• Fix a bug in selecting the best mapping pair. (#188 )

• Improve the speed when using >= 12 threads.

• Fix several issues related to deduplication #184, #185

Output peak-based QC metrics, such as estimated fraction of reads in peaks (FRiP) values, without peak callings for single-cell data (e.g. scATAC-seq) in the summary file (--summary option)

• The summary only collects information for barcodes in the whitelist, if provided. (#167 )
• Use the current directory instead /temp if the output is to /dev/stdout. (#150)
• More robust when creating too many temp files. (#142 )
• Fix an issue with the MD tag when output in SAM. (#162 )

• Support wildcard in file names. #58
• Fix the TLEN overflow issue for SAM output on Hi-C data. #139
• Remove the internal sort for --read-format option. #136
• Fix a bug in the summary file for SAM format output, where duplicate, unmapped, lowmapq read pairs are counted twice. #143
• Add the duplicate count in the bulk data BED output. #145

• Add the option "--summary" to output the mapping statistics (e.g. total reads, duplicated read, unmapped reads and low-mapq reads) summarized at the bulk or single-cell level (#107).

• Properly output the paired-end information (rnext, pnext and tlen) in SAM format
• Support the gzipped barcode whitelist and translation files (#51)
• Fix the bugs reported in #104 and #112
• Some code refactoring

This release provides a new feature that allows users to further customize the barcodes based on the original barcode input file (#42). Now multiple ranges for each sequence in the input sequence file can be given in `--read-format' option. For each sequence, Chromap will extract the specified subsequences in the ranges and combine those subsequences as a barcode.

Note that this release does not change mapping results for any input but only provides this new feature.

This release fixed the following bugs.

• When using --read-format, the quality scores are wrongly complemented, which is fixed now.
• The segfault caused by adapter trimming in #46 is fixed.

This release also improved barcode processing.

• Barcode with Ns are now not used for estimating barcode frequency.
• When correcting the barcode, its Ns are corrected first.

This release improve adapter trimming. It can now properly handle the case when one end of the read pair is a subsequence of the other in #88.

The results on mapping paired-end scATAC-seq reads would change slightly. If you previously used Chromap to process your paired-end scATAC-seq data, you may want to rerun it.

This release fixed the following bugs.

• Fixed the segfault caused by candidate cache in #78 and #59.
• Fixed some bugs on computing MAPQ for single-end reads and Hi-C reads in #79.
• Fixed the compiling issue with GCC11 in #83.