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The SAM/BAM/CRAM specification has the @CO header for one-line comments. It's defined as below:
@CO
@CO: One-line text comment. Unordered multiple @CO lines are allowed. UTF-8 encoding may be used. https://github.com/samtools/hts-specs/blob/be74ef71f3fad34eb86af83bd66338d7d569af99/SAMv1.tex#L356
However, the current implementation of the SAM/BAM reader doesn't read the @CO header properly.
$ samtools view -h header_comment.sam @SQ SN:chr1 LN:1000 M5:258e88dcbd3cd44d8e7ab43f6ecb6af0 @CO This is a comment. @CO This is also a comment.
(require '[cljam.io.sam :as sam]) (with-open [r (sam/reader "header_comment.sam")] (sam/read-header r)) ;=> {:SQ [{:SN "chr1", :LN 1000, :M5 "258e88dcbd3cd44d8e7ab43f6ecb6af0"}], :CO [{:This is a comment. nil} {:This is also a comment. nil}]}
Note that the comment contents themselves are read as keywords including whitespaces.
The text was updated successfully, but these errors were encountered:
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The SAM/BAM/CRAM specification has the
@CO
header for one-line comments. It's defined as below:However, the current implementation of the SAM/BAM reader doesn't read the
@CO
header properly.Repro
Note that the comment contents themselves are read as keywords including whitespaces.
The text was updated successfully, but these errors were encountered: