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Searched refs:itf8_size (Results 1 – 25 of 27) sorted by relevance

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/dports/biology/iolib/io_lib-io_lib-1-14-10/progs/
H A Dcram_filter.c470 itf8_size(c_hdr->content_id) + in update_slice_offsets()
471 itf8_size(c_hdr->comp_size) + in update_slice_offsets()
472 itf8_size(c_hdr->uncomp_size); in update_slice_offsets()
494 itf8_size(s->hdr_block->content_id) + in update_slice_offsets()
495 itf8_size(s->hdr_block->comp_size) + in update_slice_offsets()
496 itf8_size(s->hdr_block->uncomp_size); in update_slice_offsets()
500 itf8_size(s->block[j]->content_id) + in update_slice_offsets()
501 itf8_size(s->block[j]->comp_size) + in update_slice_offsets()
502 itf8_size(s->block[j]->uncomp_size); in update_slice_offsets()
/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/
H A Dcram_io.h107 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
344 #undef itf8_size
347 #define itf8_size uint7_size macro
H A Dcram_encode.c237 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
404 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
1721 itf8_size(c_hdr->content_id) + in cram_encode_container()
1722 itf8_size(c_hdr->comp_size) + in cram_encode_container()
1723 itf8_size(c_hdr->uncomp_size); in cram_encode_container()
1746 itf8_size(s->hdr_block->content_id) + in cram_encode_container()
1747 itf8_size(s->hdr_block->comp_size) + in cram_encode_container()
1748 itf8_size(s->hdr_block->uncomp_size); in cram_encode_container()
1752 itf8_size(s->block[j]->content_id) + in cram_encode_container()
1753 itf8_size(s->block[j]->comp_size) + in cram_encode_container()
[all …]
H A Dcram_io.c4371 itf8_size(b->content_id) + in cram_read_SAM_hdr()
4372 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
4373 itf8_size(b->comp_size); in cram_read_SAM_hdr()
4399 itf8_size(b->content_id) + in cram_read_SAM_hdr()
4400 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
4401 itf8_size(b->comp_size); in cram_read_SAM_hdr()
4552 itf8_size(b->uncomp_size) + in cram_write_SAM_hdr()
4553 itf8_size(b->comp_size); in cram_write_SAM_hdr()
4568 itf8_size(b->content_id) + in cram_write_SAM_hdr()
4569 itf8_size(padded_length)*2; in cram_write_SAM_hdr()
[all …]
H A Dcram_codecs.c637 len += itf8_put_blk(b, itf8_size(c->e_beta.offset) in cram_beta_encode_store()
638 + itf8_size(c->e_beta.nbits)); // codec length in cram_beta_encode_store()
1903 cp += itf8_put(cp, 1 + itf8_size(c->e_byte_array_stop.content_id)); in cram_byte_array_stop_encode_store()
/dports/biology/vt/vt-0.57721/lib/htslib/cram/
H A Dcram_io.c3649 itf8_size(b->content_id) + in cram_read_SAM_hdr()
3650 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
3651 itf8_size(b->comp_size); in cram_read_SAM_hdr()
3677 itf8_size(b->content_id) + in cram_read_SAM_hdr()
3678 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
3679 itf8_size(b->comp_size); in cram_read_SAM_hdr()
3845 itf8_size(b->content_id) + in cram_write_SAM_hdr()
3847 itf8_size(b->comp_size); in cram_write_SAM_hdr()
3862 itf8_size(b->content_id) + in cram_write_SAM_hdr()
3863 itf8_size(padded_length)*2; in cram_write_SAM_hdr()
[all …]
H A Dcram_encode.c249 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
450 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
1679 itf8_size(c_hdr->content_id) + in cram_encode_container()
1680 itf8_size(c_hdr->comp_size) + in cram_encode_container()
1681 itf8_size(c_hdr->uncomp_size); in cram_encode_container()
1704 itf8_size(s->hdr_block->content_id) + in cram_encode_container()
1705 itf8_size(s->hdr_block->comp_size) + in cram_encode_container()
1706 itf8_size(s->hdr_block->uncomp_size); in cram_encode_container()
1710 itf8_size(s->block[j]->content_id) + in cram_encode_container()
1711 itf8_size(s->block[j]->comp_size) + in cram_encode_container()
[all …]
H A Dcram_codecs.c575 len += itf8_put_blk(b, itf8_size(c->e_beta.offset) in cram_beta_encode_store()
576 + itf8_size(c->e_beta.nbits)); // codec length in cram_beta_encode_store()
1749 cp += itf8_put(cp, 1 + itf8_size(c->e_byte_array_stop.content_id)); in cram_byte_array_stop_encode_store()
H A Dcram_io.h264 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/
H A Dcram_io.c3671 itf8_size(b->content_id) + in cram_read_SAM_hdr()
3672 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
3673 itf8_size(b->comp_size); in cram_read_SAM_hdr()
3699 itf8_size(b->content_id) + in cram_read_SAM_hdr()
3700 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
3701 itf8_size(b->comp_size); in cram_read_SAM_hdr()
3867 itf8_size(b->content_id) + in cram_write_SAM_hdr()
3869 itf8_size(b->comp_size); in cram_write_SAM_hdr()
3884 itf8_size(b->content_id) + in cram_write_SAM_hdr()
3885 itf8_size(padded_length)*2; in cram_write_SAM_hdr()
[all …]
H A Dcram_encode.c249 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
450 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
1679 itf8_size(c_hdr->content_id) + in cram_encode_container()
1680 itf8_size(c_hdr->comp_size) + in cram_encode_container()
1681 itf8_size(c_hdr->uncomp_size); in cram_encode_container()
1704 itf8_size(s->hdr_block->content_id) + in cram_encode_container()
1705 itf8_size(s->hdr_block->comp_size) + in cram_encode_container()
1706 itf8_size(s->hdr_block->uncomp_size); in cram_encode_container()
1710 itf8_size(s->block[j]->content_id) + in cram_encode_container()
1711 itf8_size(s->block[j]->comp_size) + in cram_encode_container()
[all …]
H A Dcram_codecs.c575 len += itf8_put_blk(b, itf8_size(c->e_beta.offset) in cram_beta_encode_store()
576 + itf8_size(c->e_beta.nbits)); // codec length in cram_beta_encode_store()
1749 cp += itf8_put(cp, 1 + itf8_size(c->e_byte_array_stop.content_id)); in cram_byte_array_stop_encode_store()
H A Dcram_io.h264 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
/dports/biology/stacks/stacks-2.4/htslib/cram/
H A Dcram_io.c3602 itf8_size(b->comp_size); in cram_read_SAM_hdr()
3628 itf8_size(b->content_id) + in cram_read_SAM_hdr()
3629 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
3630 itf8_size(b->comp_size); in cram_read_SAM_hdr()
3796 itf8_size(b->content_id) + in cram_write_SAM_hdr()
3797 itf8_size(b->uncomp_size) + in cram_write_SAM_hdr()
3798 itf8_size(b->comp_size); in cram_write_SAM_hdr()
3813 itf8_size(b->content_id) + in cram_write_SAM_hdr()
3814 itf8_size(padded_length)*2; in cram_write_SAM_hdr()
3828 itf8_size(b->uncomp_size) + in cram_write_SAM_hdr()
[all …]
H A Dcram_encode.c249 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
450 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
1679 itf8_size(c_hdr->content_id) + in cram_encode_container()
1680 itf8_size(c_hdr->comp_size) + in cram_encode_container()
1681 itf8_size(c_hdr->uncomp_size); in cram_encode_container()
1704 itf8_size(s->hdr_block->content_id) + in cram_encode_container()
1705 itf8_size(s->hdr_block->comp_size) + in cram_encode_container()
1706 itf8_size(s->hdr_block->uncomp_size); in cram_encode_container()
1710 itf8_size(s->block[j]->content_id) + in cram_encode_container()
1711 itf8_size(s->block[j]->comp_size) + in cram_encode_container()
[all …]
H A Dcram_codecs.c594 len += itf8_put_blk(b, itf8_size(c->e_beta.offset) in cram_beta_encode_store()
595 + itf8_size(c->e_beta.nbits)); // codec length in cram_beta_encode_store()
1794 cp += itf8_put(cp, 1 + itf8_size(c->e_byte_array_stop.content_id)); in cram_byte_array_stop_encode_store()
H A Dcram_io.h264 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/
H A Dcram_io.c3604 itf8_size(b->comp_size); in cram_read_SAM_hdr()
3630 itf8_size(b->content_id) + in cram_read_SAM_hdr()
3631 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
3632 itf8_size(b->comp_size); in cram_read_SAM_hdr()
3794 itf8_size(b->content_id) + in cram_write_SAM_hdr()
3795 itf8_size(b->uncomp_size) + in cram_write_SAM_hdr()
3796 itf8_size(b->comp_size); in cram_write_SAM_hdr()
3811 itf8_size(b->content_id) + in cram_write_SAM_hdr()
3812 itf8_size(padded_length)*2; in cram_write_SAM_hdr()
3826 itf8_size(b->uncomp_size) + in cram_write_SAM_hdr()
[all …]
H A Dcram_encode.c249 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
450 itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
1685 itf8_size(c_hdr->content_id) + in cram_encode_container()
1686 itf8_size(c_hdr->comp_size) + in cram_encode_container()
1687 itf8_size(c_hdr->uncomp_size); in cram_encode_container()
1710 itf8_size(s->hdr_block->content_id) + in cram_encode_container()
1711 itf8_size(s->hdr_block->comp_size) + in cram_encode_container()
1712 itf8_size(s->hdr_block->uncomp_size); in cram_encode_container()
1716 itf8_size(s->block[j]->content_id) + in cram_encode_container()
1717 itf8_size(s->block[j]->comp_size) + in cram_encode_container()
[all …]
H A Dcram_io.h264 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
H A Dcram_codecs.c596 len += itf8_put_blk(b, itf8_size(c->e_beta.offset) in cram_beta_encode_store()
597 + itf8_size(c->e_beta.nbits)); // codec length in cram_beta_encode_store()
1788 cp += itf8_put(cp, 1 + itf8_size(c->e_byte_array_stop.content_id)); in cram_byte_array_stop_encode_store()
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/
H A Dcram_io.c3987 itf8_size(b->content_id) + in cram_read_SAM_hdr()
3988 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
3989 itf8_size(b->comp_size); in cram_read_SAM_hdr()
4016 itf8_size(b->content_id) + in cram_read_SAM_hdr()
4017 itf8_size(b->uncomp_size) + in cram_read_SAM_hdr()
4018 itf8_size(b->comp_size); in cram_read_SAM_hdr()
4212 itf8_size(b->content_id) + in cram_write_SAM_hdr()
4214 itf8_size(b->comp_size); in cram_write_SAM_hdr()
4229 itf8_size(b->content_id) + in cram_write_SAM_hdr()
4230 itf8_size(padded_length)*2; in cram_write_SAM_hdr()
[all …]
H A Dcram_encode.c269 r |= itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
470 r |= itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc)); in cram_encode_compression_header()
1802 itf8_size(c_hdr->content_id) + in cram_encode_container()
1803 itf8_size(c_hdr->comp_size) + in cram_encode_container()
1804 itf8_size(c_hdr->uncomp_size); in cram_encode_container()
1827 itf8_size(s->hdr_block->content_id) + in cram_encode_container()
1828 itf8_size(s->hdr_block->comp_size) + in cram_encode_container()
1829 itf8_size(s->hdr_block->uncomp_size); in cram_encode_container()
1833 itf8_size(s->block[j]->content_id) + in cram_encode_container()
1834 itf8_size(s->block[j]->comp_size) + in cram_encode_container()
[all …]
H A Dcram_io.h265 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
H A Dcram_codecs.c638 len += (n = itf8_put_blk(b, itf8_size(c->u.e_beta.offset) in cram_beta_encode_store()
639 + itf8_size(c->u.e_beta.nbits))); // codec length in cram_beta_encode_store()
1984 cp += itf8_put(cp, 1 + itf8_size(c->u.e_byte_array_stop.content_id)); in cram_byte_array_stop_encode_store()

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