libStatGen version 1.0.10 is now available

[libStatGen]

LibStatGen.1.0.10 Release Notes

• Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
  • Updates:
    • Add PhoneHome/version checking logic
  • General Updates:
    • fix use of strncpy to fix compile problem for some users
    • Fix compile problem on gcc 4.8.1 by adding -Wno-strict-overflow in general/Makefile after -Werror
    • Reduce the default IFILE read buffer size from 1MB to 64KB.
    • Fix ifclose to take a IFILE reference so it can make the pointer 0 after closing
    • StringBasics::AsInteger now returns false if the string is empty.
    • GzipFileType - update to accept -.gz as stdin/stdout
    • Remove unnecssary line from Parameters Status call
    • Fix memory leak on Tabix destructor
  • Vcf Updates:
    • VCF - add class/methods to discard records based on ID
  • Bam Updates:
    • SamFlag - add isSecondary check
    • Fix SamFile so it only allows '-', '-.sam', '-.bam', or '-.ubam' to indicate reading from stdin rather than anything that starts with '-' in order to protect it from misinterpreting another parameter as the stdin filename
    • SamRecord: Add warnings about Duplicate Tags being overwritten
    • SamFile - improve sort order validation error messages and compare using both String::Compare and strcmp to handle various sort mechanisms since neither matches samtools exactly (if either is successful, the sort order is OK)
  • Glf Updates:
    • GlfFile cleanup bugs/handle missind endMarkers & update "get" methods to be const

If you are interested in this version, it can be downloaded at:

http://genome.sph.umich.edu/wiki/LibStatGen_Download

Let me know if you have any questions.

Mary Kate Wing