Version 0.1

• Analyzes secondary alignments:
  • Keeps alignments whose alignment scores (AS) are within a specified value (-s <float>) of the best alignment. The default value of -s 0 means that only alignments judged as equivalent by the aligner will be kept.
  • Each of the n alignments for a read/fragment is counted as 1/n for the pileup.
  • To avoid excessive memory usage and the imprecision inherent in floating-point values, a maximum of 10 alignments per read is analyzed. Reads with more than 10 alignments will be subsampled based on the best alignment scores; in the case of ties, alignments appearing first in the SAM/BAM are favored.
• Input SAM/BAM files are required to be name sorted (samtools sort -n)
• A simple hashtable is implemented for efficiently compiling p-values to calculate q-values. The q-value calculation is still based on the Benjamini-Hochberg procedure.