Fixed comment typo
Merge pull request #79 from spalte/comment_typo

Fixed comment typo
hts_idx: fixed indexing of NO_COOR blocks

This also fixes indexing of bams with no mapped reads.
This resolves #49
Propagate error codes for CRAM_OPT_RANGE
vcf: Propagate error in bcf_hdr_append
Fixed off-by-one in bcf_get_format_values
Construct HTS_IDX_REST and HTS_IDX_NONE iterators without an index

These iterators never need to seek within the file, so can be
constructed even without loading/creating an index.  This means
unindexed streaming loops can be written via the iterator APIs,
simplifying programs that can process either whole files or regions.

Also implement these two special tids for CRAM files.  HTS_IDX_START
and HTS_IDX_NOCOOR remain unimplemented for CRAM and now abort if used.
Propagate error from bcf_hdr_printf
hts_readlist modifed to explicitly indicate file name vs list
make sure we have found values for AC _and_ AN before using

fixes issue samtools/bcftools#34
Merge pull request #82 from sm15/feature/bcf_calc_ac_bugfix

make sure we have found values for AC _and_ AN before using
Support for =X cigars in mpileup overlaps.

Exit on yet untreated cigars rather than silently proceeding.
faidx: Set error status if unknown seq is queried
Merge bam_dup1() addition (PR #80)
Migrate documentation from samtools bam.h to sam.h and add a few more items

(Cherry-picked from PR #31.)
bcf_hdr_subset: To allow sanity checks, mark missing samples
bcf_sr_seek to seek to start with seq=NULL
bcf_remove_alleles: Fix indexing range for Number=A alleles

This is a temporary fix only, the function will still break
on BCF output.
Silence -Wstrict-prototypes warnings

In C (but not C++), "int foo();" is a non-prototype that says nothing
about what parameters foo might or might not have.  To say that it has
no parameters and avoid warnings with the GCC option above, you need
to write "int foo(void);".  (In C++, both imply foo has no parameters.)

(Partially addresses samtools/samtools#45.)