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TextCigarCodec is stateless but has non-static methods #135

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yfarjoun opened this issue Nov 24, 2014 · 0 comments
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TextCigarCodec is stateless but has non-static methods #135

yfarjoun opened this issue Nov 24, 2014 · 0 comments
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@yfarjoun
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if encode, decode, isDigit would be made static one could use them without first creating an instance of class.
@gbggrant gbggrant self-assigned this Dec 18, 2014
@gbggrant gbggrant mentioned this issue Dec 18, 2014
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yfarjoun pushed a commit to yfarjoun/htsjdk that referenced this issue Jun 5, 2019
@jkbonfield
Changed Z and H aux types to handle zero-length strings, as these are
4bf7747 
supported in BAM implementations but not permitted in SAM.

Also changed H to require an even number of bytes as this was
(probably) an oversight and is enforced by some implementations
(htsjdk, maybe more).

Fixes samtools#135
yfarjoun pushed a commit to yfarjoun/htsjdk that referenced this issue Jun 5, 2019
@jmarshall
Minor SAM clarifications, notably allowing zero-length B arrays
c9ddec2 
Permit no numeric entries in SAM B array regexp.
Fixes samtools#135 (for B fields; already fixed for Z and H).

Describe the BAM representation of SEQ '*'.
Fixes samtools#49. Also avoid odd "odd numbered length" phrasing.

Further clarify that only @HD/SQ/RG/PG/CO are valid headers.
Explicitly list the header types in the regexp too. Apparently some were
still focussing on the [A-Z][A-Z] regexp and ignoring the surrounding
text -- see samtools-help July 2017, 'additional header lines "@ga"',
<https://sourceforge.net/p/samtools/mailman/message/35933210/>.

Remove CIGAR N intron/skip operator history note.
The N operator was in the original SAM document; its description was
merely improved in Dec 2010 (51a762b).
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