keithj / cl-sam Goto Github PK

Permitted read names have changed too. @ character is no longer allowed. Limited to between 1 and 255 chars.

The new CIGAR string operations '=' and 'X' should be supported.

Use the template/fragment notation instead of read/forward/reverse in function and argument names.

There should be functions to build PG chains from PP tags, to raise errors on orphan PP tags and to merge PP tag sets.

The reference sequence name should match the regex in the spec, or raise an error.

It fails to compile in the latest quicklisp, because it relies on CFFI declaring a version, but apparently non-release copies of CFFI, including the one in quicklisp, do not declare a :version.

Great repo! Is it still being maintained? I forked it to https://github.com/biolisp

1.3 introduces a non-backwards compatible change in permitted sequence characters; from [NTGCA=]+ to [A-Za-z=.]+. The current validation is too strict.

The sanity checks for the bitwise flags added in 1.3 should be used to avoid raising errors.

Add restarts to allow recovery from bad headers or clashes during header merging.

Hi,

The find-bam-index/1 fails for me in LispWorks. The reason is that the pathnames returned by merge-pathnames on the .bai files and the pathnames returned returned by find-bam-index don't exactly match. However, when comparing their namestrings, everything is fine. I changed the three ensure forms to this:

(ensure (equal (namestring (merge-pathnames ...))
(namestring (find-bam-index (merge-pathnames ...)))))

Then this test passes for me in LispWorks. All the other tests already pass anyway.

Best,
Pascal