[FIX] fixed test_gff_io to changed tag members
[FIX] converted alf
[FIX] removed breakpoint_calculator and variant_comp (they can be added again if Birte and Anne-Katrin have port them)
[FIX] converted fx_bam_coverage
[FIX] converted fx_fastq_stats
[FIX] fixed test_vcf_io
Merge pull request #587 from weese/feature/stream-fixes

[FIX] various new I/O related fixes