sequence-formats 1.5.0 → 1.5.1

raw patch · 2 files changed

+43/−23 lines, 2 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• Changelog.md +39/−22
• sequence-formats.cabal +4/−1

@@ -1,40 +1,57 @@-V 1.1.4.1: First entry in the Changelog. Added Haddock documentation to all modules and prepare for releasing on Hackage.+V 1.5.1: minor updates for hackage -V 1.1.4.2: Exporting readVCFfromProd+V 1.5.0: Added Plink support. -V 1.1.5: Fixed VCF parser: Now breaks if lines end prematurely+V 1.4.1:+* Added optional genetic position to FreqSumformat,+* changed various internal strings toByteStrings and vice versa. -V 1.1.6: VCF parser now allows for truncated VCF files with no Format and Genotypes (sites-only VCF files)+V 1.4.0.1: Added test file example.pileup to cabal extra-source-files to make tests work. -V 1.1.7: Added option to parse Bim file (slightly different layout to Eigenstrat Snp Format), and added genetic position and snpId to the EigenstratSnpEntry datastructure. This will cause breaking changes in code linking against this library.+V 1.4.0: Added three features:+* Chromosomes now include `X`, `Y` and `MT` (or `chrX`, `chrY`, `chrMT`), in that order after `chr22`. +* SNP rsId information is now internallyincluded as an option in the FreqSum data format.+* Pileup Format now also records strandorientation -V 1.1.8: Added more consumers for Bim and Eigenstrat Snp files+V 1.3.3: Added Pileup as new format. Changed all tests to Hspec. -V 1.1.8.1: Added Eq class to EigenstratInd and Sex+V 1.3.2.1: Fixed a hard-coded absolute path in the test-suite. -V 1.1.8.2: Added Eq and Show classes to various FreqSum entities. Fixed writing function, added tests.+V 1.3.2: Added testDat to Cabal file to make tests work off the tarball. -V 1.1.8.3: Added tests for Fasta import. Succeed.+V 1.3.1: Moved test suite outside of the main library into the test source directory. Cleaner setup. +V 1.3.0: Removed pipes-text, text and turtle dependencies and some more. Restructured all datatypes to use Bytestring instead of text. + V 1.2.0: Added tests for VCF, and several bugfixes. Now runs on LTS-14.1 with pipes-text as legacy dependency. -V 1.3.0: Removed pipes-text, text and turtle dependencies and some more. Restructured all datatypes to use Bytestring instead of text. +V 1.1.8.3: Added tests for Fasta import. Succeed. -V 1.3.1: Moved test suite outside of the main library into the test source directory. Cleaner setup.+V 1.1.8.2: Added Eq and Show classes to various FreqSum entities. Fixed writing function, added tests.+V 1.1.8.1: Added Eq class to EigenstratInd and Sex+V 1.1.8: Added more consumers for Bim and Eigenstrat Snp files+V 1.1.7: Added option to parse Bim file (slightly different layout to Eigenstrat Snp Format), and added genetic position and snpId to the EigenstratSnpEntry datastructure. This will cause breaking changes in code linking against this library.+V 1.1.6: VCF parser now allows for truncated VCF files with no Format and Genotypes (sites-only VCF files)+V 1.1.5: Fixed VCF parser: Now breaks if lines end prematurely+V 1.1.4.2: Exporting readVCFfromProd+V 1.1.4.1: First entry in the Changelog. Added Haddock documentation to all modules and prepare for releasing on Hackage. -V 1.3.2: Added testDat to Cabal file to make tests work off the tarball. -V 1.3.2.1: Fixed a hard-coded absolute path in the test-suite. -V 1.3.3: Added Pileup as new format. Changed all tests to Hspec. -V 1.4.0: Added three features:-* Chromosomes now include `X`, `Y` and `MT` (or `chrX`, `chrY`, `chrMT`), in that order after `chr22`. -* SNP rsId information is now internallyincluded as an option in the FreqSum data format.-* Pileup Format now also records strandorientation -V 1.4.0.1: Added test file example.pileup to cabal extra-source-files to make tests work. -V 1.4.1:-* Added optional genetic position to FreqSumformat,-* changed various internal strings toByteStrings and vice versa.++++++++++++++

@@ -1,5 +1,5 @@ name:                sequence-formats-version:             1.5.0+version:             1.5.1 synopsis:            A package with basic parsing utilities for several Bioinformatic data formats. description:         Contains utilities to parse and write Eigenstrat, Fasta, FreqSum, VCF, Plink and other file formats used in population genetics analyses. license:             GPL-3@@ -9,6 +9,9 @@ category:            Bioinformatics build-type:          Simple cabal-version:       >=1.10+Homepage:	           https://github.com/stschiff/sequence-formats+Bug-Reports:         https://github.com/stschiff/sequence-formats/issues+ extra-source-files:  README.md,                      Changelog.md,                      testDat/example.bim,