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.
