Tool kits for structural variation project, including
- simulation
- analysis
- validation
- tests
- miscs.
add-an-indel-to-fasta
usage: add-an-indel-to-fasta [-h] [--n_bases N_BASES] [--insert | --delete] in_fasta out_fasta out_bed
Modify a reference fasta by either inserting a substring to a reference sequence or deleting a substring from a reference sequence, make a truth SV BED file for mapping reads of the original reference to the modified reference file.
positional arguments: in_fasta Input FASTA out_fasta Output FASTA with indels out_bed Ground truth SV calls in BED if modified fasta were used as reference
optional arguments: -h, --help show this help message and exit --n_bases N_BASES Number of bases to insert to or delete from a reference sequence --insert Insert a string to a sequence in in_fasta, and make a BED file with an Deletion SV call --delete Delete a substring from a sequence in in_fasta, and make a BED file with an Insertion SV call
make-subreads-bam-from-fasta
usage: make-subreads-bam-from-fasta [-h] [--dry_run] in_fasta in_bam_fofn out_prefix
Make a subreads.bam/xml containing all reads of a fasta file
positional arguments: in_fasta Input FASTA file in_bam_fofn Input BAM fofn out_prefix Output prefix
optional arguments: -h, --help show this help message and exit --dry_run Dry run
make-subreads-bam-from-zmws
usage: make-subreads-bam-from-zmws [-h] [--dry_run] in_txt in_bam_fofn out_prefix
Make a subreads.bam/xml containing all subreads of zmws.txt
positional arguments: in_txt Input txt file containg ZMW names or read names in_bam_fofn Input BAM fofn out_prefix Output prefix
optional arguments: -h, --help show this help message and exit --dry_run Dry run, display CMDs