Release v1.6.0.0

This release adds the Variant Call Format (VCF) to its possible output options. To select it, just pass the option --vcf. The file is output to the standard-out. So you can run something like

samtools mpileup ... | pileupCaller --randomHaploid -f <snp_file> --vcf > output.vcf

You can also zip the output, by chaining it through gzip -c:

samtools mpileup ... | pileupCaller --randomHaploid -f <snp_file> --vcf | gzip -c > output.vcf

Please take a look at the README, which has been updated.

Release v1.5.4.0_more_binaries

The code hasn't changed, but I have implemented a new GitHub-action workflow, and here provide executable binaries for more platforms, including conda.

Release v1.5.4.0

• updated sequence-formats dependency allows more lenient parsing of pileup-data, now also allowing for arbitrary reference alleles (not just ACTGN). This won't affect calling (reads that support an allele that is not in the SNP-file input are treated as before), but will be less disruptive when parsing pileup-input, for example without a bed-file in samtools.
• improved error output for parsing problems with pileup-format data. Now only a small part of the problematic chunk is output, hopefully easing error interpretation in such cases
• output a useful error message if the number of samples passed in --sampleNames is inconsistent with the pileup-input
• --samplePopName now accepts multiple pop-names, separated by comma. The number of pop-names must then match the number of samples.

Fixed bug in vcf2eigenstrat

This release fixes a bug in vcf2eigenstrat, which previously would fail on missing quality fields in the VCF.

v1.5.3.1

This release just updated to the latest Compiler, with some internal code changes. No actual feature additions or patches.

v1.5.3

This release introduces an option to encode population names flexibly in plink format, and fixes a big which caused pileupCaller to exit when encountering reference-skip symbols.

v1.5.2

This version fixes a bug that --samplePopName needed to be entered after -e or -p (#23), and it links to the updated sequence-formats-1.6.3, which fixes a bug in parsing pileup-formatted data, where lower-letter reference alleles would not be properly converted to capital letters.

v1.5.1

see Changelog

v1.5.0

see Changelog

Version 1.4.0

A substantially new release that includes an option to handle single-stranded library prep data in pileupCaller.

Key updates:

• Lots of internal refactoring and addition of automatic tests.
• Different handling of triallelic sites by default. You can restore the old behaviour using --keepIncongruentReads
• Removed some dangerous options, such as running without a SNP file.
• Added option to handle single-stranded library prep (using --singleStrandMode).
• Outputting some basic statistics per sample