{"id":56886,"library":"htsjdk","title":"HTSJDK","description":"A Java API for reading and writing high-throughput sequencing data in formats like SAM, BAM, VCF, and CRAM.","status":"active","version":"5.0.0","language":"java","source_language":null,"source_url":"https://github.com/samtools/htsjdk","tags":["bioinformatics","sequencing","sam","bam","vcf"],"install":[{"cmd":"<dependency>\n  <groupId>com.github.samtools</groupId>\n  <artifactId>htsjdk</artifactId>\n  <version>5.0.0</version>\n</dependency>","lang":"xml","label":"Maven"},{"cmd":"implementation 'com.github.samtools:htsjdk:5.0.0'","lang":"groovy","label":"Gradle"}],"dependencies":[],"imports":[{"symbol":"SAMFileReader","correct":"htsjdk.samtools.SAMFileReader"}],"quickstart":{"code":"import htsjdk.samtools.SAMFileReader;\nimport htsjdk.samtools.SAMRecord;\nimport java.io.File;\n\nSAMFileReader reader = new SAMFileReader(new File(\"input.bam\"));\nfor (SAMRecord record : reader) {\n    System.out.println(record.getReadName());\n}\nreader.close();","lang":"java","description":"Read a BAM file and print read names"},"warnings":[{"fix":"Use SAMFileReader(File, ValidationStringency) or set validation stringency explicitly.","message":"HTSJDK 5.0.0 changed the default SAMFileReader constructor to require an explicit validation stringency.","severity":"breaking","affected_versions":">=5.0.0"}],"env_vars":null,"search_vec":"'api':4 'bam':18,25 'bioinformat':22 'cram':21 'data':13 'format':15 'high':10 'high-throughput':9 'htsjdk':1 'java':3 'like':16 'read':6 'sam':17,24 'sequenc':12,23 'throughput':11 'vcf':19,26 'write':8","created_at":"2026-06-15T10:54:18.775220+00:00","updated_at":"2026-06-15T10:54:18.775220+00:00","problems":[],"ecosystem":"maven","meta_description":null,"install_score":null,"quickstart_score":null,"quickstart_tag":null,"pypi_latest":null,"cli_name":null,"cli_version":null,"type":"library","homepage":"https://samtools.github.io/htsjdk/","github":"https://github.com/samtools/htsjdk","docs":"https://appdoc.app/artifact/com.github.samtools/htsjdk/","changelog":null,"pypi":null,"npm":null,"openapi_spec":null,"status_page":null,"smithery":null,"categories":["utility","other"],"base_url":null,"auth_type":null,"provenance":{"verified_status":null,"verified_at":null,"last_verified":"2026-06-15","next_check":"2026-12-12","install_tag":null}}