Io bam performance

[smehringer]

🤞

SAM

Benchmark a small SAM file (/group/ag_abi/gene/benchmark-files/io-test.bam as SAM):
Before: Elapsed (wall clock) time (h:mm:ss or m:ss): 0:10.33
After: Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.60
Seqan2: Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.19

BAM

Benchmark a small BAM file (/group/ag_abi/gene/benchmark-files/io-test.bam):
Before: Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.42
After: Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.66
Seqan2: Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.47

Looks like I need to make this pretty s.t. it can be merged.

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Name	Status	Preview	Updated
seqan3	✅ Ready (Inspect)	Visit Preview	Jan 6, 2023 at 10:29AM (UTC)

[codecov]

Codecov Report

Base: 98.22% // Head: 98.18% // Decreases project coverage by -0.03% ⚠️

Coverage data is based on head (7b762b8) compared to base (4a586be).
Patch coverage: 96.99% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3106      +/-   ##
==========================================
- Coverage   98.22%   98.18%   -0.04%     
==========================================
  Files         275      276       +1     
  Lines       12192    12277      +85     
==========================================
+ Hits        11975    12054      +79     
- Misses        217      223       +6     

Impacted Files	Coverage Δ
include/seqan3/io/sam_file/format_sam.hpp	93.68% <94.80%> (-1.42%)	⬇️
include/seqan3/io/sam_file/format_bam.hpp	94.51% <96.05%> (-0.42%)	⬇️
include/seqan3/io/detail/misc_input.hpp	96.36% <100.00%> (+0.06%)	⬆️
include/seqan3/io/sam_file/detail/cigar.hpp	95.00% <100.00%> (-5.00%)	⬇️
...lude/seqan3/io/sam_file/detail/format_sam_base.hpp	98.88% <100.00%> (+1.06%)	⬆️
...qan3/io/stream/detail/fast_istreambuf_iterator.hpp	100.00% <100.00%> (ø)
test/include/seqan3/test/literal/cigar_literal.hpp	100.00% <100.00%> (ø)
test/include/seqan3/test/streambuf.hpp	100.00% <100.00%> (ø)
include/seqan3/io/structure_file/format_vienna.hpp	96.10% <0.00%> (-1.46%)	⬇️
... and 10 more

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