Changed default reflen; more informative error message when GCD bin size too small or reflen too big
Drop empty bins from coverage distribution
Merge remote branch 'remotes/pd3master/master' into develop
bamcheck: Fixed a bug introduced by previous change igcd to uint: not a good idea to init with -1.
bamcheck: max quality value increased to 255 to handle missing qual field; pairs with IS=0 can still count as paired; output IS=0 stats as well
misc/Makefile, on behalf of ghuls: changed the order of bamcheck rules with -lz last
bamcheck: New stats, number of pairs mapped to different chromosomes
bam_plcmd.c: added sanity check in read_file_list, complain if file list is not a file list
bam_plcmd.c: more descriptive -b usage help message
ksort.h: declared __ks_insertsort_##name as static to compile with C99. (On behalf of Hanspeter Niederstrasser.)
bam2depth: Enabled reading the list of BAMs from a file list
bamcheck: New stats - the number of QC failed reads and non-primary alignments
mpileup: New --rf and --ff options for filtering reads
big fix: using samtools view file.bam gibberish returns alignments; iter not checked against kh_end
fixed missing braces
Merge branch 'vsbuffalo-master' into develop
bamcheck: new stats, number of filtered vs raw sequences
dump log-likelihood
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cont