I'm currently writing an algorithm to which the input is a large set of reads in a .sam file. I have earlier written it in matlab, but am now translating it to a java program. I have however problem to read the .sam file in java.
(I'm using Eclipse 4.6.0, Java 1.8 and the windows 10 operating system)
I've been looking around and many people seems to recommend something called "Picard tools". Many (older) links people give go to http://picard.sourceforge.net/javadoc/net/sf/samtools/SAMFileReader which seems no longer to be in use.
When I search I find it under https://broadinstitute.github.io/picard/ but the instructions there seems to be on how to use the program from the command prompt. I need a package (or something similar) which I can import in my java program and then use.
Can you still use Picard like that in some way (some old example with the non-working link seemed to have this approach). Or are the some other program/package I could use for this?
Happy if someone could help!