Update find_intersecting_snps_2.py and new filter_remapped_reads_2.py #2
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This is a longer message saying what I did.
Added run statistics and runtime to standard output. Fixed limit on number of SNPs allowed per read (default is 1024). Allowed for chromosome names that have a "." in them (e.g. NC_012920.1). Removed -s --sorted option, since it is not used.
Run statistics covers everything we need to print.
Script now tracks how many reads contain the reference SNP alleles given in the SNP files. The number of "reference matches" should ideally be 100%. If this percentage is very low, it may indicte that the SNPs are incorrect or that they are not 1-indexed, etc.
Duplicates of reads were being written to the fastq files.
Changes from original version: - No longer requires .num.gz file (now compatible with fild_intersecting_snps_2.py) - Tracks runtime and run statistics
This variable wasn't being used for anything.
Turns out we do need this.
Script now works for reads that did not remap at all, so the remapped bam file need not contain unmapped reads. Note that the remapped bam file MUST be sorted by read name.
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Updates to find_intersecting_snps_2.py:
New filter_remapped_reads_2.py: