bam-window reports the number of reads mapping within adjacent windows on the genome. It reports the number of reads overlapping the window or optionally, just reports the number whose leftmost mapping coordinate is within the window. Use -d to report only a random sampling of the reads within the window. This is useful for approximating results at lower coverage depths.
Version 0.4 Usage: bam-window <bam_file>
-q INT filtering reads with mapping quality less than INT [0]
-w INT window size to count reads within [1000]
-p only include paired reads
-P only include properly paired reads
-s only count a read as in the window if its leftmost
mapping position is within the window
-l output a column for each library in each window
-r output a column for each read length in each window
-d FLOAT probability of reporting a read [1.000000]
bam-window reports the number of reads mapping within adjacent windows on the genome. It reports the number of reads overlapping the window or optionally, just reports the number whose leftmost mapping coordinate is within the window. Use -d to report only a random sampling of the reads within the window. This is useful for approximating results at lower coverage depths.
The -l option creates separate counts for each library
The -r option creates separate counts for each read length
The -l option can be paired with the -r option to get separate counts for each read length
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