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1.15.5

  • Fix memory bug in split
  • Add debug option to setup.sh and Makefile

1.15.4

  • Fix memory bug causing crash in generateCavemanUMNormVCF
  • Add missing dependecies to install script
  • Streamline install script

1.15.3

  • Remove requirement for CWD in config ini file

1.15.2

  • Correct genotype bug since inception. Now uses / rather than | in sample genotype section (GT) of VCF.

1.15.1

  • Fixed bug in ignore region calculations where ignored regions ends at the end of a chr.

1.15.0

  • Fixed bug in fai_access test
  • Updated htslib to 1.10.2
  • Added missing libgen.h header

1.14.1

  • Adding more useful error message to cn_access file reading method

1.14.0

  • Making species and assembly required commandline arguments in the estep
  • Change method by which read position index is resolved. Results in time saving.
  • linasm is now required linasm
  • New log and exp functions from linasm

1.13.16

  • Correct occasional memory blowout caused by split step not excluding an ignore region.

1.13.15

  • Add checks to sam_iter_next to ensure result is checked for errors

1.13.14

  • Fix array length index, check loop length and error messages related to 1.13.13.

1.13.13

1.13.12

  • Correct bad malloc on sscanf.

1.13.11

  • Modify fai_access_get_count_length_all_contigs to use strtok rather than sscanf.

1.13.10

Behaviour change

Where the proper pair filter flag is used, this code now checks that the paired-end orientation is also used. This will mean that mate-pair orientation (F/F or R/R) will be rejected If you wish to use mate-pair data, please use previous version

  • Where a proper pair filter is used, now check for the correct paired-end orientation of F/R.
  • If this is not met the read is ignored.

1.13.9

  • Fix version check to allow equal to or greater than comparisons

1.13.8

  • Use gzputs instead of gzprintf when writing reference contig lines to avoid buffer overflow

1.13.7

  • Modify means by which zlib version is detected.

1.13.5

  • Remove printf that causes all contigs to be printed to stderr.

1.13.4

  • Fix incorrect file path introduced in 1.13.3
  • Fixes #82

1.13.3

  • Add gzbuffer call after gzopen to ensure we don't hit the limit where many contigs are printed
  • Added unit test for additional methods
  • Fixes #77
  • Update license dates

1.13.2

  • Futher fixes for sentinel calls.
  • Correct version of REQUIRED_MIN_LIBZ as we are looking for greater than.

1.13.1

  • Ensure all sentinel calls return non-zero exit code.

1.13.0

  • Overlapping reads now handled #78
  • Fixes for #64, #65, #61

1.12.1

  • Resolves #74

1.12.0

  • Now outputs snp and mut vcf files as gzipped.
  • Requires zlib >= 1.2.3.5

1.11.3

  • Makefile update to cope with central/prefix install of htslib

1.11.2

  • Update htslib version (1.11.1 updated an unused reference to this archive)

1.11.0

  • Rearrangement to htslib pileup code gives large speed increases

1.10.1

  • Correction to fclose checking in estep.c

1.10.0

  • Added checks to all fflush and fclose calls

1.9.5

  • Removed dependency on ENA during compilation

1.9.4

  • Correct main method to ensure failure is passed through from running the by section main methods.

1.9.3

  • Fix bug in ignore regions file reading where bed file resulted in incorrect coords

1.9.2

1.9.1

  • Removed unnecessary dependancy on rsync when cp will do.

1.9.0

  • Corrections to install methods to ensure all relevant files were installed.

1.8.0

  • Commmandline params checked
  • Readlength taken into account in split sections
  • setup.sh installs perl scripts

1.7.3

  • Fixed generateCavemanUMNormVCF - command line help has errors #28
  • Fixed check BAM headers in setup for readgroups #34

1.7.2

  • RG lane id search no longer requires ID to be at the beginning of the RG line.

1.7.1

  • Added header read to bam_access_get_by_position_counts method. Fixes #41

1.7.0

  • Updated merge script to check number of files against splitList.

1.6.4

  • Fixed #37, Fixed bug where error thrown when no CN file, and should be using default.
  • Fixed #38, removed need for stack memory usage in array reading and writing.

1.6.2

  • Fixed bug in generateCavemanVCFUnatchedNormalPanel.c where q was not read at commandline.

1.6.0

  • Cram support added using htslib
  • Added setup script to download and compile htslib with patch (required for CRAM support).
  • Added 2015 and date additional info to licenses in all files