added TwoBit parser, Bam parser and generator

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2194 93d9a472-daf7-0310-8f21-d7befa554562
added a few useful functions

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2198 93d9a472-daf7-0310-8f21-d7befa554562
more stuff moved in

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2199 93d9a472-daf7-0310-8f21-d7befa554562
one OB1 less

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2215 93d9a472-daf7-0310-8f21-d7befa554562
more convenience functions

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2218 93d9a472-daf7-0310-8f21-d7befa554562
yet more convenience functions

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2285 93d9a472-daf7-0310-8f21-d7befa554562
more convenience functions, some cleanup, separation of MPI specialties

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2290 93d9a472-daf7-0310-8f21-d7befa554562
BAM writer produces EOF marker now

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2293 93d9a472-daf7-0310-8f21-d7befa554562
experimental BAM writer w/ index

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2409 93d9a472-daf7-0310-8f21-d7befa554562
repaired EOF marker on writte BAMs

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2415 93d9a472-daf7-0310-8f21-d7befa554562
minor tweaks

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2419 93d9a472-daf7-0310-8f21-d7befa554562
added FastA/FastQ reader

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2436 93d9a472-daf7-0310-8f21-d7befa554562
added trimming functions for BAM records

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2476 93d9a472-daf7-0310-8f21-d7befa554562
fixed embarrassing space leak in isBam

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2481 93d9a472-daf7-0310-8f21-d7befa554562
support sorting by name exactly as in samtools

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2486 93d9a472-daf7-0310-8f21-d7befa554562
minor cleanup

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2507 93d9a472-daf7-0310-8f21-d7befa554562
fixed a space leak in BAM header parsing

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2605 93d9a472-daf7-0310-8f21-d7befa554562
fixed coordinate handling bug in 2bit reader

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2682 93d9a472-daf7-0310-8f21-d7befa554562
butt-ugly access to indexed bam files

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2689 93d9a472-daf7-0310-8f21-d7befa554562
corrected handling of BAM index

git-svn-id: http://biofs04/svn/bioinf/biohazard/trunk@2697 93d9a472-daf7-0310-8f21-d7befa554562