Strand

[yang-yangfeng]

two main things:
"-s" option which requires an int as argument to set strandness of rnaseq data: 0 = NONE (for unstranded), 1 = FR, 2 = RF

new function for obtaining strand info from bitwise flag, if rna prep was stranded
retains old XS function for setting strand, if rna prep was unstranded

Note: XS tags are required if data is unstranded. This is mainly an issue for STAR, which does not provide these by default. Need to mention this in documentation - if you want to use unstranded STAR bams, make sure you align with the "--outSAMstrandField intronMotif" option.

[coveralls]

Coverage decreased (-0.7%) to 88.951% when pulling a252a17 on strand into 9da076e on master.

[coveralls]

Coverage decreased (-0.6%) to 89.092% when pulling 5690304 on strand into 9da076e on master.

[coveralls]

Coverage increased (+0.2%) to 89.902% when pulling 93cd094 on strand into 9da076e on master.

[coveralls]

Coverage increased (+0.2%) to 89.932% when pulling d3b06a0 on strand into 9da076e on master.

[coveralls]

Coverage increased (+0.2%) to 89.932% when pulling d3b06a0 on strand into 9da076e on master.

[coveralls]

Coverage increased (+0.2%) to 89.911% when pulling 69f0d8a on strand into cacbb3b on master.