/dports/biology/iolib/io_lib-io_lib-1-14-10/progs/ |
H A D | cram_to_sam.c | 74 int embed_ref = 0; in main() local 108 embed_ref = 1; in main() 172 if (embed_ref) in main() 173 cram_set_option(fd, CRAM_OPT_EMBED_REF, embed_ref); in main() 177 if (!fd->refs && !embed_ref) { in main()
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H A D | sam_to_cram.c | 76 int s_opt = 0, S_opt = 0, embed_ref = 0; in main() local 115 embed_ref = 1; in main() 186 if (embed_ref) in main() 187 cram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref); in main()
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H A D | scramble.c | 148 int s_opt = 0, S_opt = 0, embed_ref = 0, ignore_md5 = 0, decode_md = 0; in main() local 226 embed_ref = 1; in main() 395 if (!in->c->refs && !embed_ref) { in main() 435 if (embed_ref) { in main() 443 if (scram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref)) in main()
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H A D | scram_merge.c | 134 int s_opt = 0, S_opt = 0, embed_ref = 0; in main() local 178 embed_ref = 1; in main() 304 if (embed_ref) in main() 305 if (scram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref)) in main()
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/dports/science/afni/afni-AFNI_21.3.16/src/scripts_install/ |
H A D | @SUMA_Make_Spec_SF | 620 set embed_ref = 2 622 set embed_ref = 3 633 echo " EmbedDimension = $embed_ref" >> $spec_file
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H A D | @SUMA_Make_Spec_Caret | 797 set embed_ref = 2 799 set embed_ref = 3 813 echo " EmbedDimension = $embed_ref" >> $spec_file
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H A D | @SUMA_Make_Spec_FS | 1168 set embed_ref = 2 1170 set embed_ref = 3 1188 echo " EmbedDimension = $embed_ref" >> $spec_file 1273 set embed_ref = 2 1275 set embed_ref = 3 1293 echo " EmbedDimension = $embed_ref" >> $spec_file
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/dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
H A D | cram_encode.c | 149 if (fd->no_ref || fd->embed_ref) { in cram_encode_compression_header() 909 int embed_ref; in cram_encode_slice() local 912 embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; in cram_encode_slice() 926 s->hdr->ref_base_id = embed_ref ? DS_ref : -1; in cram_encode_slice() 953 if (embed_ref) { in cram_encode_slice() 3088 !fd->embed_ref) { in cram_put_bam_seq() 3134 if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && in cram_put_bam_seq()
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H A D | cram_structs.h | 719 int embed_ref; member
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
H A D | cram_encode.c | 149 if (fd->no_ref || fd->embed_ref) { in cram_encode_compression_header() 909 int embed_ref; in cram_encode_slice() local 912 embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; in cram_encode_slice() 926 s->hdr->ref_base_id = embed_ref ? DS_ref : -1; in cram_encode_slice() 953 if (embed_ref) { in cram_encode_slice() 3089 !fd->embed_ref) { in cram_put_bam_seq() 3135 if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && in cram_put_bam_seq()
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H A D | cram_structs.h | 719 int embed_ref; member
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/dports/biology/stacks/stacks-2.4/htslib/cram/ |
H A D | cram_encode.c | 149 if (fd->no_ref || fd->embed_ref) { in cram_encode_compression_header() 909 int embed_ref; in cram_encode_slice() local 912 embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; in cram_encode_slice() 926 s->hdr->ref_base_id = embed_ref ? DS_ref : -1; in cram_encode_slice() 953 if (embed_ref) { in cram_encode_slice() 3082 !fd->embed_ref) { in cram_put_bam_seq() 3128 if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && in cram_put_bam_seq()
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H A D | cram_structs.h | 712 int embed_ref; member
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/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
H A D | cram_encode.c | 142 if (fd->no_ref || fd->embed_ref) { in cram_encode_compression_header() 954 int embed_ref; in cram_encode_slice() local 957 embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; in cram_encode_slice() 971 s->hdr->ref_base_id = embed_ref ? DS_ref : -1; in cram_encode_slice() 987 if (embed_ref) { in cram_encode_slice() 3086 !fd->embed_ref) { in cram_put_bam_seq() 3136 if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && in cram_put_bam_seq()
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H A D | cram_structs.h | 803 int embed_ref; member
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/ |
H A D | cram_encode.c | 149 if (fd->no_ref || fd->embed_ref) { in cram_encode_compression_header() 912 int embed_ref; in cram_encode_slice() local 915 embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; in cram_encode_slice() 929 s->hdr->ref_base_id = embed_ref ? DS_ref : -1; in cram_encode_slice() 956 if (embed_ref) { in cram_encode_slice() 3096 !fd->embed_ref) { in cram_put_bam_seq() 3142 if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && in cram_put_bam_seq()
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H A D | cram_structs.h | 713 int embed_ref; member
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/ |
H A D | cram_encode.c | 169 if (fd->no_ref || fd->embed_ref) { in cram_encode_compression_header() 960 int embed_ref; in cram_encode_slice() local 963 embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; in cram_encode_slice() 977 s->hdr->ref_base_id = embed_ref ? DS_ref : -1; in cram_encode_slice() 1003 if (embed_ref) { in cram_encode_slice() 3284 !fd->embed_ref) { in cram_put_bam_seq() 3342 if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && in cram_put_bam_seq()
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H A D | cram_structs.h | 726 int embed_ref; member
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/dports/biology/py-pysam/pysam-0.18.0/htslib/cram/ |
H A D | cram_encode.c | 161 if (fd->no_ref || fd->embed_ref) { in cram_encode_compression_header() 1081 int embed_ref; in cram_encode_slice() local 1084 embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; in cram_encode_slice() 1098 s->hdr->ref_base_id = embed_ref && s->hdr->ref_seq_span > 0 in cram_encode_slice() 1126 if (embed_ref) { in cram_encode_slice() 3363 !fd->embed_ref) { in cram_put_bam_seq() 3421 if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && in cram_put_bam_seq()
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H A D | cram_structs.h | 814 int embed_ref; member
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H A D | cram_decode.c | 2261 int embed_ref; in cram_decode_slice() local 2310 embed_ref = s->hdr->ref_base_id >= 0 ? 1 : 0; in cram_decode_slice() 2312 embed_ref = s->hdr->ref_base_id > 0 ? 1 : 0; in cram_decode_slice() 2315 if (embed_ref) { in cram_decode_slice() 2856 } else if (ref_id >= 0 && s->ref != fd->ref_free && !embed_ref) { in cram_decode_slice()
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/dports/biology/htslib/htslib-1.14/cram/ |
H A D | cram_encode.c | 161 if (fd->no_ref || fd->embed_ref) { in cram_encode_compression_header() 1081 int embed_ref; in cram_encode_slice() local 1084 embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0; in cram_encode_slice() 1098 s->hdr->ref_base_id = embed_ref && s->hdr->ref_seq_span > 0 in cram_encode_slice() 1126 if (embed_ref) { in cram_encode_slice() 3363 !fd->embed_ref) { in cram_put_bam_seq() 3421 if (bam_ref(b) >= 0 && curr_ref >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref && in cram_put_bam_seq()
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H A D | cram_structs.h | 814 int embed_ref; member
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H A D | cram_decode.c | 2261 int embed_ref; in cram_decode_slice() local 2310 embed_ref = s->hdr->ref_base_id >= 0 ? 1 : 0; in cram_decode_slice() 2312 embed_ref = s->hdr->ref_base_id > 0 ? 1 : 0; in cram_decode_slice() 2315 if (embed_ref) { in cram_decode_slice() 2856 } else if (ref_id >= 0 && s->ref != fd->ref_free && !embed_ref) { in cram_decode_slice()
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