Io bam performance

[smehringer]

:crossed_fingers:

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)

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Codecov Report

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

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

```diff @@ 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](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan) | Coverage Δ | | |---|---|---| | [include/seqan3/io/sam\_file/format\_sam.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-aW5jbHVkZS9zZXFhbjMvaW8vc2FtX2ZpbGUvZm9ybWF0X3NhbS5ocHA=) | `93.68% <94.80%> (-1.42%)` | :arrow_down: | | [include/seqan3/io/sam\_file/format\_bam.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-aW5jbHVkZS9zZXFhbjMvaW8vc2FtX2ZpbGUvZm9ybWF0X2JhbS5ocHA=) | `94.51% <96.05%> (-0.42%)` | :arrow_down: | | [include/seqan3/io/detail/misc\_input.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-aW5jbHVkZS9zZXFhbjMvaW8vZGV0YWlsL21pc2NfaW5wdXQuaHBw) | `96.36% <100.00%> (+0.06%)` | :arrow_up: | | [include/seqan3/io/sam\_file/detail/cigar.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-aW5jbHVkZS9zZXFhbjMvaW8vc2FtX2ZpbGUvZGV0YWlsL2NpZ2FyLmhwcA==) | `95.00% <100.00%> (-5.00%)` | :arrow_down: | | [...lude/seqan3/io/sam\_file/detail/format\_sam\_base.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-aW5jbHVkZS9zZXFhbjMvaW8vc2FtX2ZpbGUvZGV0YWlsL2Zvcm1hdF9zYW1fYmFzZS5ocHA=) | `98.88% <100.00%> (+1.06%)` | :arrow_up: | | [...qan3/io/stream/detail/fast\_istreambuf\_iterator.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-aW5jbHVkZS9zZXFhbjMvaW8vc3RyZWFtL2RldGFpbC9mYXN0X2lzdHJlYW1idWZfaXRlcmF0b3IuaHBw) | `100.00% <100.00%> (ø)` | | | [test/include/seqan3/test/literal/cigar\_literal.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-dGVzdC9pbmNsdWRlL3NlcWFuMy90ZXN0L2xpdGVyYWwvY2lnYXJfbGl0ZXJhbC5ocHA=) | `100.00% <100.00%> (ø)` | | | [test/include/seqan3/test/streambuf.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-dGVzdC9pbmNsdWRlL3NlcWFuMy90ZXN0L3N0cmVhbWJ1Zi5ocHA=) | `100.00% <100.00%> (ø)` | | | [include/seqan3/io/structure\_file/format\_vienna.hpp](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-aW5jbHVkZS9zZXFhbjMvaW8vc3RydWN0dXJlX2ZpbGUvZm9ybWF0X3ZpZW5uYS5ocHA=) | `96.10% <0.00%> (-1.46%)` | :arrow_down: | | ... and [10 more](https://codecov.io/gh/seqan/seqan3/pull/3106?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan)

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