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Commits on Aug 18, 2017

• update readme

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Commits on Aug 17, 2017

• Merge branch 'boolean_vectors'

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• Explaining why SRC counter may output min=0 and percentage_shared_positions=100 - commented code and README update

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Commits on Jul 19, 2017

• allow the use of a window un SRC counter. The max populated window is considered while output the percentage of positions covered by a shared kmer and this value is used for output or not a read in…

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Commits on Jul 4, 2017

• SRC Counter outputs boolean vectors in addition to previous outputfiles - now filtering is made on the -s option

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• SRC Counter outputs boolean vectors in addition to previous outputfiles

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• link jenkins

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Commits on Jul 3, 2017

• adding a new script to get reads from SRC counter output

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• adding a new script to get reads from SRC counter output

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  76e39c8

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• update README

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• src counter now outputs a percentage of positions covered by shared kmers from the bank file - .sh fix

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• src counter now outputs a percentage of positions covered by shared kmers from the bank file

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Commits on Jun 30, 2017

• correct a small output typo and add the best percentage shared when using option -r

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Commits on Jun 23, 2017

• try to optimze the case when user is interested by links but not by scores

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Commits on Jun 21, 2017

• fixed conflict

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• merging stuffs

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• tentative debug empty similar_read_ids_position 3

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• tentative debug empty similar_read_ids_position 2

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• tentative debug empty similar_read_ids_position

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• debug keep_low_complexity option

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Commits on Jun 19, 2017

• By default: threshold solidity applies only on bank. Option -A enables to take into account also counting of kmers occurring in queries. With -A option, the index depends on the query files

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Commits on Jun 16, 2017

• remove synchro - too time consumming, does not fix the issue

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• fix lock isssue

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Commits on Jun 15, 2017

• tentative bug solving - not validated - added a synchro while writing the kmer read ids

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Commits on Jun 14, 2017

• authorizing bank as file of file in case of SRC counter or when using the commet-like output (option -r))

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• update simple test wrt modifications of kmer filtration

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Commits on Jun 7, 2017

• Forbid the use of a file of file for bank

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• SRC uses only kmers present both in the bank AND in the query files. Previously indexation filtration was based only on data found in the bank file.

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• 1/ Code refactoring

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Commits on May 29, 2017

• fixing a bug due to multithreading with reads id in src linker

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• Allow the use of symbolic link @philippe Bordron

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Commits on May 16, 2017

• fixed a bug: when using fastq, there was no output

  

  MARCHET Camille

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Commits on Apr 18, 2017

• using the zero-d option for src linker ram

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Commits on Apr 7, 2017

• formating license readme

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• 1/ fixed a 0 to 1 based bug in scripts (bug appeared commit 852e05c)

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