pysam AlignedRead properties reflect old names in SAM specification

[GoogleCodeExporter]

Many of the SAM field names changed from specification 1.2 to 1.3, for instance:

MRNM (mate's reference) -> RNEXT (next fragment's reference)
MPOS (mate's position) -> PNEXT (next fragment's position)
ISIZE (insert size) -> TLEN (template length)

The AlignedRead properties reflect the old names. Also, for the FLAG helper 
methods is_read1 & is_read2, the flag bits now talk about first and last rather 
than just 1 and 2.

Perhaps the new names could be used, with the old names supported as aliases, 
later with deprecation warnings?

Original issue reported on code.google.com by p.j.a.c...@googlemail.com on 14 Oct 2011 at 1:36

[GoogleCodeExporter]

Hi,

thank for you for the suggestion. The new names have been added.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 19 Oct 2011 at 7:58

• Changed state: Fixed

[GoogleCodeExporter]

I see the RNEXT, PNEXT and TLEN change now,
http://code.google.com/p/pysam/source/diff?spec=svn66843f1a79fbd50cd9e206efb3ef0
5a53cd0ec7c&old=6480d5c5976c5df576c99c9fb6d97b54c352665a&r=66843f1a79fbd50cd9e20
6efb3ef05a53cd0ec7c&format=unidiff&path=%2Fpysam%2Fcsamtools.pyx

What about is_read1, is_read2 being switched to is_first_read and is_last_read 
or similar?

Original comment by p.j.a.c...@googlemail.com on 21 Oct 2011 at 11:13

[GoogleCodeExporter]

On second thoughts, maybe to match pysam.PileupRead use is_head and is_tail 
(assuming the meaning is close enough).

Also FLAG bit properties is_paired and is_proper_pair would need renaming, 
perhaps is_multi_segs and is_proper_segs or similar?

Original comment by p.j.a.c...@googlemail.com on 22 Oct 2011 at 12:24