Using temporary directory in assemble command.
Added a .gitignore file
Adding option of using temporary directory in popins assemble command.
Adding check for low base-calling quality in popins assemble command.
Allowing .fna ending for fasta files.
Changing to seqan version 1.4.2 instead of r14774.
Fixing file naming with temporary directory.
Writing paired fastq records immediately to files when cropping unaligned reads.
Remapping of popins assemble command uses only temporary directory if --tmpdir option specified.
Delete temporary fastq files.
Renaming variables for readability.
Introducing thresholds for number of contigs and number of branchings per component in popins merge command.
Fixing bad_alloc in popins merge command in mergeSeqWithGraph().
Adding temporary directory option to popins contigmap command.
Adding jump to chromosome when cropping mates of low quality aligned reads in popins assemble command.
Fixing tmpdir usage in popins assemble command.
Several improvements and fixes to unaligned read cropping in popins assemble command.
Comments and whitespace changes.
Resolving merge conflict.
Resolving merge conflict.