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)

Like average.py but can return different statistics according to a format string

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 167 Commits
.gitignore		.gitignore
Makefile		Makefile
N-lengths.py		N-lengths.py
NX		NX
README.org		README.org
add-missing.py		add-missing.py
average.c		average.c
average.py		average.py
bambaseatpos.c		bambaseatpos.c
bars.py		bars.py
check-ambiguity-in-ref.py		check-ambiguity-in-ref.py
cigarparse.py		cigarparse.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-rmdup.py		fasta-rmdup.py
fasta-sort.py		fasta-sort.py
fasta-subset.py		fasta-subset.py
fasta-trim.py		fasta-trim.py
fastq-rmdup.py		fastq-rmdup.py
fastq-subsample.cc		fastq-subsample.cc
fastq-subsample.py		fastq-subsample.py
generate_structure.py		generate_structure.py
gff-feature-to-svg		gff-feature-to-svg
hgrep.py		hgrep.py
homopolymer-regions.py		homopolymer-regions.py
homopolymers.py		homopolymers.py
int-count.c		int-count.c
int-hist.c		int-hist.c
n-remover.py		n-remover.py
perc-ns.py		perc-ns.py
pileupcvg.c		pileupcvg.c
resample.c		resample.c
sam-filter.py		sam-filter.py
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
soap-fix.c		soap-fix.c
sortedsam2fastq.py		sortedsam2fastq.py
split-fasta.py		split-fasta.py
split-on-ns.py		split-on-ns.py
stats.py		stats.py
subsample-pe		subsample-pe
subset-join.py		subset-join.py
vc-chunker.py		vc-chunker.py
vote.py		vote.py