v1.2.5 - 11/21/2024

The correct files to download are either falco-1.2.5.zip or falco-1.2.5.tar.gz
Please do not download the "Source code" files automatically generated by GitHub, as they do not contain all files necessary for compilation.

What's Changed

• Adding option to exit without error on empty input by @andrewdavidsmith in #78

Full Changelog: v1.2.4...v1.2.5

v1.2.4 - 9/25/2024

The correct files to download are either falco-1.2.4.zip or falco-1.2.4.tar.gz

Please do not download the "Source code" files automatically generated by GitHub, as they do not contain all files necessary for compilation.

What's Changed

• Changing adapter matching so that self-overlapping patterns are only matched once per read by @andrewdavidsmith in #71
• Fixing bug in adapter identification for BAM format by @andrewdavidsmith in #72

Full Changelog: v1.2.3...v1.2.4

v1.2.3 - 8/11/2024

The correct files to download are either falco-1.2.3.zip or falco-1.2.3.tar.gz

Please do not download the "Source code" files automatically generated by GitHub, as they do not contain all files necessary for compilation.

What's Changed

• Fixed a bug that caused access past ends of adapters in some situations
• Removed progress bar for BAM input because we can't be sure it's accurate
• Fixed a bug involving wrong strands for reads in BAM files (issue #59)
• Fixed a bug that attempted to build for BAM support even when HTSLib was not available
• Updated adapter and contaminant files from FastQC v0.12.0 (issue #64)

v1.2.2 - 3/15/2024

The correct files to download are either falco-1.2.2.zip or falco-1.2.2.tar.gz

Please do not download the "Source code" files automatically generated by GitHub, as they do not contain all files necessary for compilation.

What's Changed

• Fix error in parsing gzip file by @y9c in #48
• Added direct support for reading BAM files to improve efficiency in some situations by @masarunakajima in #53

New Contributors

• @y9c made their first contribution in #48
• @masarunakajima made their first contribution in #53

Full Changelog: v1.2.1...v1.2.2

v1.2.1 - 9/15/2022

The correct files to download are either falco-1.2.1.zip or falco-1.2.1.tar.gz

Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This is a quality-of-life release that fixes two serious bugs in 1.2.0

bug 1 (from issue #40) : falco stalls if the default configuration files are not used (e.g. when using conda)
bug 2: the file format type was not being recognized properly when using multiple inputs of different file types.

v1.2.0 - 9/11/2022

The correct files to download are either falco-1.2.0.zip or falco-2.1.0.tar.gz

Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

New in v1.2.0:

• Custom file names for summary, data and HTML reports can be provided by users
• More detailed documentation of parameters. Much of it was directly copied from FastQC v0.11.9, with flags that are not yet implemented being specifically stated as such

Bugfixes:
#39 : We fixed a bug where reads of length >1M were crashing falco. The program now allows reads of about 64M bases, but note that, since falco collects data for every read position, memory will scale accordingly. Plan the computing resources ahead!

Other changes:

• The Conda release now contains the default contaminants, adapters and limit files under the opt/falco-1.2.0/Configuration directory when installing through it, consistently with FastQC.

v1.1.0 - 09/02/2022

The correct files to download are either falco-1.1.0.zip or falco-1.1.0.tar.gz

Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

New in v1.1.0:

• Subsampling reads to improve speed for large files

Bugfixes:
#37 : adapter plot now shows range corresponding to max read length
#36 : support for multiple fastq files in a directory
#23 : html report for k-mers had a bug that is fixed

Other changes:

• modified code so falco can build with older compilers still common on some systems
• fixing a bug where the output directory was being duplicated if file is within a directory
• fixing a bug where quiet falco still displayed full progress bar
• less frequent updates to progress bar make the code faster

The added functionality is the "subsample" option, which uses every k-th read. For large files, this will give the same results (converging at the usual rate), but is faster. Thanks to @y9c for the suggestion (Issue #35).

v1.0.0 - 05/24/2022

The correct files to download are either falco-1.0.0.zip or falco-1.0.0.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

New features in 1.0.0:

• Progress bar for FASTQ, gzipped FASTQ and SAM inputs.
• Falco now runs in less than 100 MB for SAM input

Bugfixes
#18 : falco now automatically identifies quality encoding with an identical approach to FastQC
#20 : falco now recognizes filenames independent of lower/uppercase
#23 : falco can now handle adapters of varying sizes
#25 : consistency with FastQC by rounding per base sequence quality distribution to double
#24 : falco can now handle different types of newline
#26 : falco no longer crashes if a read is empty or too short
#6 and #33 : Major fixes in BAM and SAM input processing

Major thanks to @Shelestova-Anastasia for bringing up the problem and contributing to the fixes for #23 , #24 , #25 and #26 !!

v0.3.0 - 9/9/2021

The correct files to download are either falco-0.3.0.zip or falco-0.3.0.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This release adds new functionality to falco and addresses several bugs reported in the issues section, listed below

#14 : When using the --nano flag, the basic statistics file will display "Oxford Nanopore" instead of Illumina. Analysis is still done for Illumina sequences. We need a fast5 parser in C++ (or write one from scratch) to allow fast5 support, which is not yet available

#15 : The k-mer content module was implemented, but is still missing p-value calculations. For now it approximates FastQC behavior, and in the next release it will be identical. We also show 10 k-mers instead of 6 in FastQC since we can erase some of them through plotly to not make the plot so dense

#16 : Fixed a bug where, if the adapters file was not provided (which is the case in the Conda release), adapters were not being counted.

#17 : Fixed several bugs in the overrepresented sequence "hits" comparison with the contaminant list, including allowing partial overlap between sequence and contaminant.

v0.2.4 - 1/8/2021

The correct files to download are either falco-0.2.4.zip or falco-0.2.4.tar.gz
Please do not download the "Source code" files automatically generated by github, as they do not contain all files necessary for compilation

This release resolves the following issues:

• Memory usage for uncompressed FASTQ files has been drastically reduced by replacing memory mapping with standard C IO. versions <= 0.2.3 use most of the available memory in the system, whereas this version only uses about 92 MB for short reads and under 400 MB for long reads
• Base groupping has been implemented for per base sequence content and per sequence N content modules, which also drastically reduced the output size of the HTML file and the text report, especially in long-read files. We opted to leave sequence length distribution without base groupping.
• Fixed a bug in adapter content where certian long-read datasets were outputting nonsensical values.