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Searched refs:embed_ref (Results 1 – 25 of 39) sorted by relevance

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/dports/biology/iolib/io_lib-io_lib-1-14-10/progs/
H A Dcram_to_sam.c74 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()
H A Dsam_to_cram.c76 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()
H A Dscramble.c148 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()
H A Dscram_merge.c134 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()
/dports/science/afni/afni-AFNI_21.3.16/src/scripts_install/
H A D@SUMA_Make_Spec_SF620 set embed_ref = 2
622 set embed_ref = 3
633 echo " EmbedDimension = $embed_ref" >> $spec_file
H A D@SUMA_Make_Spec_Caret797 set embed_ref = 2
799 set embed_ref = 3
813 echo " EmbedDimension = $embed_ref" >> $spec_file
H A D@SUMA_Make_Spec_FS1168 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
/dports/biology/vt/vt-0.57721/lib/htslib/cram/
H A Dcram_encode.c149 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()
H A Dcram_structs.h719 int embed_ref; member
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/
H A Dcram_encode.c149 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()
H A Dcram_structs.h719 int embed_ref; member
/dports/biology/stacks/stacks-2.4/htslib/cram/
H A Dcram_encode.c149 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()
H A Dcram_structs.h712 int embed_ref; member
/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/
H A Dcram_encode.c142 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()
H A Dcram_structs.h803 int embed_ref; member
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/
H A Dcram_encode.c149 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()
H A Dcram_structs.h713 int embed_ref; member
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/
H A Dcram_encode.c169 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()
H A Dcram_structs.h726 int embed_ref; member
/dports/biology/py-pysam/pysam-0.18.0/htslib/cram/
H A Dcram_encode.c161 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()
H A Dcram_structs.h814 int embed_ref; member
H A Dcram_decode.c2261 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()
/dports/biology/htslib/htslib-1.14/cram/
H A Dcram_encode.c161 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()
H A Dcram_structs.h814 int embed_ref; member
H A Dcram_decode.c2261 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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