Add properly paired to stats and correct definition in flagstat

stats: Properly paired flag counting has been added as a summary
number.

flagstat: ensure that read with properly paired flag set is
mapped as per SAM spec.
Replace bam2fq numbers with existing constants

bam2fq:
-Replace flag constants written as numbers like 0x40 with #defines
 from htslib/sam.h like BAM_FREAD1.
Remove global variables from samtools view

view:
Removes the global variables and replaces them with a structure
containing the settings for a run.
Add ability to strip aux tags to samtools view

view:
-Add ability to strip aux tags from reads.
Fix typos in the manpage.
samtools flags: add documentation. print out decimal representation in addition to hexadecimal and string representation
Merge pull request #121 from sm15/feature/bam_flags_docs

samtools flags
Use new sam_itr_*() htslib API for BAM/CRAM iterators

Indexed view and mpileup now work with both BAM and CRAM files.
[bedcov] Use the htslib API directly, now works with BAM or CRAM files

(Also fix bam_plcmd.o dependencies, omitted when that file was previously
converted to use the htslib API directly.)
Use htslib's bam_endpos() instead of copied old bam_calend() code

Results should be unaffected except in corner cases involving unmapped
reads, which will already have been filtered out in mplp_func() anyway.

However a notable difference is that the htslib code currently does
not support the "B" CIGAR operator, BAM_CBACK.
fixed spelling mistake
Merge pull request #118, fixing man page typos
Merge pull request #141 from sb10/develop

fixed spelling mistake
Merge pull request #109 from aux_tag_strip of github.com/mp15/samtools
Merge pull request #106, properly-paired flag statistics
Shut up, clang!
mpileup: Fixed broken IMF annotation
Added mpileup tests for CRAM