/dports/biology/iolib/io_lib-io_lib-1-14-10/progs/ |
H A D | cram_filter.c | 470 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()
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/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
H A D | cram_io.h | 107 #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
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H A D | cram_encode.c | 237 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 …]
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H A D | cram_io.c | 4371 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 …]
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H A D | cram_codecs.c | 637 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()
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/dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
H A D | cram_io.c | 3649 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 …]
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H A D | cram_encode.c | 249 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 …]
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H A D | cram_codecs.c | 575 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()
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H A D | cram_io.h | 264 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
H A D | cram_io.c | 3671 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 …]
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H A D | cram_encode.c | 249 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 …]
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H A D | cram_codecs.c | 575 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()
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H A D | cram_io.h | 264 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
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/dports/biology/stacks/stacks-2.4/htslib/cram/ |
H A D | cram_io.c | 3602 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 …]
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H A D | cram_encode.c | 249 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 …]
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H A D | cram_codecs.c | 594 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()
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H A D | cram_io.h | 264 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/ |
H A D | cram_io.c | 3604 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 …]
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H A D | cram_encode.c | 249 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 …]
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H A D | cram_io.h | 264 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
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H A D | cram_codecs.c | 596 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()
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/ |
H A D | cram_io.c | 3987 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 …]
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H A D | cram_encode.c | 269 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 …]
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H A D | cram_io.h | 265 #define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?… macro
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H A D | cram_codecs.c | 638 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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