Support for multisample probing improved

When viewing a DISCOVAR de novo assembly with NhoodInfo, from multisample data, one may now flag edges having any specified pattern of presence or absence of reads from given samples. For example in a three-sample assembly of child, mother, father, the command PURPLE=100 will cause edges having only reads from the child to be flagged as purple. This change takes effect as of revision 52401.

Input spec documentation

We’re adding a detailed description of the input specification for DiscovarDeNovo. It is quite general and allows several file types as well as path descriptions. Please let us know if anything is unclear or could use improvement. The new doc will appear with release 52345.

New statistic for detecting run problems

We’ve added a new statistic ‘MPL1′, the mean length of the first read in a pair up to the first error. This turns out to be diagnostic for certain run failures. The normal range is 175-225 for 250 base reads. A much smaller value would indicate that something has gone badly wrong (which is a rare event). This stat goes live as of revision 52335.