pandepth

TAFFISH wrapper for PanDepth, an ultrafast genomic coverage and depth calculator for SAM, BAM, CRAM, and PAF alignment files.

This app packages upstream PanDepth v2.26 as pandepth 2.26-r2. The default TAFFISH command runs the upstream pandepth executable directly, and command mode remains enabled so the same container environment can also be inspected explicitly with taf-pandepth pandepth ....

Release 2.26-r2 is a help-only TAFFISH update. It keeps the upstream software, Dockerfile, runtime dependencies, smoke tests, and command behavior unchanged from 2.26-r1, and refreshes the terminal taf-pandepth --help text.

Package metadata:

name: pandepth
command: taf-pandepth
version: 2.26-r2
kind: tool
image: ghcr.io/taffish/pandepth:2.26-r2
upstream release: v2.26
upstream runtime version: [v2.26] in help banner

Quick Start

Show the TAFFISH package version:

taf-pandepth --version

Show upstream PanDepth help. PanDepth uses -h for help, which conflicts with the TAFFISH wrapper help flag, so pass it after -- or use command mode:

taf-pandepth -- -h
taf-pandepth pandepth -h

Calculate whole-reference coverage from an alignment file:

taf-pandepth -i sample.bam -o sample -t 8

Run target-specific modes:

taf-pandepth -i sample.bam -g genes.gff3 -o sample.genes -t 8
taf-pandepth -i sample.bam -b regions.bed -o sample.regions -t 8
taf-pandepth -i sample.bam -w 100000 -o sample.windows -t 8
taf-pandepth -i sample.bam -a -o sample.sites -t 8
taf-pandepth -i sample.cram -r reference.fa -c -o sample.gc -t 8

Input Notes

-i accepts SAM, BAM, CRAM, PAF, or a .list file containing one input path per line. PAF input may be gzip-compressed, but PanDepth expects PAF records to include CIGAR information. For Minimap2 or Winnowmap-generated PAF, use the aligner's CIGAR-producing option, such as Minimap2 -c.

Sorted and indexed BAM/CRAM files are not required. If matching indexes are present, PanDepth can use them for multi-threaded acceleration. CRAM decoding and GC calculation require -r reference.fa.

Main Options

-i FILE       input SAM/BAM/CRAM/PAF file, or a .list file
-o PREFIX     output prefix
-g GFF/GTF    summarize gene or transcript features
-f TYPE       GFF/GTF feature type, default CDS
-b BED        summarize BED regions
-w INT        summarize fixed windows
-a            output per-site depth
-q INT        minimum mapping quality, default 0
-d INT        minimum site depth for statistics, default 1
-x INT        exclude reads with these SAM flag bits, default 1796
-t INT        number of threads, default 3
-r FASTA      reference genome for CRAM decode or GC calculation
-c            calculate GC content, requires -r
-h            upstream help

Outputs

PanDepth writes gzip-compressed tabular outputs using the -o prefix:

PREFIX.chr.stat.gz     whole-reference coverage and mean depth
PREFIX.gene.stat.gz    feature summaries when -g is used
PREFIX.bed.stat.gz     BED-region summaries when -b is used
PREFIX.win.stat.gz     fixed-window summaries when -w is used
PREFIX.SiteDepth.gz    per-site depth when -a is used

When -c -r reference.fa is used, GC columns are added to the relevant summary files.

Container Contents

The image contains:

pandepth
gzip
Debian htslib runtime libraries
libdeflate and zlib runtime libraries

The app does not bundle aligners or alignment-preparation tools such as Samtools, Minimap2, Winnowmap, BEDTools, or index-building helpers. Prepare SAM, BAM, CRAM, PAF, BED, GFF/GTF, and reference FASTA inputs outside this app, then pass those files to taf-pandepth.

Build Notes

The Dockerfile builds from the upstream v2.26 source tag and verifies commit afc2e5f10c60384dc5574846fadf8dba67476b44. The upstream release also provides an x86_64 binary and includes prebuilt static libraries in the source tree, but this TAFFISH package compiles the source against Debian system htslib, libdeflate, and zlib libraries. A small build-time include adjustment points PanDepth at those system headers and libraries; no CLI behavior is changed.

This keeps the app native on both declared platforms:

linux/amd64
linux/arm64

Smoke Coverage

The package smoke checks are self-contained and offline. They verify:

pandepth help and upstream version banner [v2.26]
runtime linkage to libhts and libdeflate
whole-reference coverage from a tiny SAM file
per-site output with -a
BED-region summaries
fixed-window summaries
GFF feature summaries from a .list input
GC-column output with -c -r

Smoke tests validate the container and a small functional path. They do not replace full biological validation on real sequencing or assembly datasets.

Upstream

• Project: PanDepth
• Source: https://github.com/HuiyangYu/PanDepth
• Packaged release: https://github.com/HuiyangYu/PanDepth/releases/tag/v2.26
• Upstream license: MIT
• Citation: Yu et al. 2024, Briefings in Bioinformatics
• DOI: https://doi.org/10.1093/bib/bbae197
• PMID: https://pubmed.ncbi.nlm.nih.gov/38701418/

Maintainer Commands

taf check
taf build
docker build -t ghcr.io/taffish/pandepth:2.26-r2 -f docker/Dockerfile .
taf publish --release --dry-run

License

The TAFFISH packaging files are licensed under Apache-2.0. Upstream PanDepth is distributed under the MIT License.