samtools/samtools — pull request #219 by jrandall (2014-05-27 23:54:31+00:00)
Title: Fixes `samtools sort` output to always be BAM

Closes #213.

```
$ ./samtools 2>&1 |head -n 3

Program: samtools (Tools for alignments in the SAM format)
Version: 0.2.0-rc8-40-gf85fab7 (using htslib 0.2.0-rc8-18-gba16f86)
$ ./samtools sort test/dat/view.001.sam view.001.sam.sort
$ file -m ~jr17/genetic.magic view.001.sam.sort.bam
view.001.sam.sort.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 904
$ ./samtools sort -m 1K -f test/mpileup/ce#large_seq.bam large.bam
[bam_sort_core] merging from 2 files...
$ file -m ~jr17/genetic.magic large.bam
large.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 104
```