Reduce use of abort, remove assert(fp), pass one string to fprintf not multicall

Reduce use of abort to situations where you might actually want to debug.
Remove assert(fp)'s and replace with proper error messages.
Remove a few instances where fprintf is called multiple times rather than just
passing one string to it.

Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
Recanonicalise padding.c whitespace -- USE -b/-w TO DIFF/BLAME

This file had a mixture of 1-tab and 8-space indents which previously
went unnoticed.  See notes in fcb8af08a6fd3bfcf195407c4ba5bae528ee326d.
Merge abort/assert reduction (PR #290)

Also update bam_stat.c and bamshuf.c dependencies accordingly.
Fixmates ct fix

Only add ct if not already present. (Fixes #276)
Make addition of ct a non-default option.

Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
Merge fixmate ct improvements (PR #292)
Remove view -Q qual_scale option

It's unclear what it might be useful for.  Closes #154.
Free the kstring allocated in bam_fillmd1_core in all cases

Rewrote the logic to avoid unmapped reads bailing out early, negating
the (undocumented) -q and -d options.  Fixes #143, closes #293.
Describe compression level settings
Merge branch 'develop' of https://github.com/samtools/samtools into calmd