l_qname overflows for QNAMEs of 252 or more characters

[jmarshall]

5d114eb added extra NULs in memory to ensure that CIGAR data is 4-byte aligned. To avoid breaking bad code that does not use the accessor macros, these extra bytes were included in in-memory l_qname. For QNAMES of length ≥252 characters, this means that l_qname needs to have the value 256, but it is a uint8_t.

There are various ways of fixing this, though it's less straightforward to do so while minimising binary compatibility implications.

This is the cause of pysam-developers/pysam#447.

[dpryan79]

@jmarshall: Thanks for so quickly noticing this issue on the pysam repo!

[jmarshall]

PR #523 suggests a fix for this that I believe maximises binary compatibility. If the libhts .so-version were to be bumped, less convoluted fixes become available.