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sam2matrix - This program outputs for each read the ids of references it maps to.
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SYNOPSIS
sam2matrix -m a.sam -m b.sam -r reads -rf ref_a.fasta -rf ref_b.fasta -o out.csv
DESCRIPTION
This program determines for each read in the reference file if it has an entry in the provided sam files stating
that it mapped. Afterwards a file is generated containing a row for each read which contains the read ID and the
index of the mapped references.
-h, --help
Displays this help message.
--version
Display version information
-m, --mapping FILE
File containing the mappings. Valid filetype is: sam.
-r, --reads FILE
File containing the reads contained in the mapping file(s). Valid filetypes are: fa, fasta, fq, and fastq.
-rf, --reference STRING
Name of the file used as reference of the corresponding sam file.
-o, --out FILE
Output file. Valid filetype is: csv.
EXAMPLES
./sam2matrix -m a.sam -m b.sam -r reads.fasta -rf ref_a.fasta -rf ref_b.fasta -o out.csv
Storing in out.csv for each read contained in reads.fasta if it mapped to the references in ref_a.fasta or
ref_b.fasta using the corresponding sam files a.sam and b.sam.
VERSION
sam2matrix version: 0.1
Last update April 2014
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