "max_ins" ) == 0 )
{ lib_array[i].max_ins = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "avg_ins" ) == 0 )
{ lib_array[i].avg_ins = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "rd_len_cutoff" ) == 0 )
{ lib_array[i].rd_len_cutoff = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "reverse_seq" ) == 0 )
{ lib_array[i].reverse = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "asm_flags" ) == 0 )
{ lib_array[i].asm_flag = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "rank" ) == 0 )
{ lib_array[i].rank = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "pair_num_cutoff" ) == 0 )
{ lib_array[i].pair_num_cut = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "rd_len_cutoff" ) == 0 )
{ lib_array[i].rd_len_cutoff = atoi ( tabs[1] ); }
else if ( strcmp ( tabs[0], "map_len" ) == 0 )
{ lib_array[i].map_len = atoi ( tabs[1] ); }
}
fclose ( fp );
qsort ( &lib_array[0], num_libs, sizeof ( LIB_INFO ), cmp_lib );
}
