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Alignment and reference sequence from CIGAR and MD #110

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Alignment and reference sequence from CIGAR and MD #110

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07bbab5
Use CIGAR field and MD aux field to reconstruct alignments from BAM r…
ingolia Sep 1, 2018
2704703
rustfmt
ingolia Sep 4, 2018
0e98f8c
Unmangle table
ingolia Sep 5, 2018
93c268a
Moved MD accessor convenience function onto record
ingolia Sep 23, 2018
8e35160
Fix up tests and fmt
ingolia Sep 23, 2018
5d19951
Simplified Cigar/MD reconstruction interface
ingolia Sep 24, 2018
5ece794
Reference sequence reconstruction method on Record
ingolia Sep 24, 2018
1a0ee99
Better MDString newtype using standard traits
ingolia Sep 28, 2018
32086f0
Use Iter over MatchDesc rather than reified vector
ingolia Sep 28, 2018
401c58c
Generic over MatchDesc iterator type
ingolia Sep 28, 2018
c419e6a
Moved to iterator access to Cigar information
ingolia Sep 28, 2018
27939c6
fmt
ingolia Sep 28, 2018
c4510e5
Moved all read sequence lookup functions onto CigarMDPos and removed …
ingolia Sep 29, 2018
a6d8fcf
fmt
ingolia Sep 29, 2018
1d14ba7
Collecting into an Alignment now goes through FromIterator
ingolia Sep 29, 2018
8a5e3ac
Alignment reconstruction on the Record
ingolia Sep 29, 2018
5072011
Merge branch 'master' into master
johanneskoester Nov 12, 2024
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Unmangle table
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@ingolia
ingolia committed Sep 5, 2018
commit 0e98f8cf2fe43bd63aec05ccaebea5229646487d
48 changes: 25 additions & 23 deletions src/bam/md_align.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1281,29 +1281,31 @@ fn fast_compl(nt: u8) -> u8 {
}

const NT_NONE: u8 = b'*';
static COMPL: [u8; 128] = [
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, // 0x10
NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, // 0x20
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
// 0x30
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, // 0x40
NT_NONE, b'T',
NT_NONE, b'G', NT_NONE, NT_NONE, NT_NONE, b'C', NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, b'N', NT_NONE, // 0x50
NT_NONE, NT_NONE, NT_NONE, NT_NONE, b'A', NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
// 0x60
NT_NONE, b'T', NT_NONE, b'G', NT_NONE, NT_NONE, NT_NONE, b'C', NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, b'N', NT_NONE, // 0x70
NT_NONE, NT_NONE, NT_NONE,
NT_NONE, b'A', NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE,
];
#[cfg_attr(rustfmt, rustfmt_skip)]
static COMPL: [u8; 128] =
[ NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
// 0x10
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
// 0x20
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
// 0x30
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
// 0x40
NT_NONE, b'T', NT_NONE, b'G', NT_NONE, NT_NONE, NT_NONE, b'C',
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, b'N', NT_NONE,
// 0x50
NT_NONE, NT_NONE, NT_NONE, NT_NONE, b'A', NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE,
// 0x60
NT_NONE, b'T', NT_NONE, b'G', NT_NONE, NT_NONE, NT_NONE, b'C',
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, b'N', NT_NONE,
// 0x70
NT_NONE, NT_NONE, NT_NONE, NT_NONE, b'A', NT_NONE, NT_NONE, NT_NONE,
NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE, NT_NONE];

#[cfg(test)]
mod tests {
Expand Down