// Returns 0 to indicate read should be output 1 otherwise
static int process_aln(const bam_hdr_t *h, bam1_t *b, samview_settings_t* settings)
{
if (settings->remove_B) bam_remove_B(b);
if (settings->min_qlen > 0) {
int k, qlen = 0;
uint32_t *cigar = bam_get_cigar(b);
for (k = 0; k < b->core.n_cigar; ++k)
if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
qlen += bam_cigar_oplen(cigar[k]);
if (qlen < settings->min_qlen) return 1;
}
if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off))
return 1;
if (settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, h->target_name[b->core.tid], b->core.pos, bam_endpos(b))))
return 1;
if (settings->subsam_frac > 0.) {
uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed);
if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1;
}
if (settings->rghash) {
uint8_t *s = bam_aux_get(b, "RG");
if (s) {
khint_t k = kh_get(rg, settings->rghash, (char*)(s + 1));
if (k == kh_end(settings->rghash)) return 1;
}
}
if (settings->library) {
const char *p = bam_get_library((bam_hdr_t*)h, b);
if (!p || strcmp(p, settings->library) != 0) return 1;
}
if (settings->remove_aux_len) {
size_t i;
for (i = 0; i < settings->remove_aux_len; ++i) {
uint8_t *s = bam_aux_get(b, settings->remove_aux[i]);
if (s) {
bam_aux_del(b, s);
}
}
}
return 0;
}
static int packageSourceFolder(char **source, char *desintation, char *extensions[], int extCount)
{
FTS *ftsp;
FTSENT *p, *chp;
int fts_options = FTS_COMFOLLOW | FTS_LOGICAL | FTS_NOCHDIR;
int rval = 0; // remove if unused!
char line[512];
FILE *pakFile;
FILE *file;
unsigned int start_offset= 0;
unsigned int f_index=0; // file index
if (file = fopen(desintation, "r"))
{
printf("File exists, would you like to overwrite it y/n ? ");
int answer;
int loop=1;
fclose(file);
while (loop){
answer = getchar();
switch(answer){
case 'y':
loop=0;
break;
case 'n':
printf("Please run Bundle again with the correct output path.\n");
exit(1);
case 10: // \n
break;
default:
printf("not sure ? ;) \n (y/n) >");
}
}
}else {
fclose(file);
}
pakFile = fopen(desintation,"wb+");
printf("\n----------------\n");
// initialize header with nuber of files
if ((start_offset=header_init(pakFile, fileCountForHeader)) == -1){
// perror("bundler_header");
fprintf(stderr, "Cannot initialize header...exiting\n");
return 0;
}
size_t header_size = fileCountForHeader* HEADER_OFFSET_SIZE + sizeof(int);
if ((ftsp = fts_open(source, fts_options, NULL)) == NULL) {
warn("fts_open");
return -1;
}
/* Initialize ftsp with as many argv[] parts as possible. */
chp = fts_children(ftsp, 0);
if (chp == NULL) {
return 0; /* no files to traverse */
}
printf("\nCreating the Bundle\n\n");
while ((p = fts_read(ftsp)) != NULL)
{
int tempFileExists = 0; //used to flag temp file for deletion
switch (p->fts_info)
{
case FTS_D:
printf(">dir: %s\n\n", p->fts_path);
printf(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n\n");
printData(pakFile, p->fts_path);
break;
case FTS_F:
if((strstr(p->fts_path, ".DS_Store") != NULL)//ignore DS_Store and exe
|| (strstr(p->fts_path, ".exe") != NULL))
{
printf("Found file to ignore: %s\n", p->fts_path);
printf(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n\n");
}
else
{
printf("\t>file: %s\n", p->fts_path);
printData(pakFile, p->fts_path);
FILE *tempFile;
if(shouldCompressFileType(p->fts_path, extensions, extCount) == 1)
{
/* compress the fts_path file and write
the compressed data one to pak file
*/
compress_one_file(p->fts_path, "temp.txt");
tempFile = fopen("temp.txt","rb");
tempFileExists = 1;
}
else
{
tempFile = fopen(p->fts_path,"rb");
}
char byte;
fseek(pakFile, 0L, SEEK_END);
off_t offset = ftell(pakFile);
//get the size of the file
fseek(tempFile, 0L, SEEK_END);
long size = ftell(tempFile);
fseek(tempFile, 0L, SEEK_SET);
offset= offset;//-HEADER_OFFSET_SIZE;
char *fileName = p->fts_path;
char *tempFileName = strdup(fileName);
//update header
//offset_p off= malloc(HEADER_OFFSET_SIZE);
header_offset off;
off.hash = __ac_X31_hash_string( filename(fileName) );
off.size= size;
off.offset_start= offset;
header_write_offset(pakFile, &off, f_index++);
// print the file info
if(tempFileName)
{
printf("\t>The offset for %s is %d\n", tempFileName, (unsigned int)offset);
printf("\t>The written size of %s is %lu\n", basename(tempFileName), size);
printf("\t>%s was added to the bundle\n\n", basename(tempFileName));
printf(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n\n");
free(tempFileName);
}
// copy the data from the temp compressed file to the pak file
// fseek(pakFile, start_offset, SEEK_SET);
//fseek(pakFile, 0L, SEEK_SET);
fseek(pakFile, 0L, SEEK_END);
int d= 0;
while (!feof(tempFile))
{
fread(&byte, sizeof(char), 1, tempFile);
fwrite(&byte, sizeof(char), 1, pakFile);
}
fclose(tempFile); // done!
//delete the temporary file
if(tempFileExists == 1)
{
if (remove("temp.txt") == -1)
perror("Error in deleting temp file");
}
break;
}
default:
break;
}
}
fclose(pakFile);
fts_close(ftsp);
return 0;
}
