use picard to report #aln

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TOTAL_READS
PF_READS_ALIGNED

Original issue reported on code.google.com by zack...@gmail.com on 14 Jan 2014 at 10:32

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flagstat goes to advances, gets renamed tp "number of alignments"

picard moves from unused to summary, takes place of old flatstat pretty name
  (add tooltip: '1 or more mappings')

Original comment by zack...@gmail.com on 14 Jan 2014 at 10:59

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since PE is reported differently by picard: 

value_we_want = max(pf_reads_aligned_unpaired, pf_reads_aligned_paired)

Original comment by zack...@gmail.com on 15 Jan 2014 at 12:19

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1. Moved flagstat's mapped__mdups_qcpassed to Advanced and gave it a pretty
name "Number of alignments"
2. Moved Picard's pf_reads_aligned_unpaired to Summary and gave it a pretty
name Mapped reads (unpaired) and a tooltip '1 or more mappings'
3. Moved Picard's pf_reads_aligned_paired to Summary and gave it a pretty
name Mapped reads (paired) and a tooltip '1 or more mappings'

Original comment by natalia....@gmail.com on 15 Jan 2014 at 12:39

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having unpaired / paired mapped reads is proving to confusing.

try to combine into one metric.

Original comment by zack...@gmail.com on 15 Jan 2014 at 8:10

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combined pf_reads_aligned_unpaired and pf_reads_aligned_pair into max(
pf_reads_aligned_unpaired ,  pf_reads_aligned_pair)
This metric is now available in eccpgxt-beta under the name Mapped Reads in
Summary view
Moved Mapped Reads (paired) and Mapped Reads (unpaired) to Unused view

Original comment by natalia....@gmail.com on 22 Jan 2014 at 12:36

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Done. 

I implemented it as a sql query that was self-joining run_metric tables and 
inserting calculated metrics back into run_metric table. Recently, we decided 
to move away from keeping all derived  metrics in  run_metric table. So now its 
calculated in a table view. we keep the hard copy of the query generating that 
view in a seqDB scripts repository in the file: create_derived_view.sql

Original comment by natalia....@gmail.com on 5 Feb 2014 at 12:51

• Changed state: Done