* BTOF-679: bcl2fastq should fully utilize the cpus bcl2fastq2-v2.18.0.12 * BTOF-663: Revert to disallowing --use-bases-mask with UMI trimming bcl2fastq2-v2.18.0.11 * BTOF-674: ConversionResults does not have an array of objects bcl2fastq2-v2.18.0.10 * BTOF-663: Checked in missing files * BTOF-673: Update ConversionResults property in Stats.json file * BTOF-672: IndexMetricsOut.bin should concatenate indexes with a '-' * BTOF-663: Implement the TrimUMI sample sheet setting * BTOF-646: Read[1,2]StartFromCycle does not trim reads * BTOF-645: Unexpected error when index is missing from one lane bcl2fastq2-v2.18.0.9 * BTOF-635: Requesting better fail message for incorrectly specified tiles include (--tiles) * BTOF-642: Missing PF Clusters information in reports file - NextSeq Regression run * BTOF-633: Fatal Internal Error when masking single index and outputting index files for HiSeqX Smoke * BTOF-638: Mask Second Index not working for NextSeq Smoke run * BTOF-639: Empty Index 1 behavior in v2.18 different Than v2.17 * BTOF-447: Sample numbers are assigned by lane instead of order in samplesheet * BTOF-631: TrimmedBases for ReadNumber 1 is always 33 or 49 in Stats.json * BTOF-433: --create-fastq-for-index-reads does not produce index fastq files when sample sheet does not exist in the run folder bcl2fastq2-v2.18.0.8 * BTOF-463: bcl2fastq2 errors out on data with more than 8 lanes bcl2fastq2-v2.18.0.7 * BTOF-460: bcl2fastq does not properly set the number of allowed mismatches * BTOF-462: bcl2fastq throws an exception when the runfolder path contains a space bcl2fastq2-v2.18.0.6 * BTOF-459: Stats files are malformed bcl2fastq2-v2.18.0.5 * BTOF-453: Report all samples to IndexMetricsOut.bin, even ones that have 0 clusters demultiplexed. bcl2fastq2-v2.18.0.4 * BTOF-455: "Identical barcode" error for samples loaded on different lanes bcl2fastq2-v2.18.0.3 * BTOF-456: bcl2fastq throwing exception on smallRNA build bcl2fastq2-v2.18.0.2 * BTOF-455: "Identical barcode" error for samples loaded on different lanes bcl2fastq2-v2.18.0.1 * BTOF-454: bcl2fastq2 v2.18.0.0 fails with generating fastq on a smoke dataset that worked with older bcl2fastq2 bcl2fastq2-v2.18.0.0 *BTOF-452: Support multiple indexes for the same sample ID *BTOF-451: Consolidated stats format bcl2fastq2-v2.17.2.1 * BTOF-450: Improve error handling when ignoring missing/corrupt files * BTOF-449: Read number in ConversionStats.xml can be nonsense * BTOF-271: Add Visual Studio project files for Windows build * BTOF-436: Need more file handles on Windows * BTOF-435: bcl2fastq runs slowly when tiles are small (NextSeq) and there are many samples * BTOF-250: Don't throw an exception if the Interop folder is read only. (Windows) * BTOF-374: Fix to adapter trimming algorithm * BTOF-410: Add log message for bgzf compression configuration * BTOF-431: UMI sequence should not be removed from reads by default * BTOF-404: When using "-v" options, bcl2fastq output more information than expected bcl2fastq2-v2.17.1.14 * BTOF-368: The location coordinates are slightly different for MiSeq, NextSeq, and HiSeqX data bcl2fastq2-v2.17.1.13 * BTOF-392: Error message does not change when barcode collision occurs for mismatch set to > 1 * BTOF-405: Add the --no-bgzf-compression back in * BTOF-387: --tiles in command line option does not overwrite the samplesheet option. * BTOF-390: --use-bases-mask failed to parse 7bp index using "Y151, I7n, Y151" for a 8bp index run bcl2fastq2-v2.17.1.12 * BTOF-137: Improve barcode collision error message bcl2fastq2-v2.17.1.11 * BTOF-327: usebases mask '*' should match on 0 or more bcl2fastq2-v2.17.1.10 * BTOF-336: IndexMetricsOut.bin should use PF clusters * BTOF-335: HTML report improvements bcl2fastq2-v2.17.1.9 * BTOF-329: More bugs with masking index reads bcl2fastq2-v2.17.1.8 * BTOF-329: UMIs are not supported with --use-base-mask bcl2fastq2-v2.17.1.7 * BTOF-329: Handle masking an entire index bcl2fastq2-v2.17.1.6 * BTOF-329: Throw exception when index length in --use-bases-mask doesn't match sample sheet * BTOF-334: Empty index in dual index dataset makes all reads undetermined bcl2fastq2-v2.17.1.5 * BTOF-330: Masking a whole read with "--use-bases-mask" fails * BTOF-331: Fastq contains reads with duplicated names bcl2fastq2-v2.17.1.4 * BTOF-328: Move files out of share/bcl2fastq2-v* directory * BTOF-327: usebases mask '*' should match on 0 or more bcl2fastq2-v2.17.1.3 * BTOF-320: Fixed lane parsing logic bcl2fastq2-v2.17.1.2 * BTOF-322: Disallow special characters in sample sheet settings * BTOF-320: Fixed unit tests * BTOF-320: Sample ID must be a unique identifier bcl2fastq2-v2.17.1.1 * BTOF-303: Fixed unit tests * BTOF-303: Add option to automatically set allowed mismatches to 0 on barcode collision * BTOF-302: Trim white space in the settings section of the sample sheet * BTOF-192: Record barcode mismatches 1-5 in DemultiplexingStats.xml * BTOF-270: Delete --no-bgzf-compression option * BTOF-47: Use sample name and number for html report * BTOF-273: Warning message if --sample-sheet option is specified but not found * BTOF-272: Fixed empty space in sample sheet columns bcl2fastq2-v2.16.1.11 * BTOF-271: Update bcl2fastq to run on Windows * BTOF-249: DemuxSummary files' header says SampleName but lists SampleID bcl2fastq2-v2.16.1.10 * BTOF-250: Updates for accidental check in * BTOF-268: Bcl2fastq fails to read clocs files * BTOF-250: Don't throw an exception if the Interop folder is read only. * BTOF-191: Delete FASTQ files of 0 size if they exist - Fixed bug * BTOF-152: UMI support - Add '+' as delimiter, fix stats bcl2fastq2-v2.16.1.9 * BTOF-191: Delete FASTQ files of 0 size if they exist bcl2fastq2-v2.16.1.8 * BTOF-152: UMI support bcl2fastq2-v2.16.1.7 * BTOF-246: When output reverse complement reads, the quality score does not reverse * BTOF-237: Isis support - stats and barcode fix * BTOF-245: All the index reads are masked with N/# * BTOF-237: Isis support - stats fix bcl2fastq2-v2.16.1.6 *BTOF-241: Allow index2 to be used when index1 is missing in the sample sheet *BTOF-240: Compress complete fastq records for base space uploader compatibility *BTOF-239: Accept barcodes in SampleSheet.csv that are shorter than indicated by RunInfo.xml bcl2fastq2-v2.16.1.5 * BTOF-237: Isis support - Adapter trimming stats bcl2fastq2-v2.16.1.4 * BTOF-237: Isis support * BTOF-236: Support Opus+ program for HiSeq X bcl2fastq2-v2.16.1.3 * BTOF-216: Port adapter locator enhancements from Isis * BTOF-214: Avoid memory allocations on multiple threads * BTOF-215: Use c++11 * BTOF-211: Allow underscores in FASTQ file names bcl2fastq2-v2.16.1.2 * merged with bcl2fastq2-v2.16.0.10 * removed code accidentally checked in bcl2fastq2-v2.16.1.1 * Isis support - stats and sample sheet parsing bcl2fastq2-v2.16.0.10 * BTOF-198: Throw an exception for non-ACGTN characters in barcodes * BTOF-193: Separate adapters in sample sheet with '+' bcl2fastq2-v2.16.0.9 * BTOF-201: Update default values for --minimum-trimmed-read-length and --mask-short-adapter-reads * BTOF-200: bcl2fastq failed when some lanes are specified but others are not bcl2fastq2-v2.16.0.8 * BTOF-194: Fixed core dump when using --tiles bcl2fastq2-v2.16.0.7 * BTOF-190: Throw an error if a sample is missing a barcode in the sample sheet * BTOF-191: Don't generate FASTQ files of 0 size * JAS-120: Modifications to support basespace fastq uploader bcl2fastq2-v2.16.0.6 * BTOF-170: create stats directory using --stats-dir * BTOF-48: FASTQ naming convention for non-multiplexed run * BTOF-160: --ignore-missing-bcls option fixed bcl2fastq2-v2.16.0.5 * BTOF-154: Updated help text of --ignore-missing-positions * BTOF-160: --ignore-missing-bcls option is not working * BTOF-48: FASTQ naming convention is different from GenerateFASTQ * BTOF-147: Seg fault when selecting tiles * BTOF-45: Seg fault when number of lanes in RunInfo.xml doesn't match config.xml * JAS-120: Allow bgzf compression to be turned off with: --no-bgzf-compression bcl2fastq2-v2.16.0.4 * BTOF-156: Naming should fall back to SampleId if SampleName is absent * BTOF-150: Verify existence of necessary files at start of execution bcl2fastq2-v2.16.0.3 * BTOF-136: Support for differing index lengths per lane * BTOF-137: Improve barcode collisions validation * BTOF-154: Fixed RPM installation with "--prefix" * BTOF-151: Adapter trimming stats categorized by sample * BTOF-155: Make coordinates in sequence identifiers unique * BTOF-151: Adapter trimming stats bcl2fastq2-v2.16.0.2 * BTOF-146: Support for 0-padded tile numbers in filter file names * BTOF-153: Comply with bgzf standards bcl2fastq2-v2.16.0.1 * BTOF-153: Write size of compressed blocks in gzip header * BTOF-152: Improve adapter trimming logic * BTOF-149: Add table with unknown barcodes to stats * BTOF-125: Explicit mention of version in log output * BTOF-137: Improve barcode collisions validation * BTOF-135: Option for output of fastq files without lane splitting * BTOF-130: Improved automatic thread allocation logic * BTOF-148: Improved handling of corrupt files * BTOF-134: Support for --sample-sheet * BTOF-147: Speed enhancements for the FASTQ conversion stage * BTOF-144: --use-bases-mask now accepts masking all bases of a read * BTOF-126: Adjust --minimum-trimmed-read-length to size of shortest non-index read * BTOF-140: Changed config param name from --ignore-missing-locs to --ignore-missing-positions * BTOF-129: Added support for various file formats: clocs, controls, filter, pos * BTOF-142: bcl2fastq does not compile with intel compilers * BTOF-141: comma separated list now accepted for tiles option * BTOF-138: Add config parameter for fastq compression level * BTOF-131: Support for uncompressed BCLs * BTOF-139: --ignore-missing-locs does not work bcl2fastq2-v2.15.0.4 * BTOF-127: Full Hiseq X datatsets are stopping about ~75% into processing bcl2fastq2-v2.15.0.3 * BTOF-128: Sample naming convention does not follow user guide bcl2fastq2-v2.15.0.2 * BTOF-123: Lane Summary Cluster Counts in HTML report the same in Raw and Filtered sections for some datasets * BTOF-121: Boost installation is still showing a superfluous dependency on BZIP libs bcl2fastq2-v2.15.0.1 * BTOF-120: Change versioning convention for upcoming releases * BTOF-118: Bcl2fastq is masking adapters when it should be trimming them * BTOF-119: Failure to generate reports for non-multiplexed sample bcl2fastq-02.14.05.29 * BTOF-117: Internal Program Error occurring for datasets with more than 1 tile per lane * BTOF-115: logic error when dataset has no indices specified in the sample sheet bcl2fastq-02.14.05.28 * BTOF-106: Implement table with most popular index sequences * BTOF-111: Downgrade reporting failures to a warning * BTOF-116: Error message if Reports or Stats directories clash with Project bcl2fastq-02.14.05.21 * BTOF-109 %Reads identify in IndexMetrics InterOp are over 100% for certain samples/indexes * BTOF-112 'Sample_Project' or 'Project' can be used in SampleSheet.csv * BTOF-108 Add “--use-bases-mask" functionality * BTOF-105 Gather missing (PF) data in the report * BTOF-75 Generate DemultiplexSummary file bcl2fastq-02.14.05.13 * BTOF-79 Add "Processing Complete" message to all log levels * BTOF-104 HiseqX Dataset only demultiplexes lane 1 * BTOF-80 Avoid overwriting previous (especially 1.8.4) RPM installation * BTOF-82 Masking and trimming logic needs to be disabled when generating fastqs for index reads * BTOF-81 Add observed index sequence to FASTQ reference * BTOF-77 Demux by lane for hiseq datasets * BTOF-84 incorrect order of reads in fastq output files bcl2fastq-02.14.03.13 * BTOF-74 the latest build does not work on NextSeq data bcl2fastq-02.14.03.07 * BTOF-73 bcl2fastq crashes when reading bcl files with no data (registration failures/swath dropouts) bcl2fastq-02.14.02.25 * BTOF-72 avoid -static when linking cppunittest binaries * BTOF-71 --ignore-missing-filter does not work bcl2fastq-02.14.02.21 * BTOF-69 Capability to deal with tiles > 4M clusters * BTOF-66 Add support for bcl files that are in the same gzipped format as previous HiSeq models * BTOF-68 Improve auto-detection mechanism * BTOF-65 bcl2fastq should work, even when there is no config.xml file in the BaseCalls directory * BTOF-67 Patterned flowcells have only 1 locs file per run for all tiles bcl2fastq-02.14.01.17 * BTOF-59 Provide reasonable defaults for thread counts of individual stages. * BTOF-56 Default value of mask-short-adapter-reads changed to 10 (was 32). * BTOF-61 Make adapter stringency configurable. * BTOF-60 Use FastIo instead of Boost lexical casts in FASTQ creation stage. * BTOF-59 Provide reasonable defaults for thread counts of individual stages. * BTOF-58 Write FASTQ complement. * BTOF-57 Convert only selected lanes/tiles. bcl2fastq-02.14.01.07 * BTOF-56 Short read trimming special handling. * BTOF-55 Set default prefix. bcl2fastq-02.14.01.06 bcl2fastq-02.13.12.27 * BTOF-54 Include observed index in FASTQ header for Undetermined sample. bcl2fastq-02.13.12.20 * BTOF-53 Corrected FASTQ header. bcl2fastq-02.13.12.15 * BTOF-53 Corrected FASTQ header. bcl2fastq-02.13.12.14 * BTOF-50 Added linking against librt. * BTOF-48 Added support for read-specific adapters. * BTOF-48 Added options for ignoring missing positions and filter files. * BTOF-52 Corrected handling of missing BCLs. * BTOF-51 Corrected BCL file name for HiSeq. * BTOF-42 Escape underscore in FASTQ file names. bcl2fastq-02.13.12.13 * BTOF-42 Corrected default location of InterOp directory. bcl2fastq-02.13.12.12 * BTOF-42 Escape non-alphanumeric characters in FASTQ file names. * BTOF-51 Corrected BCL file name for HiSeq. bcl2fastq-02.13.12.11 * BTOF-36 HiSeq/MiSeq support. * BTOF-33 Correct positions data. * BTOF-42 ISIS-like naming scheme for output files. * BTOF-46 Corrected mismatching tiles in InterOp stats. * BOTF-49 Changed default number of allowed barcode mismatches to 1. bcl2fastq-02.13.11.15 * BTOF-45 Use gcc/g++ by default. * BTOF-44 Added legacy sample sheet option 'Adapter' for adapter trimming. * BTOF-43 Corrected value of adapter stringency. * BTOF-39 Dependency on Boost.Chrono made conditional. * BTOF-38 Include non-PF clusters. * BTOF-37 Configurable number of mismatches. bcl2fastq-02.13.11.08 * BTOF-34 Package name. * BTOF-35 Remove superfluous dependency on BZIP. * BTOF-19 Allow single sample without index in sample sheet. * BTOF-32 Do not demultiplex in case there are no index reads. * BTOF-30 Keep BCL and FASTQ files open (hacked, needs refactoring). * BTOF-30 Added fake BCL producer and FASTQ consumer. * BOTF-30 Added timing of individual stages. * BOTF-28 Solved deadlock after assertion. * BTOF-24 Merge data- and index- reads metadata into single container. * BTOF-22 Do not produce empty GZIPs. * BOTF-18 Sample sheet alternative column names "Sample_ID" and "Sample_Name". * BTOF-20 Skip only InterOp for filtered out clusters. * BTOF-20 Do not include filtered-out clusters in InterOp file. * BTOF-20 Do not include sample #0 in InterOp file. * BTOF-21 Cluster filtering. * BTOF-16 Demultiplexing statistics. * BTOF-15 Missng BCLs as no-calls. * BTOF-14 Create FASTQs for index reads. * BTOF-13 Adapter masking/trimming. * BTOF-12 Reading adapters from sample sheet. * BTOF-09 Corrected bug in initialization of lookup barcode table. * BTOF-09 Demultiplexing. * BTOF-8 Multiple barcodes per sample. * BTOF-10 Removed superfluous dependency on libgcrypt. * BTOF-8 Sample sheet parsing. * BTOF-4 Added positions handling. * BTOF-4 Added tile handling. * BTOF-4 Review amendments. * BTOF-4 Initial commit.