weeSAM | Script for parsing SAM/BAM files for coverage statistics

weeSAM is a Python library typically used in Telecommunications, Media, Advertising, Marketing applications. weeSAM has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However weeSAM build file is not available. You can download it from GitHub.

--bam : The input bam file. [file.bam] --sam : The input sam file. [file.sam] --out : The name of your output file. [myoutput.txt] --html: Generate html for each coverage plot produced by the script. [file.html] --overwrite : Add this flag to overwrite a html directory from a previous run. --mapped : Add to generate and analyse a new bam file with only mapped reads. -h : Print help function. -v : weeSAM version number. Ref_Name : The identifier of the reference. Ref_Len : The length in bases of each reference. Mapped_Reads : Number of reads mapped to each reference. Breadth : The number of sites in the genome covered by reads. %_Covered : The percent of sites in the genome which have coverage. Min_Depth : Minimum read depth observed. Max_Depth : Max read depth observed. Avg_Depth : Mean read depth observed. Std_Dev : Standard deviation of the mean (Avg_Depth). Above_0.2_Depth : Percentage of sites which have greater than 0.2 * Avg_Depth. Above_1_Depth : Percentage of sites which are above Avg_Depth. Above_1.8_Depth : Percentage of sites which have greater than 1.8 * Avg_Depth. Variation_Coefficient : The mean of Std_Dev of the mean.