Coverage parsing

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The process of coverage parsing used by blobtools create and map2cov differs depending on the file format of the coverage file.

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1. BAM files

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1.1. samtools flagstat is called on the BAM file in order to obtain:

• total number of reads
• mapped number of reads

1.2. samtools view -F 4 -F 1028 -F 256 is called on the BAM file and the output is parsed

1.3 For each read :

• read coverage of sequence increases by 1
• base coverage of sequence increases by N
• where N is the sum of alignment match positions (M/X/='s) divided by the number of AGCT's in the sequence

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2. SAM files

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2.1. Only mapped reads (where RNAME is not "*") of the SAM file

2.2 For each read :

• read coverage of sequence increases by 1
• base coverage of sequence increases by N
• where N is the sum of alignment match positions (M/X/='s) divided by the number of AGCT's in the sequence

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3. CAS files

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3.1 clc_mapping_info -s is called and the output is parsed for:

• total number of reads
• mapped number of reads

3.2 clc_mapping_info -n is called and for each sequence in the assembly the following values are parsed:

• corrected base coverage (column 6 of "Contig info")
• read coverage (column 3 of "Contig info")

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4. COV files

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• Total/mapped read count is parsed from the header
• Base/read coverage is parsed for each sequence