A new step call fastqprocessing for Optimus to speed up #82
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…oBam, Attach10XBarcodes, SplitBamFile, SplitBamByCellBarcodes--into one step in Optimus
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Are there any tests for this code? |
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I think we said we were going to add tests with this ticket https://broadinstitute.atlassian.net/browse/GL-1179 .. or at least add more if there are some already. |
…nd freeze a particular version
Codecov Report
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## master #82 +/- ##
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Coverage 88.85% 88.85%
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Files 28 28
Lines 3007 3007
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Hits 2672 2672
Misses 335 335
Continue to review full report at Codecov.
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@kishorikonwar I think you may have missed several of my comments that github had hidden, please take another look |
| // sam records in its buffer. This is the same behavior across all | ||
| // reader threads | ||
| if (r == block_size || !fastQFileR1.keepReadingFile()) { | ||
| submit_block_tobe_written(samrecord_data, tindex); |
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| submit_block_tobe_written(samrecord_data, tindex); | |
| submit_block_to_be_written(samrecord_data, tindex); |
| for (int j=0; j < 5; j++) { | ||
| char c = tp[i]; | ||
| tp[i] = ATCG[j]; | ||
| /* if the mutation in any of the positions |
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fair enough. Should we put a ticket in the backlog to look into this ?
| #!/bin/bash | ||
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| # --tool=memcheck \ |
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please remove unused code
| } | ||
| /* getopt_long already printed an error message. */ | ||
| return; | ||
| break; |
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unnecessary break; after return;
| namespace fs = std::experimental::filesystem; | ||
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| /** @copydoc filesize */ | ||
| int32_t filesize(const char *filename) { |
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Is int32 sufficient here, or is a long type needed for large files? If file size is in bytes doesn't this top out at 2.1G?
| FILE *f = fopen(filename, "rb"); /* open the file in read only */ | ||
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| int32_t size = 0; | ||
| if (fseek(f, 0, SEEK_END) ==0 ) /* seek was successful */ |
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Isn't there a better way to get a file's size, such as fstat?
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| ./fastqproc ../../L8TX/L8TX_180221_01_F12_R1.fastq.gz ../../L8TX/L8TX_180221_01_F12_I1.fastq.gz ../../L8TX/L8TX_180221_01_F12_R2.fastq.gz ../../L8TX/L8TX_171026_01_F03_R1.fastq.gz ../../L8TX/L8TX_171026_01_F03_I1.fastq.gz ../../L8TX/L8TX_171026_01_F03_R2.fastq.gz | |||
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If these scripts refer to files that aren't checked in, what use are they for developers? This script in particular doesn't seem worth checking in once the development work is complete, since it's just calling fastqproc on a list of fastqs.
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| /** | ||
| * @brief Compute the number of bam files |
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Does this match the function? It looks like it's computing the number of blocks in a bam file.
Purpose
To speed-up Optimus for large datasets