samtools/samtools — pull request #115 by lindenb (2014-01-26 11:57:24+00:00)
Title: Streamstats

Hi,
I added some new features to `samtools flagstat`.

- multiple output format (standard, json, xml)
- setting the qual for diffchrhigh
- more that one BAM file
- ouput name for report. If set, one use pipelining

## Examples:
### xml

```
$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/NA12273/alignment/NA12273.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.bam" |
./samtools view -h - |
head -n 10000 |
samtools view -Sb - |
./samtools flagstat -fX - |
xmllint --format - |
head -n 20