Changing existing code base: Difference between revisions
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There are going to be only one exercise. You have the project, and the exercise will be big.<br> | There are going to be only one exercise. You have the project, and the exercise will be big.<br> | ||
Clone Anders Gorm's repo: ''sequencelib'' and study it.<br> | Clone Anders Gorm's repo: ''sequencelib'' and study it.<br> | ||
Make it able to read FASTQ files. | '''Make it able to read FASTQ files.'''<br> | ||
This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well.<br> | |||
Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere or maybe generator, | |||
as FASTQ files get really big and can't all be in memory. Also, FASTQ are often gzipped - it is nice to read them directly from the gzip file.<br> | |||
You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help. | |||
== Exercises for extra practice == | == Exercises for extra practice == | ||
Revision as of 15:42, 30 April 2026
| Previous: Runtime evaluation | Next: Last words |
Required course material for the lesson
GitHub: Professor Anders Gorm Pedersen's repositories. Used in teaching this week.
GitHub: Gene network. A much larger and thus more complicated/confusing repo.
GitHub: The Bioinformatics Repository. Different repos, various languages.
Subjects covered
Hands-on addition to a code base,
Exercises to be handed in
There are going to be only one exercise. You have the project, and the exercise will be big.
Clone Anders Gorm's repo: sequencelib and study it.
Make it able to read FASTQ files.
This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well.
Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere or maybe generator,
as FASTQ files get really big and can't all be in memory. Also, FASTQ are often gzipped - it is nice to read them directly from the gzip file.
You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.