Bam2x

- more sqlite3 integration
- fix bugs on index number of intron and exon

- introduce sqlite3 into bam2x
- add command line program load_bed_to_db
- add command line program query_db
- now subcommand in lib/bam2x/Run directory can run as a command.

- change the interpreter method in isoforms detection.
- fixed small bugs and improve the readability of code.

pre-alpha version 0.1 for bam2x. no longer support xplib commands.
it could be installed using pip.
pip install bam2x.

<pre>
usage: bam2x [-h] [-v]
{read,cmpgene,bam2fig,getanno,query_bam,getseq,isoforms,bam2peak}
positional arguments:
read read bed or bam files.
cmpgene cmp region with gene set(bed12 format)
bam2fig draw reads distribution on chromosomes into pdf file
getanno get [utr,exon,intron] annotations from bed12 file
query_bam query bam file
getseq get sequence from twobit genome file
isoforms detect isoforms.
bam2peak bam2peak , call exon peaks and link exons
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
</pre>

bam2x subcommand is ready for most program. and final xplib and bam2x version.
the update xplib will be in xplib branch.
the update bam2x will be in bam2x branch.

<pre>
usage: bam2x [-h] [-v]
{read,cmpgene,bam2fig,getanno,query_bam,getseq,isoforms,bam2peak}
...
bam2x
positional arguments:
{read,cmpgene,bam2fig,getanno,query_bam,getseq,isoforms,bam2peak}
subcommand help
read read bed or bam files.
cmpgene cmp region with gene set(bed12 format)
bam2fig draw reads distribution on chromosomes into pdf file
getanno get [utr,exon,intron] annotations from bed12 file
query_bam query bam file
getseq get sequence from twobit genome file
isoforms detect isoforms.
bam2peak bam2peak , call exon peaks and link exons
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
</pre>