Update interleave-pairs.cpp

Fix for #27

- 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

- NH tag fixed

- bioconda

- memory leaks fixed

- salmseq related changes

Fix for paired end bs-mapping

*) Added support for reference sequences > 4 GB

*) Experimental MacOSX compatibility
*) Several Bugfixes

Intermediate dev state

*) 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

*) 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 < -Q are
reported as unmapped
*) NM tag now also includes indels
*) -n 2 --strata reports now the correct number of mapped reads

*) 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.