Updated the SamToFastq documentation

[kockan]

• Updated the SamToFastq documentation to clarify that the tool works properly for both name-sorted and coordinate-sorted inputs
• Fixed some whitespace issues

[kockan]

For #1834

[gokalpcelik]

Sorry if I forgot to mention this earlier but although mates come with the same order in both fastq files the behavior is different between name sorted vs coordinate sorted bam files. Name sorted bam files will produce the very same fastqs generated from the sequencer whereas coordinate sorted bams will result in a scrambled fastq files where mates match but reads are not sorted by name. This may result in slightly different outcomes when used with non-deterministic mappers such as bwa. Maybe we need to mention this briefly.

In summary you can still use paired fastqs generated by this tool for a reanalysis however resulting alignments may vary due to the nature of the mapper.