v0.2.6 (r486)

• 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

v0.2.5 (r473)

• 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).

v0.2.4 (r467)

• 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

v0.2.3 (r407)

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.

v0.2.2 (r388)

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.

v0.2.1 (r369)

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.

v0.2.0 (r355)

Note that two versions are attached. You should use no-cache version for now on mapping Hi-C reads or when you run the standard version of Chromap and get errors.

This release fixed the following bugs.

• SEQ and QUAL in SAM are now correct for reverse complementary mappings (#70). If you previously used Chromap to generate SAM output, you may want to rerun Chromap with the same command to get correct SEQ and QUAL in SAM.
• An issue in low memory mode was fixed. Now the memory usage for low memory mode becomes more stable and is around 20GB for all the output formats no matter what the number of reads is. This should also fix the issue in #37.
• Low memory mode for single-end data is now supported, which should fix the issue in #59.

More explanations were added for custom reference sequence order on mapping ordering and pairs flipping in the document.

v0.1.6 (r309)

This release fixed two bugs.

• --read-format was not applied when computing barcode abundance, which leads to wrong barcode abundance when --read-format is used since --read-format was introduced in v0.1.1 (#60, #15). This is now fixed and you may have to rerun Chromap if you used --read-format with v0.1.1-v0.1.5.
• With some compilers and system, --read-format is initialize to all 0s and crashes the program (#62).

Some code refactor was also done but would not affect mapping results.

v0.1.5 (r302)

This release includes the following improvement or bug fix.

• A strand field in the --read-format option was added.
• Compiling issue on macOS was fixed. And a test on macOS compiling was added in actions to avoid future issues on this.
• "Sequence and cigar lengths are not equal" problem in Hi-C SAM output was resolved.
• Some code refactor was performed, which does not affect the mapping results.

v0.1.4 (r284)

This release includes the following improvement or bug fix.

• Chromap can warn the users and stop mapping when most barcodes are not in the whitelist.
• Chromap can process single-cell data without input barcode whitelist and only warn the users.
• Chromap can translate the barcode for 10x Multiome and SHARE-seq data.
• From this version, the license is MIT.
• Some issues on processing single-end data is fixed.
• Code is partially refactored which should not affect the results.