wtwhite

Example code for Gaps docs says one thing and does another

1

The documentation at http://docs.seqan.de/seqan/master/class_Gaps.html gives some nice example code, but in the last line before the `return;` in `main()` there is a small but confusing error: The program says it...

StringSet tutorial example uses deprecated functions like positionToId()

1

The "Working with StringSets" section of the [StringSet tutorial page](http://seqan.readthedocs.io/en/master/Tutorial/DataStructures/Sequence/StringSets.html) explains how to use several functions like `positionToId()`, although these functions are listed as deprecated in the `StringSet` docs. If...

AlignmentGraph tutorial refers to undocumented 3-parameter version of addVertex()

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The [Alignment (Graph) tutorial page](http://seqan.readthedocs.io/en/master/Tutorial/DataStructures/Alignment/AlignmentGraph.html) makes heavy use of a 3-argument form of `addVertex()` that takes start position and length parameters in addition to the usual graph parameter. I could...

Commit b09e87e0 causes link error "undefined reference to `pthread_create'" on Linux

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On Linux, SeqAn seems to need libpthread for multithreaded BAM file I/O (at least). But since commit b09e87e0 (I think; I haven't tried git bisect to verify), using any SeqAn...

Java: Please either autodetect the needed JDK version from `pom.xml` or document that `setup-java` must be called manually

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For CodeQL runs on Maven Java projects, the default-generated workflow, which runs autobuild, fails with `error: invalid target release: 17` if the project requires JDK 17 (or, apparently, any version...