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smithlabcode / walt

WALT is a read mapping program for bisulfite sequencing DNA methylation studies.
GNU General Public License v3.0
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support SAM output format #5

Closed acgtun closed 9 years ago

acgtun commented 9 years ago

most of the bisulfite sequencing mapper support SAM output format. In order to support downstream analysis, bsmapper will be support SAM format, too.

acgtun commented 9 years ago

supports SAM format

mengzhou commented 9 years ago

I noticed that the CIGAR string is always * in WALT. Could it be (read_length)M, e.g. 50M, instead of ? I just have a little bit of concern that a \ might not be as compatible.

mengzhou commented 9 years ago

also MAPQ should not be 0. If it is not available, the value should be 255.

acgtun commented 9 years ago

@mengzhou

Hi, Meng, good catch. Thanks.