From c65f20626d9fe96633181c4ab90f07b5560ddf5a Mon Sep 17 00:00:00 2001 From: faithokamoto Date: Tue, 30 Jun 2026 08:39:22 -0700 Subject: [PATCH 1/4] duplicate name handling --- contrib/fastahack | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/contrib/fastahack b/contrib/fastahack index d9aa0a2e..5b89a739 160000 --- a/contrib/fastahack +++ b/contrib/fastahack @@ -1 +1 @@ -Subproject commit d9aa0a2ed3fb6a772566173943428bebb307b3a6 +Subproject commit 5b89a73915b28a1ea68ee45198e21666bd73522b From d43f5c41a2195e2fe4002795c6b865180791a94c Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Wed, 1 Jul 2026 14:59:41 -0400 Subject: [PATCH 2/4] Point at vgteam fastahack repo that has the new commit we need --- .gitmodules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index 70add79b..8cb34105 100644 --- a/.gitmodules +++ b/.gitmodules @@ -6,7 +6,7 @@ url = https://github.com/ekg/multichoose.git [submodule "fastahack"] path = contrib/fastahack - url = https://github.com/ekg/fastahack.git + url = https://github.com/vgteam/fastahack.git [submodule "intervaltree"] path = contrib/intervaltree url = https://github.com/ekg/intervaltree.git From 63252752d66aab4bcad5d3294d374a918cef0eb5 Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Wed, 1 Jul 2026 17:03:09 -0700 Subject: [PATCH 3/4] Use fastahack that can catch duplicate names at index build and at index load --- contrib/fastahack | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/contrib/fastahack b/contrib/fastahack index 5b89a739..b469d1b5 160000 --- a/contrib/fastahack +++ b/contrib/fastahack @@ -1 +1 @@ -Subproject commit 5b89a73915b28a1ea68ee45198e21666bd73522b +Subproject commit b469d1b55c694937b6be1f81c3794fe521186c9d From 81624a203ec372703c4731424995e246a504b0fe Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Wed, 1 Jul 2026 17:19:23 -0700 Subject: [PATCH 4/4] Use fastahack that can copy index entries --- contrib/fastahack | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/contrib/fastahack b/contrib/fastahack index b469d1b5..524a976f 160000 --- a/contrib/fastahack +++ b/contrib/fastahack @@ -1 +1 @@ -Subproject commit b469d1b55c694937b6be1f81c3794fe521186c9d +Subproject commit 524a976f26d2c8bb62dc3a98bf8089cba57f85ec