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If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.
[samopen] SAM header is present: 1 sequences.
[bam_sort_core] merging from 2 files...
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bam_pileup_core] the input is not sorted (reads out of order)
[afs] 0:0.000 1:0.000 2:0.000
[bam_plp_destroy] memory leak: 1. Continue anyway.