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guanchangge / mosaik-aligner

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erroneous/buggy NM:i:66545 values in MosaikText -bam output #24

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Any read that isn't aligned end-to-end (i.e. globally) has a faulty NM tag
in the output BAM, e.g.:

10 3LHet 715307 715368 208_USI-EAS034_1_PE1_FC304J0AAXX:3:1:1408:2015 2 63
+ 43 DGRP_208_3_PE_EAS034_080702
GATGTGCTAGAATATTTCACAAGAATAATAATTCCATCAGTTCGGGGAAATCATTGGTATTT
GATGTGCTAGAATATTTCACAAGAATAATAATTCCATCAGTTCGTGGAAATCTTTGGTATTT
777777777777777777777777777777777711111(.11+.&.1111/%/1+.11111

Looks like this in BAM:

208_USI-EAS034_1_PE1_FC304J0AAXX:3:1:1408:2015  9   3LHet   715307  43
62M *   0   0   GATGTGCTAGAATATTTCACAAGAATAATAATTCCATCAGTTCGTGGAAATCTTTGGTATTT
777777777777777777777777777777777711111(.11+.&.1111/%/1+.11111
RG:Z:DGRP_208_3_PE_EAS034_080702    NM:i:65538

Original issue reported on code.google.com by ajmac...@gmail.com on 9 Dec 2009 at 4:28

GoogleCodeExporter commented 8 years ago 
The bug has now been fixed in version 1370. Please download the latest version 
and
give it another try :-)

Cheers,

// Michael

Original comment by snowneb...@gmail.com on 16 Jan 2010 at 1:53