covstats denominator

v0.2.6

• covstats: fix denominator in unmapped (#73)

cram scaling

Indexcov was tuned on bam indexes. The cram (crai) indexes always looked much worse.
See below for a before and after on the same data.

This required indexcov to be run with the --extranormalize flag. This is highly recommended if you are using crai files. It can clean up bam data as well. A reason to not use it would be if you want to do your own scaling/cleanup on the (more) raw data.

before:

after:

header fix

v0.2.3

fix header bug

indexcov maintenance

v0.2.2

• indexcov: better message on empty crai
• indexcov: allow sending indexes as globs (to avoid argument length limit)
• indexcov: if expected sex chroms are X,Y also find chrX,chrY (and use sorted order for output)

support for bai without .bams

v0.2.1

• indexcov:more defense for bad crai's
• indexcov: now works on just *.bai if a .fai is also given with -f.

minor bugfixes for indexcov and indexsplit

v0.2.0

• indexcov: better error message and handling of excluded chromosomes.
• indexcov: if given crais and no fai, indexcov will try to read the cram header using samtools view.
• indexsplit: fix rare panic in CRAI files due to an off-by-one error (thanks Lavanya for reporting and providing a test-case).

crai with long reads

v0.1.19

• indexcov: fix for long reads with cram. (#43)

more cram fixes for indexcov

v0.1.18

• indexsplit: fix off-by-one that resulted in double-counting some regions.
• indexcov: cram edge-cases.
• indexcov: better normalization to 1 for all cases. Fixes bug for bams with
  many (e.g. > 10K) chromosomes of which many have very low or normalization
  coverage. (#36)

CRAI fixes, better sex CN counting

v0.1.17

• indexcov: dont error when no sex chromosomes are found (#27).
• indexcov: dont error when some chromosomes have a single region and others have 0.
• indexcov: better checking on short sex chroms and other CRAI fixes.

(thanks to Javier Prado for several test-cases on CRAM)

v0.1.16

v0.1.16

• indexcov: report and plot number of mapped and unmapped reads as reported by the index.
• covmed: rename to covstats
• covstats: report samplename(s) from read groups as well as bam path.
• covstats: skip first 100K reads to give better estimates of depth.
• covstats: report percent of bad (QC-Fail|Duplicate) and of umapped reads.
• indexcov: automatically exclude chromosomes that match pattern: ^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d$.
  this can be adjusted from the command-line.