Source: ea-utils
Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:
 Andreas Tille <tille@debian.org>,
Section: science
Build-Depends:
 debhelper-compat (= 13),
 libbam-dev,
 zlib1g-dev,
 libgsl-dev,
 libsparsehash-dev,
 architecture-is-64-bit,
 architecture-is-little-endian,
Vcs-Browser: https://salsa.debian.org/med-team/ea-utils
Vcs-Git: https://salsa.debian.org/med-team/ea-utils.git
Homepage: https://expressionanalysis.github.io/ea-utils/
Rules-Requires-Root: no

Package: ea-utils
Architecture: any
Depends:
 ${shlibs:Depends},
 ${misc:Depends},
 r-base-core,
 r-cran-getopt,
 r-cran-hmisc,
 r-cran-lattice,
 r-cran-survival,
 r-cran-formula,
 r-cran-ggplot2,
Recommends:
 med-config,
Description: command-line tools for processing biological sequencing data
 Ea-utils provides a set of command-line tools for processing biological
 sequencing data, barcode demultiplexing, adapter trimming, etc.
 .
 Primarily written to support an Illumina based pipeline - but should work with
 any FASTQs.
 .
 Main Tools are:
 .
  * fastq-mcf
 Scans a sequence file for adapters, and, based on a log-scaled threshold,
 determines a set of clipping parameters and performs clipping. Also does
 skewing detection and quality filtering.
  * fastq-multx
 Demultiplexes a fastq. Capable of auto-determining barcode id's based on a
 master set fields. Keeps multiple reads in-sync during demultiplexing. Can
 verify that the reads are in-sync as well, and fail if they're not.
  * fastq-join
 Similar to audy's stitch program, but in C, more efficient and supports some
 automatic benchmarking and tuning. It uses the same "squared distance for
 anchored alignment" as other tools.
  * varcall
 Takes a pileup and calculates variants in a more easily parameterized manner
 than some other tools.
