NOTE: This is a working specification, and is subject to modifications and revisions. However, to the extent possible, this specification aims to agree with and conform to the RAD files currently being produced by the tools using this format (the otherwise de facto specification). Data types Shorthand for the data types of fields used in this spec. (x1, x2, ... , xn) — a tuple of n data types (simply encoded as x1 followed by x2, etc.) The following data types can be specified by their corresponding assigned type id specified below. b — boolean (type id 0)

Topics What are the biggest challenges facing the adoption of rust in genomics? Which of these challenges can be met by the community? Interest in a general "rust for genomics working group"? What would the structure look like? What mechanism for communication and decision making? What specific libraries / data structure do we most need (or cases where there are many and we need to "bless" one)?encodings minimizers / super-kmers / ... Library of common reusable types in APIs? (Like pa-types) intervals (noodles)? Should there be a blessed.rs specifically for genomics / bioinformatics?

template <typename T_idx_> inline T_idx_ Suffix_Array<T_idx_>::lcp_opt_avx(const char* str1, const char* str2, const idx_t len_in) { int64_t i = 0; int64_t len = static_cast<int64_t>(len_in); if ((len - i)>= 256) { for (; i <= len - 256; i += 256) { __m256i v1 = _mm256_loadu_si256((__m256i*)(str1 + i)); __m256i v2 = _mm256_loadu_si256((__m256i*)(str2 + i)); __m256i cmp = _mm256_cmpeq_epi8(v1, v2);

The sequence fragment geometry descriptions language (FGDL) is a basic grammar designed to describe the layout of information encoded in sequenced fragments. Specifically, it is initially designed to support parsing different sequencing chemistries that are common in single-cell transcriptomics. It is capable of processing both "simple" and "complex" geometries — where the definitions of these terms are outlined below. Examples of some geometries in this format. Below are examples of some common geometries (chemistries) and how they are translated into FGDL. 10x Chromium v3 3' : 1{b[16]u[12]}2{r:} 10x Chromium v2 3' : 1{b[16]u[10]}2{r:} SciSeq3 : 1{b[9-10]f[CAGAGC]u[8]b[10]}2{r:} Preventing improper parsing