Merge rust-toolbox into this repo. #372
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Rather than a git revision. vdj_ann should depend on published align_tools.
Bumps [itertools](https://github.com/rust-itertools/itertools) from 0.10.5 to 0.11.0.
Hold back to versions - thiserror 1.0.39 - serde 1.0.156 to stay on syn 1.0.109
build(deps): bump bio-types from 0.13.0 to 1.0.0
Avoid duplication.
Add an optional sample field to ContigAnnotation
Package Before After aho-corasick 1.0.2 1.1.1 anyhow 1.0.71 1.0.75 bio-types 1.0.0 1.0.1 bytemuck 1.13.1 1.14.0 bytes 1.4.0 1.5.0 cc 1.0.79 1.0.83 cpp_demangle 0.4.1 0.4.3 cpufeatures 0.2.8 0.2.9 crossbeam-epoch 0.9.13 0.9.15 either 1.8.1 1.9.0 errno 0.3.1 0.3.4 fastrand 1.9.0 2.0.1 hashbrown 0.14.0 0.14.1 indexmap 2.0.0 2.0.2 itoa 1.0.6 1.0.9 linux-raw-sys 0.3.8 0.4.8 log 0.4.19 0.4.20 matrixmultiply 0.3.7 0.3.8 memchr 2.5.0 2.6.4 memoffset 0.7.1 0.9.0 num-complex 0.4.3 0.4.4 paste 1.0.12 1.0.14 quote 1.0.28 1.0.33 rayon 1.7.0 1.8.0 rayon-core 1.11.0 1.12.0 regex 1.8.4 1.9.6 regex-syntax 0.7.2 0.7.5 rustix 0.37.20 0.38.15 rustversion 1.0.12 1.0.14 ryu 1.0.13 1.0.15 safe_arch 0.7.0 0.7.1 scopeguard 1.1.0 1.2.0 sha2 0.10.7 0.10.8 smallvec 1.10.0 1.11.1 strum_macros 0.24.3 0.25.2 symbolic-common 12.2.0 12.4.1 symbolic-demangle 12.2.0 12.4.1 tempfile 3.6.0 3.8.0 thiserror 1.0.39 1.0.49 thiserror-impl 1.0.39 1.0.49 typenum 1.16.0 1.17.0 unicode-ident 1.0.1 1.0.12 uuid 1.3.4 1.4.1 which 4.4.0 4.4.2 wide 0.7.10 0.7.12 windows-targets 0.48.0 0.48.5 windows_aarch64_gnullvm 0.48.0 0.48.5 windows_aarch64_msvc 0.48.0 0.48.5 windows_i686_gnu 0.48.0 0.48.5 windows_i686_msvc 0.48.0 0.48.5 windows_x86_64_gnu 0.48.0 0.48.5 windows_x86_64_gnullvm 0.48.0 0.48.5 windows_x86_64_msvc 0.48.0 0.48.5
Consistently handle FR3 start window bounds in the face of sequences that are possibly shorter than the window we're searching in. Bail out early if the full search window does not overlap with the sequence, to ensure that the FR3 start computed based on a given contig is the same irrespective of the amount of prefix clipped in the contig.
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