Tools

Some tools that I wrote.

pileupcvg.c

Take as input a bam file and a chromosome id and outputs the coverage at each nucleotide position in the chromosome.

Reads a table from standard input and resamples it into bins.

Reads table from standard input and calculates average (mean, median or mode)

Prints in SAM format those alignments from a BAM file which contain a given base (or indel) at a given reference position

Name		Name	Last commit message	Last commit date
Latest commit History 82 Commits
.gitignore		.gitignore
Makefile		Makefile
NX		NX
README.org		README.org
average.py		average.py
bambaseatpos.c		bambaseatpos.c
bamvcftool.c		bamvcftool.c
bars.py		bars.py
consensus.c		consensus.c
fasta-filter.py		fasta-filter.py
fasta-index-get.py		fasta-index-get.py
fasta-lengths.py		fasta-lengths.py
fasta-regex.py		fasta-regex.py
fasta-sort.py		fasta-sort.py
fasta-subset.py		fasta-subset.py
fasta-trim.py		fasta-trim.py
fastq-subsample.py		fastq-subsample.py
gff-feature-to-svg		gff-feature-to-svg
homopolymers.py		homopolymers.py
perc-ns.py		perc-ns.py
pileupcvg.c		pileupcvg.c
resample.c		resample.c
sam-to-svg.py		sam-to-svg.py
simple-bowtie2-pe-to-ref		simple-bowtie2-pe-to-ref
simple-bwamem-asm-to-ref		simple-bwamem-asm-to-ref
sortedsam2fastq.py		sortedsam2fastq.py
split-fasta.py		split-fasta.py
stats.py		stats.py
vote.py		vote.py