v1.18.0

New in 1.18.0

• New awk functions getAlnEnd() and getAlnLen() to get the end and
  length of a SAM aligmment, respectively. Useful to filter for alignments
  above/below a cutoff, especially handy with Nanopore reads. E.g.

awk 'getAlnLen() > 2000 && getAlnEnd() < 12345'

• Use the operating system's awk instead of the built-in Java Jawk. OS's
  awk appears to be 5-10x faster than Jawk. The flip side is that we assume
  users have awk on their PATH.

• Add configuration parameter low_mapq to set what you consider as low
  mapping quality. Default is 5 which was the setting hardcoded until now.

• Use false in config shade_structural_variant to omit shading of
  structural variants

• New command nextChrom moves to the next chromosome without the need of
  typing its name. Useful to quickly flip through several chromosomes.

• Can read CRAM files (finally!)

• New command addHeader inserts one or more lines of text before a track.
  Useful to add a header or legend-like text to groups of tracks.

• Accept bed/bedgraph with space as column separator (see old issue #12)

• print decodes URL character to readable character (e.g. it prints , instead of %2C)

• Improved command show genome: Add option -n to limit the number of
  contigs; sort by size; add percentage and cumulative percentage of genome
  covered by each contig; add indicator of current contig. E.g.:

show genome
Genome size: 3095693983; Number of contigs: 25                                                                                                                           
chr1  249250621 |||||||||||||||||||||||||||||| 8.1%; 8.1%                                                                                                                
chr2  243199373 |||||||||||||||||||||||||||||  7.9%; 15.9%                                                                                                               
chr3  198022430 ||||||||||||||||||||||||       6.4%; 22.3%                                                                                                               
chr4  191154276 |||||||||||||||||||||||        6.2%; 28.5%                                                                                                               
chr5  180915260 ||||||||||||||||||||||         5.8%; 34.3%                                                                                                               
chr6  171115067 |||||||||||||||||||||          5.5%; 39.9%                                                                                                               
chr7  159138663 |||||||||||||||||||            5.1%; 45.0% <==                                                                                                  
chrX  155270560 |||||||||||||||||||            5.0%; 50.0%                                                                                                               
chr8  146364022 ||||||||||||||||||             4.7%; 54.7%                                                                                                               
chr9  141213431 |||||||||||||||||              4.6%; 59.3%                                                                                                               
chr10 135534747 ||||||||||||||||               4.4%; 63.7%                                                                                                               
chr11 135006516 ||||||||||||||||               4.4%; 68.0%                                                                                                               
chr12 133851895 ||||||||||||||||               4.3%; 72.4%                                                                                                               
chr13 115169878 ||||||||||||||                 3.7%; 76.1%                                                                                                               
chr14 107349540 |||||||||||||                  3.5%; 79.5%                                                                                                               
chr15 102531392 ||||||||||||                   3.3%; 82.9%                                                                                                               
chr16 90354753  |||||||||||                    2.9%; 85.8%                                                                                                               
chr17 81195210  ||||||||||                     2.6%; 88.4%                                                                                                               
chr18 78077248  |||||||||                      2.5%; 90.9%                                                                                                               
chr20 63025520  ||||||||                       2.0%; 93.0%                                                                                                               
chrY  59373566  |||||||                        1.9%; 94.9%                                                                                                               
chr19 59128983  |||||||                        1.9%; 96.8%                                                                                                               
chr22 51304566  ||||||                         1.7%; 98.4%                                                                                                               
chr21 48129895  ||||||                         1.6%; 100.0%                                                                                                              
chrM  16571                                    0.0%; 100.0%