| /dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
| H A D | cram_structs.h | 733 unsigned int cram_flag_swap[0x1000];// bam -> cram flags member
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| H A D | cram_encode.c | 581 i32 = fd->cram_flag_swap[cr->flags & 0xfff]; in cram_encode_slice_read()
2537 cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]); in process_one_read()
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| H A D | cram_io.c | 3987 fd->cram_flag_swap[i] = g; in cram_init_tables()
3994 fd->cram_flag_swap[i] = i; in cram_init_tables()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/ |
| H A D | cram_structs.h | 740 unsigned int cram_flag_swap[0x1000];// bam -> cram flags member
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| H A D | cram_encode.c | 611 i32 = fd->cram_flag_swap[cr->flags & 0xfff]; in cram_encode_slice_read()
2727 if (cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]) < 0) in process_one_read()
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| H A D | cram_io.c | 4357 fd->cram_flag_swap[i] = g; in cram_init_tables()
4364 fd->cram_flag_swap[i] = i; in cram_init_tables()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
| H A D | cram_structs.h | 733 unsigned int cram_flag_swap[0x1000];// bam -> cram flags member
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| H A D | cram_encode.c | 581 i32 = fd->cram_flag_swap[cr->flags & 0xfff]; in cram_encode_slice_read()
2537 cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]); in process_one_read()
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| H A D | cram_io.c | 4009 fd->cram_flag_swap[i] = g; in cram_init_tables()
4016 fd->cram_flag_swap[i] = i; in cram_init_tables()
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| /dports/biology/stacks/stacks-2.4/htslib/cram/ |
| H A D | cram_structs.h | 724 unsigned int cram_flag_swap[0x1000];// bam -> cram flags member
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| H A D | cram_encode.c | 581 i32 = fd->cram_flag_swap[cr->flags & 0xfff]; in cram_encode_slice_read()
2553 cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]); in process_one_read()
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| H A D | cram_io.c | 3938 fd->cram_flag_swap[i] = g; in cram_init_tables()
3945 fd->cram_flag_swap[i] = i; in cram_init_tables()
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/ |
| H A D | cram_structs.h | 725 unsigned int cram_flag_swap[0x1000];// bam -> cram flags member
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| H A D | cram_encode.c | 583 i32 = fd->cram_flag_swap[cr->flags & 0xfff]; in cram_encode_slice_read()
2565 cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]); in process_one_read()
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| H A D | cram_io.c | 3936 fd->cram_flag_swap[i] = g; in cram_init_tables()
3943 fd->cram_flag_swap[i] = i; in cram_init_tables()
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/cram/ |
| H A D | cram_structs.h | 831 unsigned int cram_flag_swap[0x1000];// bam -> cram flags member
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| H A D | cram_encode.c | 568 i32 = fd->cram_flag_swap[cr->flags & 0xfff]; in cram_encode_slice_read()
2740 if (cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]) < 0) in process_one_read()
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| H A D | cram_io.c | 5096 fd->cram_flag_swap[i] = g; in cram_init_tables()
5103 fd->cram_flag_swap[i] = i; in cram_init_tables()
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| /dports/biology/htslib/htslib-1.14/cram/ |
| H A D | cram_structs.h | 831 unsigned int cram_flag_swap[0x1000];// bam -> cram flags member
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| H A D | cram_encode.c | 568 i32 = fd->cram_flag_swap[cr->flags & 0xfff]; in cram_encode_slice_read()
2740 if (cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]) < 0) in process_one_read()
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| H A D | cram_io.c | 5096 fd->cram_flag_swap[i] = g; in cram_init_tables()
5103 fd->cram_flag_swap[i] = i; in cram_init_tables()
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| /dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
| H A D | cram_structs.h | 818 unsigned int cram_flag_swap[0x1000];// bam -> cram flags member
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| H A D | cram_encode.c | 551 i32 = fd->cram_flag_swap[cr->flags & 0xfff]; in cram_encode_slice_read()
2534 cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]); in process_one_read()
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| H A D | cram_io.c | 4692 fd->cram_flag_swap[i] = g; in cram_init_tables()
4699 fd->cram_flag_swap[i] = i; in cram_init_tables()
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