A Java API for high-throughput sequencing data (HTS) formats.
active 2023-08-16 → 2026-07-26 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 1076 days from 2023-08-16 to 2026-07-26. Pushes: 166 total, peak 6 in a day. Pull requests: 82 total, peak 5 in a day. Issues: 26 total, peak 2 in a day. Comments: 301 total, peak 16 in a day. Stars: 31 total, peak 1 in a day.
- Pushes
- Pull requests
- Issues
- Comments
- Stars
Stars, PRs, issues and forks are under-captured in the later part of this window. GH Archive progressively stopped capturing non-push events during 2026 — −95% or worse by the end of the window. Every series here except Pushes fades for that reason, so a decline above reflects the archive, not this repository. Pushes stay reliable throughout, so read them, and the contributor counts derived from them, as the real signal. Data health has the measurements.
Top contributors
Pushes, PRs, issues, reviews and comments — stars and forks excluded, so this is contribution rather than popularity
| Contributor | Contributions | Pushes | PRs | Comments |
|---|---|---|---|---|
| cmnbroad | 236 | 82 | 18 | 71 |
| lbergelson | 200 | 46 | 41 | 62 |
| yash-puligundla | 89 | 0 | 1 | 43 |
| tfenne | 55 | 28 | 7 | 13 |
| droazen | 49 | 1 | 1 | 35 |
| takutosato | 47 | 3 | 1 | 22 |
| yfarjoun | 24 | 3 | 2 | 12 |
| nh13 | 18 | 0 | 2 | 13 |
| lindenb | 6 | 0 | 4 | 2 |
| KevinCLydon | 6 | 3 | 1 | 1 |
| jamesemery | 3 | 0 | 0 | 1 |
| bartcharbon | 3 | 0 | 0 | 2 |
| jkbonfield | 3 | 0 | 0 | 2 |
| kshakir | 3 | 0 | 1 | 1 |
| karlestira | 3 | 0 | 0 | 1 |
| jmarshall | 2 | 0 | 0 | 2 |
| meganshand | 2 | 0 | 1 | 1 |
| jerryliu2005 | 2 | 0 | 0 | 2 |
| pgrt | 2 | 0 | 0 | 1 |
| AlessandroBalestrucci | 2 | 0 | 0 | 1 |
Recent activity
Latest issues, pull requests and releases
- Issue comment#1557tfenne2026-07-14 01:37convert Runtime exceptions in the CRAM code into CRAMExceptions (also…
- Issue comment#1784jonn-smith2026-06-16 01:39Migrate from java.io.File to java.nio.file.Path for NIO SPI support (6.0.0)
- Issue comment#1782yfarjoun2026-06-12 02:23Optimize SAM text parsing (~2.2x throughput)
- Pull request#1781tfenne2026-05-01 22:09
- Pull request#1770tfenne2026-04-25 10:31
- Pull request#1763tfenne2026-04-25 10:29
- Issue comment#1763tfenne2026-04-25 10:28Full CRAM 3.1 support & performance tuning of CRAM read/write
- Issue comment#1413codecov-commenter2026-04-13 08:23Allow partially spanned alleles.
- Pull request#1769tfenne2026-04-11 12:24
- Pull request#1768tfenne2026-04-11 03:18
- Pull request#1767tfenne2026-04-11 02:24
- Issue comment#1763jkbonfield2026-03-31 09:06Full CRAM 3.1 support & performance tuning of CRAM read/write
- Pull request#1758tfenne2026-03-24 00:32
- Issue#1756karlestira2026-03-10 07:42Extremly high random I/O in query overlaping API for CRAM
- Issue#1756karlestira2026-03-10 03:51Extremly high random I/O in query overlaping API for CRAM
- Issue comment#1756karlestira2026-03-10 03:51Extremly high random I/O in query overlaping API for CRAM
- Issue comment#1755yfarjoun2026-02-15 23:08Any objection to creating a release for CRAM 3.1 inclusion
- Issue comment#1755cmnbroad2026-02-15 22:18Any objection to creating a release for CRAM 3.1 inclusion
- Issue#1752dariober2026-01-11 16:33Fast way to get number of aligned reads in indexed CRAM file.
- Issue#1750Lenbok2025-11-17 21:13Incorrect error message for out of order SAM file alignments
- Issue#1749tfenne2025-10-24 14:58ReferenceSequenceFile is thread-safe for uncompressed FASTA but decidedly non-threadsafe for bgzipped FASTA files
- Pull request#876nh132025-09-26 00:32
- Issue comment#1745lbergelson2025-05-19 19:36feat: Add sanity check to indexed FASTA file
- Issue comment#1745lbergelson2025-05-19 19:23feat: Add sanity check to indexed FASTA file
- Issue comment#1745yfarjoun2025-05-15 19:36feat: Add sanity check to indexed FASTA file
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 31 stars here means stars gained during the window, not the repo's star count.