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Ongoing transition to DB backend (SQLite) #184

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Ongoing transition to DB backend (SQLite) #184

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Commits on Mar 9, 2021

  1. DataStore: small fix in SQL query, add to-do comment

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    hendrikweisser committed Mar 9, 2021
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  2. Eventalign_collapse: add flag for writing to DB (or TSV file), fix er… 

    …ror in DataStore call ('add_read' renamed to 'store_read')
    @hendrikweisser
    hendrikweisser committed Mar 9, 2021
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  3. Merge branch 'new_data_store' of https://github.com/tleonardi/nanocom… 

    …pore into new_data_store
    @hendrikweisser
    hendrikweisser committed Mar 9, 2021
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Commits on Mar 10, 2021

  1. better log message in 'DataStore.__init__'

    @hendrikweisser
    hendrikweisser committed Mar 10, 2021
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  2. Merge branch 'new_data_store' of https://github.com/tleonardi/nanocom… 

    …pore into new_data_store
    @hendrikweisser
    hendrikweisser committed Mar 10, 2021
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Commits on Mar 11, 2021

  1. coding style (added spaces for readability)

    @hendrikweisser
    hendrikweisser committed Mar 11, 2021
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  2. store read-level kmer stats in database (needed for whitelisting)

    @hendrikweisser
    hendrikweisser committed Mar 11, 2021
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Commits on Mar 12, 2021

  1. Whitelist: read data from SQLite, filter reads during query

    @hendrikweisser
    hendrikweisser committed Mar 12, 2021
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Commits on Mar 16, 2021

  1. add function to check validity of sample dictionary to 'common.py'

    @hendrikweisser
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  2. new class 'DatabaseWrapper' for reusable DB interaction code; adapt '… 

    …Whitelist' accordingly
    @hendrikweisser
    hendrikweisser committed Mar 16, 2021
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Commits on Mar 17, 2021

  1. Whitelist: fix filtering condition for sample subsets

    @hendrikweisser
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  2. consolidate database code in 'DataStore', remove 'DatabaseWrapper' (n… 

    …ot yet tested)
    @hendrikweisser
    hendrikweisser committed Mar 17, 2021
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Commits on Mar 23, 2021

  1. DataStore: small fixes, move 'DBCreateMode' (enum) to top level

    @hendrikweisser
    hendrikweisser committed Mar 23, 2021
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  2. Eventalign_collapse: small fix in 'DataStore' call

    @hendrikweisser
    hendrikweisser committed Mar 23, 2021
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  3. Whitelist: updated 'DataStore' call

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    hendrikweisser committed Mar 23, 2021
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  4. SampComp: get data from SQLite DB; some refactoring

    @hendrikweisser
    hendrikweisser committed Mar 23, 2021
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  5. TxComp: update to changes in 'SampComp'; some refactoring

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    hendrikweisser committed Mar 23, 2021
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Commits on Mar 29, 2021

  1. refactor DataStore, create child classes 'DS_EventAlign' and 'DS_Samp… 

    …Comp'
    @hendrikweisser
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  2. use 'DataStore_EventAlign' in 'Eventalign_collapse' and 'Whitelist'

    @hendrikweisser
    hendrikweisser committed Mar 29, 2021
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  3. TxComp: simplify 'txCompare' results data structure (remove 'lowCov' … 

    …elements)
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    hendrikweisser committed Mar 29, 2021
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  4. SampComp: small logging fix and update of 'txCompare' results

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    hendrikweisser committed Mar 29, 2021
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Commits on Mar 31, 2021

  1. DataStore: add functions to store sample information and whitelisted … 

    …reads
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    hendrikweisser committed Mar 31, 2021
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  2. SampComp: store whitelisted reads in SQLite DB

    @hendrikweisser
    hendrikweisser committed Mar 31, 2021
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Commits on Apr 6, 2021

  1. TxComp: use 'ST' as abbrev. for (Student) t-test

    @hendrikweisser
    hendrikweisser committed Apr 6, 2021
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  2. DataStore: fix DB init (tables creation), rework DB schema for SampCo… 

    …mp results
    @hendrikweisser
    hendrikweisser committed Apr 6, 2021
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  3. SampComp: remove unused parameters, write output to SQLite

    @hendrikweisser
    hendrikweisser committed Apr 6, 2021
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Commits on Jul 16, 2021

  1. TxComp: coding style - added whitespace

    @hendrikweisser
    hendrikweisser committed Jul 16, 2021
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  2. DataStore: split 'gmm_results' SQL table into two; improve error logg… 

    …ing during table creation
    @hendrikweisser
    hendrikweisser committed Jul 16, 2021
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  3. add new class 'PostProcess' for data export etc. (work in progress)

    @hendrikweisser
    hendrikweisser committed Jul 16, 2021
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Commits on Jul 21, 2021

  1. SampComp/TxComp/DataStore: limit to one univariate and one GMM-based … 

    …statistical test per k-mer
    @hendrikweisser
    hendrikweisser committed Jul 21, 2021
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  2. DataStore: improve definition of SQL tables

    @hendrikweisser
    hendrikweisser committed Jul 21, 2021
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  3. TxComp: cosmetic changes

    @hendrikweisser
    hendrikweisser committed Jul 21, 2021
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  4. DataStore/SampComp: add DB columns for adj. p-values, adapt DB schema… 

    … based on processing options
    @hendrikweisser
    hendrikweisser committed Jul 21, 2021
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  5. TxComp: combine collection of functions into class 'TxComp'

    @hendrikweisser
    hendrikweisser committed Jul 21, 2021
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  6. DataStore: small bug fixes (add 'self' for method calls)

    @hendrikweisser
    hendrikweisser committed Jul 21, 2021
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  7. SampComp: use new 'TxComp' class, simplify parameter handling

    @hendrikweisser
    hendrikweisser committed Jul 21, 2021
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  8. TxComp/DataStore: bug fixes (use of 'sequence_context')

    @hendrikweisser
    hendrikweisser committed Jul 21, 2021
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Commits on Jul 23, 2021

  1. SampComp: add multiple testing correction, remove 'shelve' export

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  2. PostProcess: implement 'save_report' for SQLite data

    @hendrikweisser
    hendrikweisser committed Jul 23, 2021
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  3. PostProcess: remove 'save_shift_stats' (now included in 'save_report')

    @hendrikweisser
    hendrikweisser committed Jul 23, 2021
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Commits on Aug 12, 2021

  1. Eventalign_collapse: remove TSV output option, simplify parameters

    @hendrikweisser
    hendrikweisser committed Aug 12, 2021
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  2. SampComp: remove irrelevant data from output queue tuple (thanks Tomm… 

    …aso!)
    @hendrikweisser
    hendrikweisser committed Aug 12, 2021
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Commits on Aug 16, 2021

  1. common: update function to build dict. with sample information

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  2. DataStore: add to-do comment

    @hendrikweisser
    hendrikweisser committed Aug 16, 2021
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  3. main: update command line options

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Commits on Aug 17, 2021

  1. main: fix PostProcess (TSV export) usage

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  2. main: update CLI documentation (minimal examples), make report genera… 

    …tion optional
    @hendrikweisser
    hendrikweisser committed Aug 17, 2021
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Commits on Aug 25, 2021

  1. Eventalign_collapse: small optimization (input file reading)

    @hendrikweisser
    hendrikweisser committed Aug 25, 2021
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  2. SuperParser: add spaces (coding style)

    @hendrikweisser
    hendrikweisser committed Aug 25, 2021
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Commits on Aug 26, 2021

  1. Whitelist: add to-do comment

    @hendrikweisser
    hendrikweisser committed Aug 26, 2021
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  2. DataStore: reduce file size of 'eventalign_collapse' output DB (by ab… 

    …out 20%)
    @hendrikweisser
    hendrikweisser committed Aug 26, 2021
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