v0.5.5

• Fix missing defines using latest Intel compiler #28
• --broken-pairs added #25
• Build error using Clang 5.0.0 #27

v0.5.4

• Segfault when mapping paired end with BAM output fixed (Issue #22)
• --broken-pairs added. Allows mixing paired and single-end reads in interleaved input files. (Issues #24)
• Dockerfile added
• Switched to MIT license

v0.5.3

• NH tag fixed
• bioconda

v0.5.2

• memory leaks fixed
• salmseq related changes

v0.5.0

*) Added support for reference sequences > 4 GB
*) Experimental MacOSX compatibility
*) Several Bugfixes

v0.4.12

*) Filter settings fixed for data sets with reads that don't have the
same length
*) BAM support improved
*) Better paired end support for BAM/SAM
*) Added parameters for read groups
*) Commandline output is now written to stderr
*) SAM/BAM output is written to stdou if -o/--output is omitted
*) Better handling of empty reads in FASTA/Q files
*) Change NAME filed to PN in SAM/BAM header
*) Fixed a bug that prevented NextGenMap from terminating when executed
in python scripts

v0.4.11

• bs-mapping: fixed bug that caused only 50% of reads to align when
  using -1 and -2
• bs-mapping: fixed wrong strand information in ZS flag for single end
  data
• bs-mapping: bs-cutoff default value set to 6 (instead of 8)
• Support for read groups (--rg-*)
• Parameter --keep-tags added. When specified NextGenMap copies all
  tags from the input SAM/BAM file to the output file
• Fixed segmentation fault when specifying a reference sequence that is
  < 2bp
• Fixed header information form output BAM files
• New parameter -Q/--min-mq . All reads with mapping quality < are
  reported as unmapped
• NM tag now also includes indels
• -n 2 --strata reports now the correct number of mapped reads

v0.4.10

*) When using SAM/BAM as input the strand of the reads is now taken into account
*) In paired end mode the alignment filter is now applied to both mates individually.
*) When using FASTA/Q as input in paired end mode NextGenMap now removes /1 and /2 which marks the right and the left mate from the names when writing SAM/BAM files.
*) The AMD APP SDK required to run OpenCL code is now part of the project.
*) LibSatGen library was removed from the source code.

v0.4.9

*) libStatGen source code added to project
*) alignment batch size reduced to fix "Unable to create buffer" error
*) max length of help text set to 80

v0.4.8

*) 32k limit for number of reference sequences removed
*) Endfree alignments fixed for reads with very low similarity to the
reference
*) Placement of gaps in endfree alignments changed to match gap
placement in local alignments
*) Paired-end BAM output fixed
*) Number of written lines output fixed
*) Fixed opencl/lib folder permission problem
*) --no-progress parameter added (suppress NextGenMap progress output)
*) OpenCL code cleanup