{"push_id":2616616389,"size":1,"distinct_size":1,"ref":"refs/heads/devel","head":"6df64f9fdccda8a120edcc61912ea7334501c25e","before":"d54f405951d0f4fef057b3f3e86752b386d82fff","commits":[{"sha":"6df64f9fdccda8a120edcc61912ea7334501c25e","author":{"name":"daviesrob","email":"3243a2766bb737188235920577f6adab5919ad82@sanger.ac.uk"},"message":"Enable barcode decoding in i2b. (#113)\n\n* Enable barcode decoding in i2b\r\n\r\nAdd an interface to decode so that i2b can call into it.  To avoid\r\na clash with i2b, its opts_t struct is renamed to decode_opts_t.\r\n\r\nAdd decoding options to i2b.  Options (long only) are copied from\r\ndecode.  Decoding is enabled by using the --barcode-file option.\r\n\r\nMake addHeader() write a read group header for each barcode\r\nif decoding is enabled instead of a single one for the whole file.\r\n\r\nUpdate processRecordGroup() to make it look up the barcodes and\r\nalter the read group and optionally the read name to say which\r\ntag was found.  The actual decoding is done by decode_tags().\r\nCurrently the call data is not shared with bam_write_barcode_tag()\r\nso the barcode bcl files get converted twice.  While not quite\r\nas efficient, it's simpler to keep both separate.\r\n\r\nprocessTile() now recycles processRecordJob_struct structures\r\nusing a free-list so that it can reuse barcode metrics structures.\r\n\r\nBarcode metrics are accumulated in the same way as for decode and\r\nprinted out at the end if the --metrics-file option is used.\r\n\r\nIn a small test, decoding in i2b saves about 30% CPU compared\r\nto i2b piped into decode.\r\n\r\n* Add compare on sequence as last tie-breaker for sorting tag hops\r\n\r\nMainly so files can be easily compared when running tests.\r\n\r\n* Add tests for i2b barcode decoding","distinct":true,"url":"https://api.github.com/repos/wtsi-npg/bambi/commits/6df64f9fdccda8a120edcc61912ea7334501c25e"}]}
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